This study used molecular dynamics simulations and mutagenesis experiments to investigate the interaction between adenylyl cyclase (AC) from Bordetella pertussis and calmodulin (CaM). Based on previous simulations, three residues in AC that interact with CaM were identified and substituted with alanine. Biochemical assays showed that mutating all three residues greatly reduced the affinity between AC and CaM, while mutating one or two residues did not significantly affect affinity. New molecular dynamics simulations of the mutant complexes provided insight into how the mutations weakened the interaction by increasing fluctuations in CaM. The results suggest the mutated residues in AC play an important role in stabilizing CaM binding and the active conformation of the AC catalytic
This document summarizes a study on the kinetics and mechanism of the acetyl transfer partial reaction of the acetyl-CoA decarbonylase/synthase (ACDS) complex from Methanosarcina barkeri. The study found that acetyl transfer activity required strongly reducing conditions and exhibited a ping-pong kinetic mechanism consistent with formation of an acetyl-enzyme intermediate. Analysis of inhibitory effects provided values for substrate binding and isotope exchange experiments provided information about the stability of the acetyl-enzyme intermediate. The results help characterize the acetyl-enzyme intermediate and have implications for understanding the mechanism of C-C bond cleavage catalyzed by the ACDS complex.
Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymerDarren Martin Leith
This document summarizes molecular dynamics simulations of two forms of an electroactive polymer interacting with ions. In one simulation, an amphiphilic polymer forms a charged monolayer interface between a vacuum and an aqueous layer containing ions. The stability of the monolayer under hydrostatic pressure and charge imbalance is investigated. In another simulation, a polythiophene oligomer is twisted into a helix serving as an ion channel between two aqueous regions separated by a phospholipid bilayer membrane.
1) Lipases are water-soluble enzymes that catalyze the hydrolysis of ester bonds in triacylglycerols and belong to the alpha/beta hydrolase fold family. They contain a catalytic triad of Ser-His-Asp/Glu and undergo conformational changes through a flexible lid region.
2) Lipases exist in both closed and open conformations, with the closed state shielding the active site and the open state exposing a hydrophobic surface upon lid movement. This lids movement is important for catalytic activity and binding to interfaces.
3) Molecular modeling was used to study the reaction mechanism and conformational preferences of Candida antarctica lipase B. The results supported a
This document describes applying the quantum mechanical/molecular mechanical (QM/MM) replica path method to study the Claisen rearrangement of chorismate to prephenate catalyzed by chorismate mutase. Specifically, it explores optimizing a reaction pathway for this reaction using the QM/MM replica path method. The optimized pathway yielded an activation enthalpy of 14.9 kcal/mol, consistent with the experimental value of 12.7 ± 0.4 kcal/mol. This demonstrates the ability of the QM/MM replica path method to accurately model enzyme-catalyzed reactions.
Some reactions seem to obvious to fail, so what happens when they do? Quantum calculations yield invaluable insight to the nature of a reaction mechanism.
Presented at the Virtual Conference on Computational Chemistry VCCC 2014
Credit due to Guillermo Caballero on whose BSc thesis this presentation is based.
This study used NMR spectroscopy to measure hydrogen exchange rates of backbone amide protons in two disordered proteins, a-synuclein and FlgM, in buffer and inside Escherichia coli cells. The rates were similar in buffer and cells, and close to rates predicted from studies of unstructured peptides. This suggests that true disorder can persist inside the crowded cellular interior, and that weak interactions between proteins and macromolecules in cells do not necessarily affect intrinsic exchange rates. However, the C-terminal region of FlgM showed some evidence of transient structure formation in buffer that was not observed inside cells.
Protein Secondary Structure Prediction using HMMAbhishek Dabral
This document describes using hidden Markov models to predict protein secondary structure from amino acid sequences. It discusses:
1) Performing statistical correlation analysis to identify significant correlations between amino acid pairs in different secondary structure types. This found correlations between positions in alpha helices, beta strands, and coils.
2) Building a semi-Markov hidden Markov model to represent secondary structure assignments as segments defined by type and endpoint. The model considers correlations at segment borders and within segments.
3) Training the model by iteratively predicting secondary structure, removing inaccurate predictions from the training set, and re-estimating model parameters.
4) Evaluating prediction accuracy using Q3 scores, which measure the percentage of residues correctly
This document summarizes a study on the kinetics and mechanism of the acetyl transfer partial reaction of the acetyl-CoA decarbonylase/synthase (ACDS) complex from Methanosarcina barkeri. The study found that acetyl transfer activity required strongly reducing conditions and exhibited a ping-pong kinetic mechanism consistent with formation of an acetyl-enzyme intermediate. Analysis of inhibitory effects provided values for substrate binding and isotope exchange experiments provided information about the stability of the acetyl-enzyme intermediate. The results help characterize the acetyl-enzyme intermediate and have implications for understanding the mechanism of C-C bond cleavage catalyzed by the ACDS complex.
Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymerDarren Martin Leith
This document summarizes molecular dynamics simulations of two forms of an electroactive polymer interacting with ions. In one simulation, an amphiphilic polymer forms a charged monolayer interface between a vacuum and an aqueous layer containing ions. The stability of the monolayer under hydrostatic pressure and charge imbalance is investigated. In another simulation, a polythiophene oligomer is twisted into a helix serving as an ion channel between two aqueous regions separated by a phospholipid bilayer membrane.
1) Lipases are water-soluble enzymes that catalyze the hydrolysis of ester bonds in triacylglycerols and belong to the alpha/beta hydrolase fold family. They contain a catalytic triad of Ser-His-Asp/Glu and undergo conformational changes through a flexible lid region.
2) Lipases exist in both closed and open conformations, with the closed state shielding the active site and the open state exposing a hydrophobic surface upon lid movement. This lids movement is important for catalytic activity and binding to interfaces.
3) Molecular modeling was used to study the reaction mechanism and conformational preferences of Candida antarctica lipase B. The results supported a
This document describes applying the quantum mechanical/molecular mechanical (QM/MM) replica path method to study the Claisen rearrangement of chorismate to prephenate catalyzed by chorismate mutase. Specifically, it explores optimizing a reaction pathway for this reaction using the QM/MM replica path method. The optimized pathway yielded an activation enthalpy of 14.9 kcal/mol, consistent with the experimental value of 12.7 ± 0.4 kcal/mol. This demonstrates the ability of the QM/MM replica path method to accurately model enzyme-catalyzed reactions.
Some reactions seem to obvious to fail, so what happens when they do? Quantum calculations yield invaluable insight to the nature of a reaction mechanism.
Presented at the Virtual Conference on Computational Chemistry VCCC 2014
Credit due to Guillermo Caballero on whose BSc thesis this presentation is based.
This study used NMR spectroscopy to measure hydrogen exchange rates of backbone amide protons in two disordered proteins, a-synuclein and FlgM, in buffer and inside Escherichia coli cells. The rates were similar in buffer and cells, and close to rates predicted from studies of unstructured peptides. This suggests that true disorder can persist inside the crowded cellular interior, and that weak interactions between proteins and macromolecules in cells do not necessarily affect intrinsic exchange rates. However, the C-terminal region of FlgM showed some evidence of transient structure formation in buffer that was not observed inside cells.
Protein Secondary Structure Prediction using HMMAbhishek Dabral
This document describes using hidden Markov models to predict protein secondary structure from amino acid sequences. It discusses:
1) Performing statistical correlation analysis to identify significant correlations between amino acid pairs in different secondary structure types. This found correlations between positions in alpha helices, beta strands, and coils.
2) Building a semi-Markov hidden Markov model to represent secondary structure assignments as segments defined by type and endpoint. The model considers correlations at segment borders and within segments.
3) Training the model by iteratively predicting secondary structure, removing inaccurate predictions from the training set, and re-estimating model parameters.
4) Evaluating prediction accuracy using Q3 scores, which measure the percentage of residues correctly
Exam 2 structure function Protiens Biochem f2016 Syed A JamalSayed Jamal
This document contains a 26 question biochemistry exam covering topics like protein structure, binding, kinetics, hemoglobin function, and diseases. The exam tests understanding of key concepts like protein folding, ligand binding, allosteric regulation, oxygen transport, sickle cell anemia, and prion diseases through calculation, graph, and diagram analysis questions. Students must demonstrate their mastery of biochemistry fundamentals and their ability to apply knowledge to clinical scenarios.
tuning the pH Response of i-Motif DNA Oligonucleotides_Lannes_et_al-2015-Chem...saheli halder
This document discusses tuning the pH response of i-motif DNA oligonucleotides. The authors introduced 5-methylcytosines (5-MeC) and 5-bromocytosines (5-BrC) into the human telomeric i-motif sequence to shift its pH response range. They found that 5-MeC shifted the pH response towards more basic values, while 5-BrC shifted it towards more acidic values. Additionally, lengthening the sequence shifted the pH response in a more basic direction. The modifications did not thermally destabilize the i-motifs. 5-BrC substitution led to a ten-fold increase in folding kinetics compared to the other sequences.
A molecular-dynamics-investigation-of-the-stability-of-a-charged-electroactiv...Darren Martin Leith
1) A molecular dynamics simulation investigates the stability of a charged electroactive polymer monolayer consisting of an amphiphilic polythiophene on a sodium chloride solution.
2) When the monolayer is chemically reduced, negative charges are conferred on the thiophene rings. This leads to a loss of planarity and buckling of the monolayer, eventually causing it to rupture. It also attracts excess sodium ions to the interface.
3) At low levels of reduction, interface sodium ions are more mobile than sodium ions in the NaCl solution, responding to electric fields by jumping between sites with an energy barrier of 0.33 eV. The instability of the charged polymer membrane is discussed using Gou
Computational and Experimental Studies of MTO Catalyzed Olefin HydrogenationKaram Idrees
The poster that I presented at the 253rd American Chemical Society National Meeting and Exposition in San Francisco,
CA. It highlights some of my REU research at North Carolina State University under the mentorship of Dr. Elon Ison.
Inhibition of μ-calpain; towards treatment of rheumatoid arthritis (2)Hala Issa
1. Rheumatoid arthritis is an inflammatory disease where neutrophils migrate to sites of inflammation facilitated by the action of μ-calpain, a calcium-dependent protease. Inhibiting μ-calpain could help treat rheumatoid arthritis.
2. Monohalogenated α-mercaptoacrylates are potent and selective inhibitors of calpain that bind to the PEF(S) domain, interrupting conformational changes needed for activity. Compound 2 was shown to impair neutrophil spreading.
3. The aim of the study is to further elucidate the interactions of α-mercaptoacrylate inhibitors with calpain domains to optimize them as drug candidates for treating rheumatoid arthritis and other
Inhibition of μ-calpain; towards treatment of rheumatoid arthritisHala Issa
This document summarizes research on calpain inhibition for the treatment of rheumatoid arthritis. Calpains are calcium-dependent cysteine proteases implicated in inflammatory diseases. The large subunit of μ- and m-calpains contains catalytic domains and calcium binding domains. Calpastatin inhibits activated calpains. Overactivation of calpains is associated with rheumatoid arthritis due to calcium imbalance. Newly synthesized mono-halogenated α-mercaptoacrylate derivatives potently inhibit calpains by binding calcium binding domains. This study examines the interactions of these inhibitors with the PEF(L) and PEF(S) calcium binding domains.
The document discusses fluorescent proteins and their ability to undergo photo-switching based on the conformation of their chromophores. It analyzed 338 fluorescent protein structures to determine if their shape, as measured by eccentricity and cross-sectional size, correlates with whether the chromophore is in the cis or trans conformation. Logistic regression found that chromophores are more likely to be trans if the ratio of major to minor axis is above 1.10747, and more likely to be cis if the minor axis is above 9.202. Higher ratios and minor axes were statistically associated with trans and cis conformations, respectively.
This document discusses using a Loop Power Controller (LPC) and fuel cell system to improve load balancing and reduce power losses in a distribution system. It first provides background on fuel cells and how they can provide continuous power generation. It then discusses how an LPC works by adjusting voltage ratio and phase shift to control real and reactive power flow between two distribution feeders. The document presents a case study where an LPC is used to balance the loads between two feeders that also have intermittent power injection from a fuel cell system. Simulation results show the LPC is able to improve load balancing and reduce overall power losses in the distribution system compared to using only fuel cell generation.
This document discusses quantitative structure-activity relationships (QSAR) modeling for drug discovery. It describes how QSAR has evolved from using 2D descriptors to 3D modeling that accounts for molecular shape and conformation. Accurately positioning molecules in 3D space relative to a reference molecule is important. Various algorithms are used to measure conformational and shape similarities between molecules. Database searching involves fitting candidate molecules to a template that represents the dimensions and physicochemical properties of a drug target's active site. High-throughput screening and virtual screening are approaches to evaluating large numbers of molecules from databases. The concept of isosterism, where structural components impart similar properties, is also important for database searching and analog design.
34th Annual Mid-West Photosynthesis Conference at Turkey Run State Park, INSean Padden
The document reports on a study of mutations to the arginine residue at position 257 (R257) of the D1 protein in Photosystem II in Chlamydomonas reinhardtii. Three mutations were made - R257E, R257K, and R257Q. Thermoluminescence and fluorescence measurements showed that the redox potential of the QB/QB- pair was lowered by 20-40 mV in the mutants. This suggests the size and charge of the residue at position 257 modulates the redox potential of QB/QB-. Growth rates and oxygen evolution were negatively impacted in the mutants compared to wild type.
The document summarizes research conducted by Alejandro Gil Villegas of the University of Guanajuato's Department of Physical Engineering on predicting phase diagrams of fluids using thermodynamic perturbation theory and Monte Carlo simulations. Some key points:
- The research combines thermodynamic perturbation theory and Monte Carlo simulations to predict phase diagrams of mixtures of fluids.
- Gil Villegas' department offers degrees in physics, physical engineering, chemical engineering, and biomedical engineering at both the undergraduate and postgraduate levels.
- The research focuses on associating fluids, using theories like SAFT (Statistical Associating Fluid Theory) to model interactions.
- Applications include modeling asphaltene precipitation and predicting phase equ
The document discusses the mechanism of aggregation of amyloid beta monomers to form amyloid fibrils. It states that monomers first aggregate to form a high-energy nucleus of a few chains, represented by a hexagonal arrangement. Once this nucleus is formed, aggregation proceeds energetically downhill to create the amyloid fibril. However, the structure of the nucleus and the steps between unstructured monomers and amyloid form are still unknown.
This document summarizes a knowledge discovery method for characterizing protein unfolding processes using molecular dynamics simulations. The method analyzes simulation data on the unfolding of the transthyretin protein (TTR), which is responsible for amyloid diseases. It clusters amino acids based on their distance to the protein's center over time in the simulations. It then identifies representative amino acids and events characterizing unfolding. Association rules are used to relate unfolding events to wild-type and mutant TTR variants, helping understand their amyloidogenic behaviors at a molecular level. The method aims to extract useful insights from large and complex simulation datasets on protein unfolding and misfolding, which are important for developing treatments for amyloid diseases.
1) Size-exclusion chromatography (SEC) and strong anion exchange chromatography (SAX) are used to separate enoxaparin oligosaccharides based on size and charge, but some oligosaccharides have similar properties and cannot be fully resolved. 2) Capillary electrophoresis (CE) using histamine in the running buffer exploits differences in histamine binding affinity to provide additional separation. 3) Preliminary results show histamine increases migration time of an enoxaparin tetrasaccharide in CE, and binding constants were calculated from isotherm graphs, confirming histamine interacts with heparin oligosaccharides.
1) Burst phase kinetic analysis was used to evaluate the rate of deamination (k3) of the aminated−methyl-idene imidazolone (NH2−MIO) adduct in the Taxus phenylalanine aminomutase (TcPAM) enzyme.
2) The analysis showed that TcPAM forms a transient NH2−MIO adduct during catalysis, resulting in an initial burst of product formation followed by a slower steady-state rate.
3) The deamination rate of the NH2−MIO adduct (k3 = 0.041 ± 0.002 s−1) was determined, demonstrating that the adduct and subsequent reaction
Prion diseases can affect various animal species, including sheep (scrapie), mink (TME), deer and elk (CWD), and cows (BSE). In humans, prion diseases include CJD, FFI, and kuru. The pathogenic prion protein (PrPSc) differs from the normal prion protein (PrPC) in having a higher beta-sheet content, being insoluble and able to aggregate, and being infectious. PrPSc converts PrPC into more PrPSc, propagating the disease. Hemoglobin and myoglobin are oxygen carrier proteins that contain heme groups and have similar alpha-helical structures, but hemoglobin is a heterotetramer that binds oxygen cooperatively
Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
Este documento resume las causas y consecuencias del cambio climático. Explica que el aumento de gases como el CO2 debido a la quema de combustibles fósiles y la deforestación están calentando el planeta y causando sequías, inundaciones y la extinción de especies. Propone crear conciencia sobre este problema y desarrollar soluciones como reducir las emisiones de carbono para prevenir mayores daños ambientales y a la salud humana.
Este documento resume las causas y consecuencias del cambio climático. Explica que el calentamiento global está causado por las emisiones de gases de efecto invernadero como el CO2 producidas por la quema de combustibles fósiles y la deforestación. Esto está ocasionando el derretimiento de los polos, la subida del nivel del mar, sequías más frecuentes y otros desastres ambientales. Propone acciones como el uso de energías renovables y el reciclaje para mitigar este problema.
Creative and Profitable Ways in which to Use AutoReponderszackm1982
This document provides 15 creative ways to use auto responders to transform casual visitors into profitable customers. Some suggestions include using auto responders to publish and distribute newsletters, articles, advertising, and email courses on various topics. Auto responders can also be used to automate sales processes by exposing visitors to testimonials and product descriptions, and to distribute free reports, trials, contests and quizzes to capture email addresses. Overall, the document advocates using auto responders to engage with and follow up on visitors in a variety of ways to increase sales.
This document contains a series of photo credits citing various photographers and their works licensed under Creative Commons licenses, including Attribution, Non-Commercial, and Share-Alike restrictions. The photos span multiple subjects and were sourced from Flickr for use in a Haiku Deck presentation.
Pompeii was destroyed by the eruption of Mount Vesuvius in 79 AD, which buried the city under ash and rock. The eruption petrified the bodies of the people who were unable to escape. Now, the excavated city of Pompeii has been preserved and is open for tours, revealing glimpses into ancient Roman life.
Exam 2 structure function Protiens Biochem f2016 Syed A JamalSayed Jamal
This document contains a 26 question biochemistry exam covering topics like protein structure, binding, kinetics, hemoglobin function, and diseases. The exam tests understanding of key concepts like protein folding, ligand binding, allosteric regulation, oxygen transport, sickle cell anemia, and prion diseases through calculation, graph, and diagram analysis questions. Students must demonstrate their mastery of biochemistry fundamentals and their ability to apply knowledge to clinical scenarios.
tuning the pH Response of i-Motif DNA Oligonucleotides_Lannes_et_al-2015-Chem...saheli halder
This document discusses tuning the pH response of i-motif DNA oligonucleotides. The authors introduced 5-methylcytosines (5-MeC) and 5-bromocytosines (5-BrC) into the human telomeric i-motif sequence to shift its pH response range. They found that 5-MeC shifted the pH response towards more basic values, while 5-BrC shifted it towards more acidic values. Additionally, lengthening the sequence shifted the pH response in a more basic direction. The modifications did not thermally destabilize the i-motifs. 5-BrC substitution led to a ten-fold increase in folding kinetics compared to the other sequences.
A molecular-dynamics-investigation-of-the-stability-of-a-charged-electroactiv...Darren Martin Leith
1) A molecular dynamics simulation investigates the stability of a charged electroactive polymer monolayer consisting of an amphiphilic polythiophene on a sodium chloride solution.
2) When the monolayer is chemically reduced, negative charges are conferred on the thiophene rings. This leads to a loss of planarity and buckling of the monolayer, eventually causing it to rupture. It also attracts excess sodium ions to the interface.
3) At low levels of reduction, interface sodium ions are more mobile than sodium ions in the NaCl solution, responding to electric fields by jumping between sites with an energy barrier of 0.33 eV. The instability of the charged polymer membrane is discussed using Gou
Computational and Experimental Studies of MTO Catalyzed Olefin HydrogenationKaram Idrees
The poster that I presented at the 253rd American Chemical Society National Meeting and Exposition in San Francisco,
CA. It highlights some of my REU research at North Carolina State University under the mentorship of Dr. Elon Ison.
Inhibition of μ-calpain; towards treatment of rheumatoid arthritis (2)Hala Issa
1. Rheumatoid arthritis is an inflammatory disease where neutrophils migrate to sites of inflammation facilitated by the action of μ-calpain, a calcium-dependent protease. Inhibiting μ-calpain could help treat rheumatoid arthritis.
2. Monohalogenated α-mercaptoacrylates are potent and selective inhibitors of calpain that bind to the PEF(S) domain, interrupting conformational changes needed for activity. Compound 2 was shown to impair neutrophil spreading.
3. The aim of the study is to further elucidate the interactions of α-mercaptoacrylate inhibitors with calpain domains to optimize them as drug candidates for treating rheumatoid arthritis and other
Inhibition of μ-calpain; towards treatment of rheumatoid arthritisHala Issa
This document summarizes research on calpain inhibition for the treatment of rheumatoid arthritis. Calpains are calcium-dependent cysteine proteases implicated in inflammatory diseases. The large subunit of μ- and m-calpains contains catalytic domains and calcium binding domains. Calpastatin inhibits activated calpains. Overactivation of calpains is associated with rheumatoid arthritis due to calcium imbalance. Newly synthesized mono-halogenated α-mercaptoacrylate derivatives potently inhibit calpains by binding calcium binding domains. This study examines the interactions of these inhibitors with the PEF(L) and PEF(S) calcium binding domains.
The document discusses fluorescent proteins and their ability to undergo photo-switching based on the conformation of their chromophores. It analyzed 338 fluorescent protein structures to determine if their shape, as measured by eccentricity and cross-sectional size, correlates with whether the chromophore is in the cis or trans conformation. Logistic regression found that chromophores are more likely to be trans if the ratio of major to minor axis is above 1.10747, and more likely to be cis if the minor axis is above 9.202. Higher ratios and minor axes were statistically associated with trans and cis conformations, respectively.
This document discusses using a Loop Power Controller (LPC) and fuel cell system to improve load balancing and reduce power losses in a distribution system. It first provides background on fuel cells and how they can provide continuous power generation. It then discusses how an LPC works by adjusting voltage ratio and phase shift to control real and reactive power flow between two distribution feeders. The document presents a case study where an LPC is used to balance the loads between two feeders that also have intermittent power injection from a fuel cell system. Simulation results show the LPC is able to improve load balancing and reduce overall power losses in the distribution system compared to using only fuel cell generation.
This document discusses quantitative structure-activity relationships (QSAR) modeling for drug discovery. It describes how QSAR has evolved from using 2D descriptors to 3D modeling that accounts for molecular shape and conformation. Accurately positioning molecules in 3D space relative to a reference molecule is important. Various algorithms are used to measure conformational and shape similarities between molecules. Database searching involves fitting candidate molecules to a template that represents the dimensions and physicochemical properties of a drug target's active site. High-throughput screening and virtual screening are approaches to evaluating large numbers of molecules from databases. The concept of isosterism, where structural components impart similar properties, is also important for database searching and analog design.
34th Annual Mid-West Photosynthesis Conference at Turkey Run State Park, INSean Padden
The document reports on a study of mutations to the arginine residue at position 257 (R257) of the D1 protein in Photosystem II in Chlamydomonas reinhardtii. Three mutations were made - R257E, R257K, and R257Q. Thermoluminescence and fluorescence measurements showed that the redox potential of the QB/QB- pair was lowered by 20-40 mV in the mutants. This suggests the size and charge of the residue at position 257 modulates the redox potential of QB/QB-. Growth rates and oxygen evolution were negatively impacted in the mutants compared to wild type.
The document summarizes research conducted by Alejandro Gil Villegas of the University of Guanajuato's Department of Physical Engineering on predicting phase diagrams of fluids using thermodynamic perturbation theory and Monte Carlo simulations. Some key points:
- The research combines thermodynamic perturbation theory and Monte Carlo simulations to predict phase diagrams of mixtures of fluids.
- Gil Villegas' department offers degrees in physics, physical engineering, chemical engineering, and biomedical engineering at both the undergraduate and postgraduate levels.
- The research focuses on associating fluids, using theories like SAFT (Statistical Associating Fluid Theory) to model interactions.
- Applications include modeling asphaltene precipitation and predicting phase equ
The document discusses the mechanism of aggregation of amyloid beta monomers to form amyloid fibrils. It states that monomers first aggregate to form a high-energy nucleus of a few chains, represented by a hexagonal arrangement. Once this nucleus is formed, aggregation proceeds energetically downhill to create the amyloid fibril. However, the structure of the nucleus and the steps between unstructured monomers and amyloid form are still unknown.
This document summarizes a knowledge discovery method for characterizing protein unfolding processes using molecular dynamics simulations. The method analyzes simulation data on the unfolding of the transthyretin protein (TTR), which is responsible for amyloid diseases. It clusters amino acids based on their distance to the protein's center over time in the simulations. It then identifies representative amino acids and events characterizing unfolding. Association rules are used to relate unfolding events to wild-type and mutant TTR variants, helping understand their amyloidogenic behaviors at a molecular level. The method aims to extract useful insights from large and complex simulation datasets on protein unfolding and misfolding, which are important for developing treatments for amyloid diseases.
1) Size-exclusion chromatography (SEC) and strong anion exchange chromatography (SAX) are used to separate enoxaparin oligosaccharides based on size and charge, but some oligosaccharides have similar properties and cannot be fully resolved. 2) Capillary electrophoresis (CE) using histamine in the running buffer exploits differences in histamine binding affinity to provide additional separation. 3) Preliminary results show histamine increases migration time of an enoxaparin tetrasaccharide in CE, and binding constants were calculated from isotherm graphs, confirming histamine interacts with heparin oligosaccharides.
1) Burst phase kinetic analysis was used to evaluate the rate of deamination (k3) of the aminated−methyl-idene imidazolone (NH2−MIO) adduct in the Taxus phenylalanine aminomutase (TcPAM) enzyme.
2) The analysis showed that TcPAM forms a transient NH2−MIO adduct during catalysis, resulting in an initial burst of product formation followed by a slower steady-state rate.
3) The deamination rate of the NH2−MIO adduct (k3 = 0.041 ± 0.002 s−1) was determined, demonstrating that the adduct and subsequent reaction
Prion diseases can affect various animal species, including sheep (scrapie), mink (TME), deer and elk (CWD), and cows (BSE). In humans, prion diseases include CJD, FFI, and kuru. The pathogenic prion protein (PrPSc) differs from the normal prion protein (PrPC) in having a higher beta-sheet content, being insoluble and able to aggregate, and being infectious. PrPSc converts PrPC into more PrPSc, propagating the disease. Hemoglobin and myoglobin are oxygen carrier proteins that contain heme groups and have similar alpha-helical structures, but hemoglobin is a heterotetramer that binds oxygen cooperatively
Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
Este documento resume las causas y consecuencias del cambio climático. Explica que el aumento de gases como el CO2 debido a la quema de combustibles fósiles y la deforestación están calentando el planeta y causando sequías, inundaciones y la extinción de especies. Propone crear conciencia sobre este problema y desarrollar soluciones como reducir las emisiones de carbono para prevenir mayores daños ambientales y a la salud humana.
Este documento resume las causas y consecuencias del cambio climático. Explica que el calentamiento global está causado por las emisiones de gases de efecto invernadero como el CO2 producidas por la quema de combustibles fósiles y la deforestación. Esto está ocasionando el derretimiento de los polos, la subida del nivel del mar, sequías más frecuentes y otros desastres ambientales. Propone acciones como el uso de energías renovables y el reciclaje para mitigar este problema.
Creative and Profitable Ways in which to Use AutoReponderszackm1982
This document provides 15 creative ways to use auto responders to transform casual visitors into profitable customers. Some suggestions include using auto responders to publish and distribute newsletters, articles, advertising, and email courses on various topics. Auto responders can also be used to automate sales processes by exposing visitors to testimonials and product descriptions, and to distribute free reports, trials, contests and quizzes to capture email addresses. Overall, the document advocates using auto responders to engage with and follow up on visitors in a variety of ways to increase sales.
This document contains a series of photo credits citing various photographers and their works licensed under Creative Commons licenses, including Attribution, Non-Commercial, and Share-Alike restrictions. The photos span multiple subjects and were sourced from Flickr for use in a Haiku Deck presentation.
Pompeii was destroyed by the eruption of Mount Vesuvius in 79 AD, which buried the city under ash and rock. The eruption petrified the bodies of the people who were unable to escape. Now, the excavated city of Pompeii has been preserved and is open for tours, revealing glimpses into ancient Roman life.
The document is a collection of 16 photos from Flickr shared under various Creative Commons licenses. The photos show a variety of subjects like nature, cities, and people. Attribution is required for some photos while others can be shared non-commercially or require attribution and sharing under the same license.
Este documento describe un proyecto llamado "En la lucha a favor de la inclusión" que tiene como objetivo mejorar la calidad de vida de comunidades necesitadas y excluidas mediante la educación y la salud. El proyecto se llevará a cabo en el municipio de Piñón, Magdalena, Colombia y contará con financiamiento de $70 millones de pesos. El proyecto se enfocará en brindar capacitación e inclusión a niños con discapacidades intelectuales durante un período de un año a través de
C multiple choice questions and answers pdfchoconyeuquy
The document contains 20 coding questions and explanations of their answers in C programming. It discusses concepts like data types, operators, loops, functions, pointers, macros, structures and more. The questions test understanding of how C code is compiled and executed, and what output would result from each code snippet.
This document discusses negation in Prolog. It begins by explaining how to use the not operator to avoid wrong answers when replacing cuts, and gives an example using not for inequality checks. It then discusses negation as failure in Prolog, and how the closed world assumption can lead to surprises. It provides examples and advice on the safe use of negation, and explains that double negation does not cancel out in Prolog. It also introduces the fail predicate and shows how it can be used to define falsehoods and represent exceptions. Throughout it traces examples to illustrate Prolog's behavior with negation.
Adam's presentation on Alternate Day and Intermittent Fasting ADF/IFBernie Williams
ADF/IF refers to nutrition protocols that extend the usual daily fasting period. ADF involves fasting whole days, while IF extends the ordinary fasting period by delaying the first meal. Both aim to reduce total caloric intake. Studies show calorie restriction can increase lifespan and reduce disease risk. IF methods include 16/8 fasting and alternate-day fasting. Purported benefits include improved blood glucose, reduced inflammation, and weight loss. The best protocol is one that can be consistently followed while still reducing weekly calorie intake.
Rubber Flooring UK is a leading supplier of rubber flooring products for industrial, commercial, public, sporting, and institutional facilities. They offer a range of rubber flooring options including matting, flooring rolls, sheets, grass mats, and gym mats. The company's products are made from recycled rubber and are suitable for both indoor and outdoor applications. More information can be found on their website at http://www.rubberflooringuk.com.
Dokumen tersebut membahas tentang logika pernyataan dan bukan pernyataan, pernyataan majemuk, serta penarikan kesimpulan. Secara singkat, dokumen tersebut menjelaskan bentuk-bentuk pernyataan seperti pernyataan tunggal, pernyataan majemuk, negasi, konjungsi, disjungsi, implikasi, dan kuantor; serta penarikan kesimpulan melalui modus ponens, modus tollens, dan silogisme.
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Dynamic Simulation of a Hybrid Solar and Ocean Thermal Energy Conversion SystemIJRES Journal
Ocean thermal energy conversion (OTEC) is à system in which electricity is produced using small temperature difference of warm surface water and deep cold water in oceans. This paper analyzes the dynamic stability and performance simulation results of a solar and ocean thermal energy conversion (SOTEC) system connected to a power grid through undersea cables. In SOTEC, the temperature of warm sea water was boosted by using a typical low-cost solar thermal collector. The complete system model is established from the dynamics of each subsystem and their interconnections. Specifically, we examine stability and performance of the power system against such disturbance conditions as slow variations of solar radiation and severe three-phase short-circuit fault at the power grid. Simulation results indicate that the design of a power system stabilizer can improve the damping of power system under various disturbance conditions.
Neuronal modeling of patch-clamp data is based on approximations which are valid under specific assumptions regarding cell properties and morphology. Certain cells, which show a biexponential capacitance transient decay, can be modeled with a two-compartment model. However, for parameter-extraction in such a model, approximations are required regarding the relative sizes of the various model parameters. These approximations apply to certain cell types or experimental conditions and are not valid in the general case. In this paper, we present a general method for the extraction of the parameters in a two-compartment model without assumptions regarding the relative size of the parameters. All the passive electrical parameters of the two-compartment model are derived in terms of the available experimental data.
Abstract
Neuronal modeling of patch-clamp data is based on approximations which are valid under specific assumptions regarding cell properties and morphology. Certain cells, which show a biexponential capacitance transient decay, can be modeled with a two-compartment model. However, for parameter-extraction in such a model, approximations are required regarding the relative sizes of the various model parameters. These approximations apply to certain cell types or experimental conditions and are not valid in the general case. In this paper, we present a general method for the extraction of the parameters in a two-compartment model without assumptions regarding the relative size of the parameters. All the passive electrical parameters of the two-compartment model are derived in terms of the available experimental data. The experimental data is obtained from a DC measurement (where the command potential is a hyperpolarizing DC voltage) and an AC measurement (where the command potential is a sinusoidal stimulus on a hyperpolarized DC potential) performed on the cell under test. Computer simulations are performed with a circuit simulator, XSPICE, to observe the effects of varying the two-compartment model parameters on the capacitive transients of the current response. Our general solution for the parameter-estimation of a two-compartment model may be used to model any neuron, which has a biexponential capacitive current decay. In addition, our model avoids the need for simplifying and perhaps erroneous approximations. Our equations may be easily implemented in hardware/software compensation schemes to correct the recorded currents for any series resistance or capacitive transient errors. Our general solution reduces to the results of previous researchers under their approximations.
1) Researchers developed a new structure to immobilize the Rhodobacter sphaeroides reaction center (RC) protein on a gold electrode using cytochrome c (cyt c) as a linker. Cytochrome c was attached to a self-assembled monolayer on the electrode, which then bound the RC protein.
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The document summarizes heat and mass transfer characteristics of direct methanol fuel cells (DMFCs) based on experiments and modeling. Key points:
- A 3D non-isothermal model is developed to predict methanol and temperature distributions in the anode. Experimental results validate the model.
- Increasing methanol concentration does not significantly impact net water generation but does increase methanol crossover, affecting cell performance.
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This document summarizes a study that used molecular docking to test three porphyrin compounds (TPPS, FeTPPS, and FeNOTPPS) as potential inhibitors of acetylcholinesterase (AChE) to treat Alzheimer's disease. FeNOTPPS was found to form the most stable complex with the AChE enzyme from Drosophila melanogaster. The scoring functions indicated that FeNOTPPS had the highest binding affinity and was therefore predicted to be the most efficacious inhibitor of the three compounds tested. The breakdown of cholinergic neurons in Alzheimer's disease reduces AChE activity, and inhibiting AChE with porphyrin compounds may help increase acetylcholine levels in the brain
This document summarizes research on a series of siloxane-based side chain liquid crystal polymers where the length of the coupling chain between the mesogenic unit and polymer backbone was systematically varied. All polymers exhibited a smectic phase and the nematic-isotropic transition temperature increased with longer coupling chain length. Electro-optic measurements found that threshold voltage for reorientation decreased with increasing chain length due to changes in intrinsic curvature elasticity rather than orientational order. A model is presented where constraints from coupling the mesogenic units to the backbone influence the observed electric-optic properties as chain length varies.
A series of siloxane based side chain liquid crystal polymers have been prepared with asystematic variation in spacer length. Nematic liquid crystal polymers possess large optical nonlinearities owing to their large refractive index anisotropy coupled with the collective molecular reorientation. All the polymer exhibited a smectic phase, for which the Nematic -isotropic transition temperature increased as the spacer length increased. Electro-optic measurements are used to evaluate the threshold voltages for this series of polymers. It is found that with increasing spacer length (n) of polymer the threshold voltage is lowered and that the variation of the threshold voltage arises from changes to the intrinsic curvature elasticity rather than to differences in orientational order. A simple model is used to indicate the origion of the effects observed which appear to arise from the constraints offered by the coupling of the mesogenic units to the polymer backbone.
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J. biol. chem. 2014-selwa-jbc.m113.530410
1. Daniel Ladant and Thérèse E. Malliavin
Chenal, Ana-Cristina Sotomayor-Perez,
Edithe Selwa, Marilyne Davi, Alexandre
Studies
Molecular Dynamics and Mutagenesis
Adenylyl Cyclase by Calmodulin:
Bordetella pertussisAllosteric Activation of
Molecular Biophysics:
published online June 6, 2014J. Biol. Chem.
10.1074/jbc.M113.530410Access the most updated version of this article at doi:
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2. Mutants of AC and AC/CaM interaction 1
June 5, 2014
Allosteric activation of Bordetella pertussis adenylyl
cyclase by calmodulin: molecular dynamics and
mutagenesis studies
Edithe Selwa1,3, Marilyne Davi2, Alexandre Chenal2, Ana-Cristina Sotomayor-P´erez2,
Daniel Ladant*2 and Th´er`ese E Malliavin*1
1 Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unit´e de Bioinformatique Struc-
turale, 75015 Paris, France
2
Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unit´e de Biochimie des Interactions
Macromol´eculaires, 75015 Paris, France
3
Universit´e Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Dr Roux, 75015 Paris, France
Corresponding authors:
Th´er`ese E Malliavin, Unit´e de Bioinformatique Structurale, UMR CNRS 3528, rue du Dr
Roux, 75015 Paris, France; mail: therese.malliavin@pasteur.fr, tel.: 00 33 1 45 68 88 54
Daniel Ladant, Unit´e de Biochimie des Interactions Macromol´eculaires, UMR CNRS 3528,
rue du Dr Roux, 75015 Paris, France; mail: daniel.ladant@pasteur.fr, tel.: 00 33 1 45 68
84 00
Keywords: adenylyl cyclase,Bordetella pertussis, calcium, calmodulin affin-
ity, allostery, molecular dynamics
June 5, 2014
Running Title: AC mutants and AC/CaM interaction
Background: Adenylyl cyclase (AC)
from Bordetella pertussis is activated when
it interacts with calmodulin (CaM).
Results: A triple mutant of AC, which
was predicted by molecular modeling, exhib-
ited a highly reduced affinity for CaM.
Conclusion: This study suggests that
a long-range connection between CaM and
the AC catalytic loop is crucial for AC acti-
vation.
Significance: Molecular modeling
identified critical molecular determinants for
the allosteric activation of AC.
ABSTRACT
Adenylyl cyclase (AC) toxin is an es-
sential toxin that allows Bordetella per-
tussis to invade eukaryotic cells, where
it is activated after binding to calmod-
ulin (CaM). Based on the crystal
structure of the AC catalytic domain
in complex with the C-terminal half
of CaM (C-CaM), our previous molec-
ular dynamics simulations (Selwa et
al., Proteins 80, 1028–1040, 2012) sug-
gested that three residues, i.e., Arg338,
http://www.jbc.org/cgi/doi/10.1074/jbc.M113.530410The latest version is at
JBC Papers in Press. Published on June 6, 2014 as Manuscript M113.530410
Copyright 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
3. Mutants of AC and AC/CaM interaction 2
Asn347, and Asp360, might be impor-
tant for stabilizing the AC/CaM in-
teraction. These residues belong to a
loop-helix-loop motif (LHL) at the C-
terminal end of AC, which is located
at the interface between CaM and the
AC catalytic loop. In the present
study, we conducted the in silico and
in vitro characterization of three AC
variants, where one (Asn347; ACm1A),
two (Arg338 and Asp360; ACm2A), or
three residues (Arg338, Asn347, and
Asp360; ACm3A) were substituted
with Ala. Biochemical studies showed
that the affinities of ACm1A and
ACm2A for CaM were not affected
significantly, whereas that of ACm3A
was reduced dramatically. To under-
stand the effects of these modifica-
tions, molecular dynamics (MD) sim-
ulations were performed based on the
modified proteins. The MD trajecto-
ries recorded for the ACm3A/C-CaM
complex showed that the calcium-
binding loops of C-CaM exhibited
large fluctuations, which could be
related to the weakened interaction
between ACm3A and its activator.
Overall, our results suggest that the
LHL motif at the C-terminal end of
AC is crucial during CaM-binding for
stabilizing the AC catalytic loop in an
active configuration.
INTRODUCTION
The adenylyl cyclase toxin (CyaA) from
Bordetella pertussis, the causative agent of
whooping cough, plays an essential role
in host invasion [1–3]. CyaA is able to
invade eukaryotic target cells where it is
activated by interacting with calmodulin
(CaM), thereby overproducing cAMP, which
disorganizes cellular signaling processes and
triggers host cell death [4–12]. Several crys-
tallographic structures have been reported
of the CyaA catalytic domain (AC) in com-
plex with the C terminal moiety of CaM
(C-CaM) [13] (Figure 1). These structures
are physiologically relevant because C-CaM
has been shown [14] to be as potent in acti-
vating the enzymatic activity of AC as the
full-length CaM. In the AC/C-CaM com-
plex (Figure 1a), the AC domain includes
three main regions, CA (residues 7–61, 187–
197, 261–299, and 313–345; colored in green)
in the middle of the structure, and CB
(residues 62–186, colored in orange) and
SA (residues 192–254, colored in purple) at
the two extremities. The C-terminal tail
(residues 346–364, colored in cyan) and the
C-loop of the catalytic site (residues 300–
312, colored in yellow) are found in the CA
region. At the C-terminal end of AC, a
loop-helix-loop motif (LHL) that includes
residues from Arg338 to Asp360 (Figure 1c)
is present at the interface between C-CaM
and a major AC catalytic loop that spans
residues 300–312. In C-CaM, the calcium
ions are bound to EF-hands 3 and 4, where
EF-hand 3 is close to the interaction inter-
face with AC.
In a previous study [15], we analyzed
the interaction between the catalytic do-
main of AC from B. pertussis and C-CaM
based on the molecular dynamics (MD) tra-
jectories using maps of the energetic influ-
ences [16, 17]. Three residues in the LHL
motif, i.e., Arg338, Asn347, and Asp360 (Fig-
ure 1b), were predicted to be important for
the stability of the AC/CaM interaction,
where Arg338 and Asp360 make contact with
C-CaM, whereas Asn347 is in direct contact
with the AC catalytic loop. In the present
study, to further characterize the potential
roles of these residues in AC/CaM interac-
tions, we performed in silico MD simulations
and in vitro biochemical and biophysical
studies of the three modified AC proteins,
where one (Asn347; ACm1A), two (Arg338
and Asp360; ACm2A), or three residues
(Arg338, Asn347, and Asp360; ACm3A) were
substituted with Ala. We found that the
ACm3A variant exhibited a strongly re-
duced affinity for CaM, whereas the affini-
ties of the ACm1A and ACm2A variants
were similar to that of the wild-type enzyme.
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4. Mutants of AC and AC/CaM interaction 3
This demonstrated the strong synergistic ef-
fects of the three mutations. The MD sim-
ulations showed that the differences in the
behavior of the modified and wild-type com-
plexes were related to differences in the in-
ternal mobility of the C-CaM calcium loops.
These differences in mobility may induce di-
rect or indirect weakening of the C-CaM/AC
interaction observed in the ACm3A modi-
fied protein. These results, as well as an
analysis of the geometrical strain, suggest
that the LHL motif at the C-terminal end
of AC is important for establishing a long-
range connection between CaM binding and
the stabilization of the AC catalytic loop in
an active configuration, thus it is a criti-
cal module during the allosteric activation
of AC by CaM.
1 EXPERIMENTAL PRO-
CEDURES
MD simulations
The wild-type AC/C-CaM complexes in
the presence (ACwt 2Ca) and absence
(ACwt 0Ca) of calcium were prepared as de-
scribed previously [15] and the three mod-
ified systems, i.e., ACm1A, ACm2A, and
ACm3A, were generated in the following
manner. The last snapshot of the simula-
tion WT2Ca T1 (see Table I for the defi-
nition of this trajectory) was extracted and
the sidechains of the modified residues were
replaced by Ala sidechains using the LEaP
module from AMBER 10 [18] and the force
field FF99SB [19]. Na+ counterions were
added to neutralize the system.
The five systems, i.e., ACwt 2Ca,
ACwt 0Ca, ACm1A, ACm2A, and ACm3A
(Table I) were then hydrated in a box of
TIP3P [20] water molecules using cutoff val-
ues of 10 or 12.5 ˚A and periodic boundary
conditions. The calcium Lennard-Jones pa-
rameters of the Ca2+ ions comprised a van
der Waals radius R of 1.7131 ˚A, and a well
depth of 0.459789 kcal/mol [21].
The MD trajectories were initiated and
ran as described previously 15. For each sys-
tem, two simulations were recorded, which
were labeled using the system name and the
strings “T1” and “T2” (Table I).
The formation of hydrogen bonds be-
tween protein acceptor and donor groups
was monitored by selecting donor and ac-
ceptor pairs with a proximity of less than 3
˚Aevery ten recorded frames. This selection
was implemented using the Biskit python li-
brary [22]. In the following, the AC and
C-CaM residues are labeled based on their
numbers in the crystallographic structure
1YRT [13] and the C-CaM residue numbers
are followed by the letter a.
Along the MD trajectories, the geomet-
ric strain [23] of a residue i was calculated
using the following equation:
p(i) =
j
(dij − dij )2
[1−tanh( dij −7)]/2
(1)
where (dij − dij )2 is the intantaneous de-
viation from the average of the distance dij
between the α carbons of residues i and
j. It was shown previously [23] that hinge
residues are characterized by large p(i) val-
ues.
Plasmids
Plasmid pTRAC384GK was used to express
the wild-type AC (corresponding to the first
384 codons of CyaA, followed by the two
residues Gly and Lys), as described pre-
viously 24. Plasmids pKTRACm2A and
pKTRACm3A, which were used to express
ACm2A and ACm3A, respectively, were
constructed from plasmid pKTRAC, an ex-
pression vector for the CyaC and CyaA pro-
teins of B. pertussis. This plasmid was ob-
tained from plasmid pTRACG [25] by re-
placing the ampicillin (Amp) resistance gene
with a kanamycin (Kan) resistant gene from
plasmid pKT25 [26]. In pKTRAC, both the
cyaC and cyaA genes are expressed under
the control of the λ phage Pr promoter. The
plasmid has a ColE1 replication origin and it
also expresses a thermosensitive λ repressor
cI857, which strongly represses gene tran-
scription at the λ Pr promoter at tempera-
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5. Mutants of AC and AC/CaM interaction 4
tures below 32 ◦C. Thus, expression of the
CyaC and CyaA proteins can be triggered
by shifting the cells to 37–42 ◦C.
Plasmid pKTRACm3A was constructed
by subcloning between the unique AgeI and
BamHI sites of pKTRAC, a synthetic gene
(synthesized by GeneArt, Life Technologies
SAS, France) that encodes CyaA residues
320–384, followed by the two residues Gly
and Lys, and where the three codons,
Arg338, Asn347, and Asp360, were changed
to Ala codons (the sequence of the ACm3A
gene is available upon request).
Plasmid pKTRACm2A was constructed
by subcloning between the unique SnaBI
and BsiWI sites of plasmid pKTRACm3A
using a double-stranded synthetic oligonu-
cleotide produced via the hybridization
of the following two oligonucleotides: 5’-
GTTTTCTACGAAAACCGCGC-3’ and 5’-
GTACGCGCGGTTTTCGTAGAAAAC-3’
(Eurofins MWG GmbH, Ebersberg, Ger-
many), thereby restoring the wild-type
Asn347 codon (the SnaBI site was abol-
ished after oligonucleotide insertion; see
Figure S1). The DNA sequences of the
modified cyaA’ genes in pKTRACm2A and
pKTRACm3A were confirmed by DNA se-
quencing (Eurofins MWG GmbH, Ebers-
berg, Germany).
Plasmid pKT7AC contained a synthetic
AC gene (synthesized by GeneArt, Life
Technologies SAS, France) that encoded the
first 384 codons of CyaA, which was op-
timized for high expression in Escherichia
coli, followed by the two residues Gly and
Lys (the full DNA sequence is available
upon request). This synthetic AC gene was
cloned under the control of a T7 promoter
and a synthetic RBS sequence in the vector
pMK-RQ (GeneArt, Life Technologies SAS,
France), a plasmid with a ColE1 replication
origin and a Kan resistance gene.
Plasmid pKT7ACm1A was used
to express ACm1A and it was con-
structed by subcloning between the
unique SnaBI and BsiWI sites of plas-
mid pKT7AC, a double-stranded syn-
thetic oligonucleotide, which was obtained
by hybridizing two oligonucleotides: 5’-
GTGTTCTACGAAGCTCGCGC-3’ and 5’-
GTACGCGCGAGCTTCGTAGAACAC-3’
(Eurofins MWG GmbH, Ebersberg, Ger-
many), thereby replacing the wild-type
Asn347 codon with an Ala codon (sequence
available upon request). The DNA sequence
of the modified cyaA’ gene in pKT7ACm1A
was confirmed by DNA sequencing (Eurofins
MWG GmbH, Ebersberg, Germany).
Purification of AC proteins
The wild-type AC, ACm2A, and ACm3A
were expressed in the E. coli BLR
strain (Novagen, Darmstadt, Germany)
by transformation with the plasmids
pTRAC384GK, pKTRACm2A, and pK-
TRACm3A, respectively. The transfor-
mants were grown at 30 ◦C in LB medium
that contained either 100 µg/mL Amp
(for plasmid pTRAC384GK) or 50 µg/mL
Kan (for plasmids pKTRACm2A or pK-
TRACm3A). When the culture reached an
optical density of 0.6–0.8 at 600 nm, expres-
sion of the proteins was triggered by shifting
the growth temperature to 42 ◦C. After 150
min of additional growth at 42 ◦C, the cells
were collected by centrifugation (20 min,
10,000 × g, 4 ◦C) and the cell pellets were
frozen at -20 ◦C.
ACm1A was expressed in the E. coli
KRX strain (Promega, Madison, USA),
which was transformed with the plas-
mid pKT7ACm1A. The transformants were
grown at 37 ◦C in LB medium containing
50 µg/mL Kan to an optical density of 0.6–
0.8. Next, expression of the proteins was
triggered by the addition of 0.1% rhamnose
(to induce the expression of the chromoso-
mally encoded T7 RNA polymerase). After
180 min of additional growth at 37 ◦C, the
cells were collected by centrifugation, as de-
scribed above.
The cell pellets were resuspended in 20
mM HEPES-Na, pH 7.5, and disrupted by
sonication at 4 ◦C. The sonicated suspen-
sion was centrifuged for 20 min at 13,000 ×
g and 4 ◦C. The supernatant was discarded
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6. Mutants of AC and AC/CaM interaction 5
and the pellet was resuspended in 8 M urea
with 20 mM HEPES-Na (pH 7.5), and ag-
itated overnight at 4 ◦C. After 20 min of
centrifugation at 13,000 × g at 4 ◦C, the su-
pernatant (“urea extract”) that contained
the solubilized AC proteins was collected.
The AC proteins were purified accord-
ing to a previously described protocol us-
ing two sequential chromatographic treat-
ments with DEAE-Sepharose [24]. Briefly,
the urea extract was first loaded onto a
DEAE-Sepharose column (20 mL packed
resin) equilibrated in 8 M urea with 20
mM HEPES-Na (pH 7.5). In these con-
ditions, the AC protein did not bind to
the resin and it was recovered in the flow-
through (FT) fractions. The collected FT
fractions were then diluted five times with
20 mM HEPES-Na (pH 7.5) and applied to
a second DEAE-Sepharose column (20 mL
packed resin), which had been equilibrated
in 20 mM HEPES-Na (pH 7.5). In these
conditions, the AC proteins were retained
on the resin and, after extensive washing
with 20 mM HEPES-Na (pH 7.5), the pro-
teins were eluted in a soluble form using 20
mM HEPES-Na (pH 7.5) containing 100–
200 mM NaCl. All of the AC protein prepa-
rations exceeded a purity of 95% according
to SDS-PAGE analysis (Figure 6A). The AC
protein content was determined based on the
absorption spectra using an extinction coef-
ficient at 278 nm of 28,000 M−1/cm−−1.
AC enzymatic activity assays
The activity of AC was measured using a
sensitive colorimetric assay, which was re-
ported recently [27]. AC converts ATP into
cAMP and pyrophosphate (PPi), and the
latter can be hydrolyzed further by an ex-
ogenously added pyrophosphatase into two
phosphate molecules (Pi), which can be
quantified using a standard colorimetric as-
say based on the change in the absorbance of
malachite green dye in the presence of phos-
phomolybdate complexes. The amount of
Pi produced was determined using the Pi
color Lock TM ALS colorimetric assay from
Innova Biosciences (Cambridge, UK).
The AC enzymatic assays were per-
formed using a 96-well microtiter plate at
30◦C in a final volume of 50 µL, which con-
tained 50 mM Tris-HCl (pH 8.0), 10 mM
MgCl2, 0.1 mM CaCl2, 0.5 mg/mL bovine
serum albumin, 2 Unit/mL of E. coli inor-
ganic pyrophosphatase (Sigma-Aldrich; the
amount of pyrophosphatase added to the re-
action medium was found to be sufficient
to ensure the immediate and complete con-
version of the released PPi into Pi), 0–1
µM of CaM, and 0.1–1 nM (depending on
the specific activity) of AC proteins (di-
luted from stock solutions in 10 mM Tris-
HCl with 0.2% Tween 20, pH 8.0). The mix-
tures were pre-incubated for 10 min at 30◦C.
Then, the enzymatic reactions were initiated
by adding 2 mM ATP (final concentration)
and the microplate was incubated at 30◦C
with agitation. At various incubation times
(typically 2–10 min), 10 µL samples were
taken from each well and transferred into a
second 96-well microtiter plate, where each
well contained 100 µL of a Pi-ALS mixture
made of 2 volumes of H2O plus 8 volumes
of Pi ColorLock ALS reagent (provided in
the Pi-ALS kit from Innova Biosciences).
The enzymatic reaction was stopped imme-
diately by the acidic conditions of the Pi-
ALS mixture. After 10–13 min incubation
at room temperature, 10 µL of stabilizer so-
lution (from the Pi-ALS kit) was added to
prevent further nonenzymatic breakdown of
the phosphorylated substrate in acidic con-
ditions (according to the kit instructions).
After further incubation for 30–60 min at
room temperature, the optical density at
595 nm (OD595) was recorded using a mi-
croplate reader (Tecan, Lyon, France). A
standard curve was obtained in parallel by
adding known concentrations of Pi to the
Pi-ALS mixture, which was used to convert
the OD595values into moles of PPi produced.
The enzymatic activity was calculated based
on the initial velocity of PPi synthesis (in
the conditions described above, the accumu-
lation of PPi was linear with time).
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7. Mutants of AC and AC/CaM interaction 6
Biophysical characterization of AC
proteins
Size exclusion chromatography (SEC) was
performed using a Superdex 200 column
(GE Healthcare), which was controlled by
a GPCmax module that was connected on-
line to a triple detector array (TDA) model
302 (Viscotek Ltd, Houston, Basingstoke,
U.K.), as described previously [28]. The
running buffer was buffer A (20 mM Hepes,
100 mM NaCl, pH 7.4) and the protein
concentrations were 10–20 µM. Synchrotron
radiation circular dichroism (SR-CD) ex-
periments were conducted at the SOLEIL
synchrotron facility (DISCO beamline, Gif-
sur-Yvette, France), as described previ-
ously [29]. Briefly, the SR-CD spectra were
recorded at 25◦C using an integration time
of 1.2 s and a bandwidth of 1 nm, with a
1-nm resolution step. Each far-UV spec-
trum represented the average of at least
three individual scans. Optical cells with
a 26 µm path-length and CaF2 windows
(Hellma) were used for recording CD sig-
nals in the far-UV region (180–260 nm).
The protein concentrations were 25–50 µM
for AC proteins and 250 µM for CaM in
buffer A. Equimolar mixtures of enzyme and
activator were used to obtain the AC-CaM
and ACm3A-CaM spectra. The thermo-
dynamic stability of the AC proteins was
investigated by following their urea-induced
denaturation (at 25◦C, in buffer A), which
was monitored by tryptophan fluorescence
spectroscopy as described previously [30]
using an FP-6200 spectrofluorimeter (Jasco,
Japan) in a Peltier-thermostated cell holder,
with a 1-cm path length quartz cell (101.QS,
Hellma). The thermodynamic parameters
(urea concentration required to unfold half
the population of native proteins, [urea]1/2,
the cooperativity, m, and free energy, ∆G)
were deduced from the fluorescence data, as
described previously 30.
RESULTS
C-CaM/AC interface in the crystal-
lographic structures
To explore the potential role of AC residues
Arg338, Asn347, and Asp360 in CaM-induced
activation, as suggested previously [15], we
first checked the conservation of the atomic
contacts established by these residues in
the crystallographic structures of the AC/C-
CaM complex [13]. The analysis of the
hydrogen bonds and water-mediated con-
tacts established between C-CaM and AC
residues showed that the residues Arg338
and Asp360 were often involved in hydrogen
bonds or in water-mediated contacts with
C-CaM (data not shown, but available on
request). Furthermore, most of the contacts
and hydrogen bonds between the LHL mo-
tif (residues 338–360) (Figure 1c) and other
AC residues were present in more than three
crystallographic structures (data not shown,
but available on request), thereby suggest-
ing that the LHL motif plays an important
role in the stabilization of the AC structure.
C-CaM/AC interaction along MD
trajectories
Six independent MD simulations were
recorded using the AC/C-CaM complex,
where AC was modified in three dif-
ferent ways. Two simulations, i.e.,
”T1” and ”T2,” were performed for each
AC variant, ACm1A (N347A), ACm2A
(R338A, D360A), and ACm3A(R338A,
N347A, D360A) (Figure 1b). The aim of
these simulations was to analyze the rela-
tive stability of the different ACm/C-CaM
complexes and to relate these to the obser-
vations described previously based on the X-
ray crystallographic structures.
The conformational drift of the AC/C-
CaM complex was monitored during
trajectories ACm1A T1, ACm2A T1,
ACm3A T1, ACm1A T2, ACm2A T2, and
ACm3A T2 (Figure 2). The global RMSD
calculated for the different AC/C-CaM com-
plexes (Figures 2a and 2e) were similar
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8. Mutants of AC and AC/CaM interaction 7
for all variants and they rapidly reached
a plateau around 3 ˚A. The RMSD plateau
was similar to that obtained based on the
MD trajectories of the wild-type AC/C-
CaM complex (Figure 2a in Ref [15]). Thus,
these modifications did not destabilize the
overall AC structure at least during the
timescales considered by the MD trajecto-
ries.
The conformational drifts (RMSD) of
the different protein regions in the two sets
of simulations (Figures 2b-d and 2f-h) were
very similar for CB (orange curves), the C
loop (yellow curves), the F, G, H, and H’
α helices, and the loop at the extremity of
SA, which all had RMSD plateaus that were
similar to or less than 2 ˚A. The CA region
(green curves), SA region (violet curves),
and C-terminal tail (cyan curves) had more
significant drifts, where the RMSD values
were larger than 4 ˚A. The CA and C ter-
minal drifts are not surprising because the
modified residues were located in these re-
gions. Interestingly, the increased internal
mobility of the C terminal tail is analogous
to that observed in a wild-type AC/C-CaM
complex (Figure 3a, b of Ref [15]) when the
Ca2+ ions were removed (Figure 3a, b of
Ref [15]). The latter had a lower affinity
in vitro, thus the modifications of residues
Arg338, Asn347, and Asp360 may have de-
creased the affinity of C-CaM for AC.
The water-mediated connections be-
tween AC and C-CaM were also ana-
lyzed along the MD trajectories (data not
shown). The connections that involved the
C-terminal tail of AC were present mainly
in one or two trajectories, which shows that
the interaction at this interface underwent
reorganizations.
C-CaM and AC fluctuations in the
MD trajectories
The behavior of C-CaM was monitored
along the two series of mutant trajectories
and compared with previous observations
[15] obtained using the wild type AC/C-
CaM complex.
In the simulation of the wild-type AC/C-
CaM complex in the absence of calcium ions
(WT0Ca T1) (Figure 3a, solid red curve),
the calcium loop of EF-hand 3 (i.e., between
α helices V and VI) and the C-terminal part
of α helix V exhibited highly increased fluc-
tuations (RMSF). A similar increase was ob-
served in ACm3A T1 (Figure 3b, solid red
curve) but in ACm2A T2 and ACm3A T2
(Figure 3b, dashed green and red curves),
increased fluctuations were found in the cal-
cium loop of EF-hand 4 (i.e., between α
helices VII and VIII). Interestingly, the in-
creased fluctuations in the C-terminal part
of α helix V in ACm3A T1 was associated
with the small number of hydrogen bonds
that connect C-CaM and C tail, i.e., only a
single hydrogen bond is present for over 80%
of the trajectory length between Arg90a and
Glu346.
Analysis of the internal fluctuations of
AC along the various trajectories (data not
shown) detected no major variations be-
tween the different modified proteins, which
agreed with the similar global RMSD that
was observed for all trajectories (Figure 2).
The fluctuations measured in the wild-type
systems were similar to those observed in
the modified proteins, where the largest dif-
ferences were observed for the 226–232 loop
and the C-terminal tail of the protein. It
should be noted that the loop 226–232 is not
visible in the X-ray crystallographic struc-
tures, thereby indicating that it is probably
a highly flexible region.
The coordination of calcium ions by the
C-CaM residues was stable in the EF-hand
3 along the trajectories of the modified pro-
teins (data available on request), but there
were some variations in the EF-hand 4. In-
deed, the calcium coordination by Asp133
in the EF-hand 4 was perturbed in the
two series of simulations. This perturba-
tion agrees with the increased fluctuation
observed in the calcium loop of EF-hand
4 for ACm2A T2 and ACm3A T2 (Figure
3b), and with the increase in the EF-hand 4
angle up to about 100◦.
The C-CaM conformations were ex-
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9. Mutants of AC and AC/CaM interaction 8
tracted from ACm2A T2 and ACm3A T2
(Figure 4) at times when different distances
were observed between Asp133-Oδ1/Oδ2 and
the calcium ion. In both simulations, the
sidechain of Asp133 moved apart and at
the end of the trajectory, the calcium ion
was coordinated by the backbone carbonyl,
instead of the sidechain. This conforma-
tional tendency of Asp133 was increased in
ACm3A T2 compared with ACm2A T2. In-
terestingly, in a steered MD study of the cal-
cium dissociation in CaM [31], it was found
that Asp133 was among the latest residues to
lose calcium coordination. The destabiliza-
tion of the calcium/Asp133 interaction ob-
served in the present study corresponds to
the destabilization of one of the strongest
interactions that defines the calcium coor-
dination in EF-hand 4. Thus, this desta-
bilization indicates that the AC mutations
decreased the calcium binding to CaM.
Overall, the perturbations of the EF-
hand angles and calcium coordination are
precursory indicators of the decrease in the
C-CaM affinity for calcium ions [32,33]. On
longer time scales, this decrease could lead
to the dissociation of calcium ions from C-
CaM and to a decrease in the affinity of AC
for C-CaM, as shown previously [14].
Network of interactions involving
LHL along the MD trajectories
The LHL motif, which contains the three
modified residues, lies at the interface be-
tween C-CaM and the AC catalytic loop.
The hydrogen bonds established by the
residues in the LHL motif were analyzed
in the different AC/C-CaM complexes (data
available on request). Only long-range hy-
drogen bonds (that connected residues sep-
arated by more than ten residues in the
protein sequence) were considered in order
to exclude interactions related to local sec-
ondary structures. Most of these hydrogen
bonds were conserved along the MD tra-
jectories, except for one hydrogen bond be-
tween Asn35 and Tyr342, which was present
only in the modified complexes, and two hy-
drogen bonds between Glu346 and Leu357,
and between Tyr350 and Glu308, which were
observed in less than two simulations. A
lower number of stable hydrogen bonds that
involved modified residues were observed
in the ACm3A T1 and ACm3A T2 simula-
tions. Indeed, Asn347 established hydrogen
bonds with the residues Glu301, Gln302, and
Asn304, which are located in the catalytic
loop. These hydrogen bonds were disrupted
by the change from Asn347 to Ala, except for
the hydrogen bonds that involved the Asn347
backbone hydrogen. Similarly, the hydro-
gen bonds between Asp360 and Arg338 dis-
appeared when Asp360 or Arg338 were mod-
ified to Ala. These observations show that
the overall structure of the LHL motif is con-
served in all systems, and that the LHL con-
nection to C-CaM on one side, as well as to
the C-loop on the other side, were signifi-
cantly weakened in the presence of the triple
modification.
The hydrogen bonds that involved LHL
residues, as well as the protein fluctua-
tions and the correlations in the fluctua-
tion, indicated that there was limited vari-
ation among the protein variants (data not
shown). Thus, the possibility of long-range
communication through LHL was investi-
gated using a parameter that was poten-
tially more sensitive to small variations in
geometry. The geometric strain, as defined
by Chiappori et al. [23] (see Materials and
Methods), exhibits sufficient sensitivity be-
cause it depends on the geometry of the en-
vironment of the analyzed residue within a
sphere of 7 ˚A while it also follows the dis-
tance variations with respect to the average
distance values.
The variations in the geometric strain
along the MD trajectories exhibited corre-
lated transitions between the given residues,
which were due to simultaneous displace-
ments of the environments of these residues.
To summarize these variations, the time
correlation matrices of the geometric strain
were analyzed. The strain correlation peaks
(in pink/yellow) correspond to residue pairs
that are undergoing correlated displace-
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10. Mutants of AC and AC/CaM interaction 9
ments in their environment, thus they are
mechanically correlated. In order to esti-
mate the reliability of the correlation pre-
dictions, the calculation was repeated five
times by selecting at each time, one data-
point over five along the analyzed time
interval. The average values were calcu-
lated among LHL residues (Figure 5) and
among the LHL, C-loop and calcium loop
residues (data not shown but available on
request). The standard deviations obtained
from the repeated calculation of the corre-
lations allowed us to estimate the error on
the correlation, which was 4–6.5% for cor-
relations greater than 0.15. In all trajecto-
ries, the peaks were observed repeatedly be-
tween residues in the α-helix at 346–355. A
general attenuation of the correlations, with
pixel colors changing from pink to yellow,
was observed for the trajectories recorded
in the protein variants compared with those
recorded in the wild type. This suggests
that there was a decrease in the long-range
correlation along the LHL for the modified
proteins.
In vitro characterization of AC vari-
ants that harbored mutations at po-
sitions 338, 347 or 360
To further delineate the effect of the muta-
tions on the activity of AC and its affinity for
CaM, the three variants ACm1A, ACm2A,
and ACm3A were characterized in vitro (see
Materials and Methods). The three modi-
fied proteins and the wild-type catalytic do-
main (AC) were overexpressed in E. coli and
purified to homogeneity, as described pre-
viously ( [24], see Materials and Methods).
The results of the SDS-PAGE analysis of the
purified preparations are shown in Figure
6A.
The enzymatic activities of each AC
variant were determined at different CaM
concentrations, which ranged from 0.03
nM to 1 µM. Figure 6B shows the CaM-
dependency of the enzymatic activity for
each variant as a percentage of the maximal
activity (100 %) determined at the saturat-
ing CaM concentration of 1 µM. The affini-
ties of the AC enzymes for CaM, which were
defined as the CaM concentration at half-
maximal activation K1/2, were determined
(Figure 6C) by curve-fitting with a single
binding isotherm, according to A = AMax
(C/C+ K1/2) where C is the concentration
of CaM, A is the activity at the concentra-
tion C of CaM, and AMax is the maximal
activity measured in the presence of 1 µM
CaM.
As shown in Figures 6B and C, wild-type
AC (labeled ACWT in Figure 6C) exhibited
a kcat of 4600 s−1 (at saturating CaM and 2
mM ATP) and a half-maximal CaM activa-
tion K1/2 of 0.11 nM, which agreed well with
previous studies [13, 24, 34]. The ACm1A
variant, where the Asn347 residue that in-
teracted with the catalytic loop was mod-
ified to Ala, exhibited an enzymatic activ-
ity that was reduced by about half (kcat ∼
2250 s−1) compared with the wild type and
a ∼ five-fold lower affinity for CaM (KCaM
1/2
of 0.61 nM). The dual mutations R338A and
D360A in the ACm2A variant did not af-
fect the catalytic efficiency (kcat ∼ 6000 s−1
was even slightly higher than that of the
wild type) but the affinity for CaM was re-
duced by about six-fold (KCaM
1/2 of 0.66 nM),
as might be expected with modifications at
the CaM interface. Finally, the triple mu-
tant ACm3A was the enzyme that was af-
fected most significantly, where its catalytic
turnover (kcat ∼ 650 s−1) was decreased sig-
nificantly compared with the wild-type AC
(ca 15% of the wild type turnover) and its
affinity for CaM (KCaM
1/2 of 26 nM) was re-
duced by more than 200 times.
These data indicate that the separate
single (N347A) and dual (R338A, and
D360A) modifications had limited effects on
the catalytic and CaM-binding properties of
AC, whereas their combination in a single
enzyme (ACm3A) had strong synergistic ef-
fects on both the enzymatic activity and the
affinity for CaM. This fully supports our pre-
diction that the LHL region is critical for
the allosteric coupling of CaM binding to the
stabilization of the catalytic loop in an enzy-
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11. Mutants of AC and AC/CaM interaction 10
matically active configuration. The two- to
five-fold higher KATP
M levels of all the mod-
ified AC enzymes compared with the wild-
type AC also demonstrate that the LHL mo-
tif is important for maintaining the optimal
conformation of the active site.
To verify that the triple modification of
R338A, N347A, and D360A in ACm3A did
not affect the structural integrity of the pro-
tein, we performed the following biophysi-
cal analyses. First, the proteins were ana-
lyzed by SEC followed by triple detector ar-
ray (SEC-TDA) to determine whether the
mutations affected their oligomeric status.
SEC-TDA provides the molecular masses
of the eluted species by combining static
right angle light scattering with UV ab-
sorbance. The results showed that both
the wild-type and ACm3A proteins were
monomeric species in solution (Figure 7A).
The secondary structure contents of the
CaM and AC proteins, either isolated or in
complexes, were analyzed by SRCD in the
far-UV range. The shapes of the far-UV
CD spectra of wild-type AC and ACm3A
were similar (Figure 7B). The addition of
CaM induced similar changes in the over-
all secondary structure content of both AC
proteins. These results clearly indicate that
the secondary structure content of ACm3A
was not affected by the mutations. Fi-
nally, the thermodynamic stability of both
AC proteins was characterized. The urea-
induced denaturation of the AC proteins
was monitored by tryptophan fluorescence.
The denaturation profiles (Figure 7C). and
the thermodynamic parameters (Figure 7D)
obtained for both proteins were very similar.
Overall, these experiments indicate that the
three modifications in ACm3A did not af-
fect the structural properties or the overall
stability of the protein.
DISCUSSION
Maps of the energetic influences [16, 17]
that were calculated [15] previously using
the AC/C-CaM complex allowed us to iden-
tify three residues, i.e., Arg338, Asn347, and
Asp360, that might affect the interaction be-
tween AC and C-CaM. In the present study,
we characterized three modified proteins,
i.e., ACm1A (N347A), ACm2A (R338A,
D360A), and ACm3A (R338A, N347A and
D360A), using in silico MD simulations and
based on in vitro biochemical and biophysi-
cal studies.
Our in vitro studies showed that the
affinity of the triple mutant ACm3A for
CaM was greatly reduced whereas that
of the single (ACm1A) or dual mutant
(ACm2A) was not affected significantly
compared with that of the wild-type en-
zyme. These results indicate that these
three mutations had a strong synergistic ef-
fect on the CaM-binding affinity. A similar
synergistic effect was noted for the catalytic
efficiency of the enzyme because the enzy-
matic activity of ACm3A was also reduced
significantly (about 15% of the wild-type en-
zyme activity), whereas that of ACm1A was
about 50% of the wild-type activity. The
lower activity of the ACm1A and ACm3A
variants might be expected because the
Asn347 residue interacts directly with the
catalytic loop. Thus, any perturbation of
the interaction between Asn347 and the cat-
alytic loop might directly affect the catalytic
efficiency of AC.
The dynamical behaviors of the three
modified proteins in complex with C-CaM
were also analyzed in silico based on two
series of MD simulations. High variabil-
ity in the establishment of hydrogen bonds
in the complex was observed in the dif-
ferent modified proteins, as well as among
repeated trajectories. However, this vari-
ability could not be assigned to simula-
tion artifacts because similar variability was
observed among the four crystallographic
structures of the complex AC/C-CaM [13].
The analysis of the trajectories recorded
using modified and wild-type AC/C-CaM
complexes, which were conducted in paral-
lel with the experimental characterization
of the AC/CaM interaction, identified two
different routes that allowed the affinity of
AC for C-CaM to decrease. In the first
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12. Mutants of AC and AC/CaM interaction 11
simulation of the triple modified protein
(ACm3A T1), a destabilization of the cal-
cium loop of EF-hand 3 was observed, as
well as a large decrease in the interactions
between C-CaM and the CA region. In the
second trajectory recorded using ACm3A
(ACm3A T2), a destabilization of the cal-
cium coordination in the EF-hand 4 of C-
CaM led to the disruption of the hydrogen
bond between the Asp133 sidechain and cal-
cium. This could be the first step in the pos-
sible dissociation of calcium from C-CaM. It
is known that calcium-free CaM has a lower
affinity for AC [14], thus the destabilization
of calcium coordination would result in a re-
duction of the CaM affinity for AC.
Guo et al. [13] described the crys-
tallographic structure of the complex
AC/C-CaM and characterized one AC
modification: the double modification
E346A/R348A in the C terminal tail. The
modified protein exhibited a reduced enzy-
matic activity as well as a reduced affinity
for CaM. The two amino acids changed
in the E346A/R348A mutant flanked the
Asn347 residue that was modified in the
present study. The hydrogen bonds that in-
volve Glu346 and Arg348 residues varied in
the wild-type AC when calcium ions or C-
CaM were removed from the system, as well
as in the trajectories of the modified AC pro-
tein, but no systematic variations were de-
tected. However, the observations of Guo
et al. [13] based on the E346A/R348A AC
variant agree well with our present study,
as well as supporting the hypothesis that
the LHL motif is critical for linking CaM
binding with the stabilization of the AC cat-
alytic loop in a configuration that is favor-
able for catalysis. Indeed, the LHL mo-
tif is in direct contact with C-CaM on one
side via the Arg338 and Asp360 residues,
as well as the catalytic loop on the other
side via the Asn347 residue. Thus, it is
ideally positioned to relay information re-
lated to CaM-binding on the distant cat-
alytic site of the AC enzyme via a dense
network of atomic contacts, which primar-
ily involve the Arg338, Asn347, and Asp360
residues, as demonstrated in our MD simu-
lations. Long-range communications within
the LHL motif were further suggested by our
analysis of the geometric strain along the
MD trajectories of the different ACs. There-
fore, the LHL motif appears to be a crit-
ical module for the allosteric activation of
AC by CaM. The analysis performed in the
present study was more qualitative than the
method proposed recently by Weinkam et
al. [35,36], but we should note that the avail-
ability of only one structure of AC in com-
plex with Ca2+-loaded C-CaM, as well as
the conformational equilibrium that is prob-
ably adopted by AC in the unbound state,
prevent a more straightforward application
of this method.
From a more general perspective, the de-
tection of the residue networks that are re-
sponsible for long-range communication in-
side a given protein has been attracting
much interest during the last decade [37–41].
These networks are thought to be involved
in biomolecular interactions [42] with fun-
damental roles in many biological processes
[43]. Homologous protein sequence align-
ments [44–46] or analysis of the covariance of
the NMR chemical shifts [47] have predicted
long-range protein communication networks
that agree with experimental observations.
Some of these analyses have facilitated pro-
tein engineering [48]. In the present study,
we combined MD and mutagenesis to iden-
tify a long-range communication network re-
lated to the activation of a key virulence
factor derived from a bacterial pathogen.
This investigation may facilitate new meth-
ods for interfering with the AC-CaM inter-
action, thereby allowing a novel drug discov-
ery approach [49].
ACKNOWLEDGMENTS
We acknowledge SOLEIL for providing the
synchrotron radiation facilities (Proposal
IDs 20110586 and 20120444) and we thank
Frank Wien for assistance with using the
DISCO beamline. Edithe Selwa was sup-
ported by an allocation doctorale from
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13. Mutants of AC and AC/CaM interaction 12
MENRT, which was distributed by Uni-
versit´e Pierre et Marie Curie (Paris VI).
Ana Cristina Sotomayor P´erez was sup-
ported by an Institut Pasteur PTR grant
(PTR#374). This project was supported by
the Institut Pasteur and the Centre National
de la Recherche Scientifique (CNRS UMR
3528, Biologie Structurale et Agents Infec-
tieux). Data not shown in the manuscript
may be obtained from the authors (Daniel
Ladant: daniel.ladant@pasteur.fr; Th´er`ese
Malliavin: therese.malliavin@pasteur.fr) on
request.
References
[1] Ladant, D. and Ullmann, A. (1999) Bordetella pertussis adenylate cyclase: a toxin
with multiple talents. Trends Microbiol 7, 172–176
[2] Vojtova, J., Kamanova, J., and Sebo, P. (2006) Bordetella adenylate cyclase toxin: a
swift saboteur of host defense. Curr Opin Microbiol 9, 69–75
[3] Carbonetti, N. (2010) Pertussis toxin and adenylate cyclase toxin: key virulence
factors of Bordetella pertussis and cell biology tools. Future Microbiol 5, 455–469
[4] Wolff, J., Cook, G., Goldhammer, A., and Berkowitz, S. (1980) Calmodulin activates
prokaryotic adenylate cyclase. Proc Natl Acad Sci USA 77, 3841–3844
[5] Confer, D. and Eaton, J. (1982) Phagocyte impotence caused by an invasive bacterial
adenylate cyclase. Science 217, 948–950
[6] Rogel, A., Schultz, J., Brownlie, R., Coote, J., Parton, R., and Hanski, E. (1989)
Bordetella pertussis adenylate cyclase: purification and characterization of the toxic
form of the enzyme. EMBO J 8, 2755–2760
[7] Goodwin, M. and Weiss, A. (1990) Adenylate cyclase toxin is critical for colonization
and pertussis toxin is critical for lethal infection by Bordetella pertussis in infant
mice. Infect Immun 58, 3445–3447
[8] Khelef, N., Zychlinsky, A., and Guiso, N. (1993) Bordetella pertussis induces apoptosis
in macrophages: role of adenylate cyclase-hemolysin. Infect Immun 61, 4064–4071
[9] Harvill, E., Cotter, P., Yuk, M., and Miller, J. (1999) Probing the function of Bor-
detella bronchiseptica adenylate cyclase toxin by manipulating host immunity. Infect
Immun 67, 1493–1500
[10] Hewlett, E., Donato, G., and Gray, M. (2006) Macrophage cytotoxicity produced by
adenylate cyclase toxin from Bordetella pertussis: more than just making cyclic AMP!
Mol Mic 59, 447–459
[11] Cheung, G., Dickinson, P., Sing, G., Craigon, M., Ghazal, P., Parton, R., and Coote,
J. (2008) Transcriptional responses of murine macrophages to the adenylate cyclase
toxin of Bordetella pertussis. Microb Pathog 44, 61–70
[12] Kamanova, J., Kofronova, O., Masin, J., Genth, H., Vojtova, J., Linhartova, I., Be-
nada, O., Just, I., and Sebo, P. (2008) Adenylate cyclase toxin subverts phagocyte
function by RhoA inhibition and unproductive ruffling. J Immunol 181, 5587–5597
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
14. Mutants of AC and AC/CaM interaction 13
[13] Guo, Q., Shen, Y., Lee, Y., Gibbs, C., Mrksich, M., and Tang, W. (2005) Structural
basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.
EMBO J. 24, 3190–3201
[14] Shen, Y., Lee, Y., Soelaiman, S., Bergson, P., Lu, D., Chen, A., Beckingham, K.,
Grabarek, Z., Mrksich, M., and Tang, W. (2002) Physiological calcium concentrations
regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins. EMBO J 21,
6721–6732
[15] Selwa, E., Laine, E., and Malliavin, T. (2012) Differential role of Calmodulin and
Calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from
Bordetella pertussis. Proteins 80, 1028–1040
[16] Hamacher, K., Trylska, J., and McCammon, J. (2006) Dependency map of proteins
in the small ribosomal subunit. PloS Comput. Biol. 2, e10
[17] Laine, E., Blondel, A., and Malliavin, T. (2009) Dynamics and Energetics: A Con-
sensus Analysis of the Impact of Calcium on EF-CaM Protein Complex. Biophysical
Journal 96, 1–15
[18] Case, D., Cheatham, T., Darden, T., Gohlke, H., Luo, R., Merz, K., Onufriev, A.,
Simmerling, C., Wang, B., and Woods, R. (2005) The AMBER biomolecular simula-
tion programs. J Computat Chem 26, 1668–1688
[19] Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C.
(2006) Comparison of multiple AMBER force fields and development of improved
protein backbone parameters. Proteins 65, 712–725
[20] Jorgensen, W. (1981) Transferable intermolecular potential functions for water, alco-
hols and ethers. application to liquid water. J. Am. Chem. Soc. 103, 335–340
[21] Aqvist, J. (1990) Ion-water interaction potentials derived from free energy perturba-
tion simulations. J Phys Chem 94, 8021–8024
[22] Grunberg, R., Nilges, M., and Leckner, J. (2007) Biskit–a software platform for struc-
tural bioinformatics. Bioinformatics 23, 769–770
[23] Chiappori, F., Merelli, I., Colombo, G., Milanesi, L., and Morra, G. (2012) Molecular
mechanism of allosteric communication in Hsp70 revealed by molecular dynamics
simulations. PLoS Comput Biol 8, e1002844
[24] Vougier, S., Mary, J., Dautin, N., Vinh, J., Friguet, B., and Ladant, D. (2004) Essen-
tial role of methionine residues in calmodulin binding to Bordetella pertussis adeny-
late cyclase, as probed by selective oxidation and repair by the peptide methionine
sulfoxide reductases. J Biol Chem 279, 30210–30218
[25] Gmira, S., Karimova, G., and Ladant, D. (2001) Characterization of recombinant
Bordetella pertussis adenylate cyclase toxins carrying passenger proteins. Research
in microbiology 152, 889–900
[26] Karimova, G., Ullmann, A., and Ladant, D. (2001) Protein-protein interaction be-
tween Bacillus stearothermophilus tyrosyl-tRNA synthetase subdomains revealed by
a bacterial two-hybrid system. Journal of molecular microbiology and biotechnology
3, 73–82
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
15. Mutants of AC and AC/CaM interaction 14
[27] Laine, E., Goncalves, C., Karst, J., Lesnard, A., Rault, S., Tang, W., Malliavin,
T., Ladant, D., and Blondel, A. (2010) Use of allostery to identify inhibitors of
calmodulin- induced activation of Bacillus anthracis Edema Factor. Proc. Natl. Acad.
Sci. U.S.A. 107, 11277–11282
[28] Karst, J., Sotomayor-P´erez, A., Guijarro, J., Raynal, B., Chenal, A., and Ladant,
D. (2010) Calmodulin-induced conformational and hydrodynamic changes in the cat-
alytic domain of Bordetella pertussis adenylate cyclase toxin. Biochemistry 49, 318–
328
[29] Sotomayor-P´erez, A., Subrini, O., Hessel, A., Ladant, D., and Chenal, A. (2013)
Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State
and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein. J Am
Chem Soc 135, 11929–11934
[30] Chenal, A., Karst, J., Sotomayor-P´erez, A., Wozniak, A., Baron, B., England, P.,
and Ladant, D. (2010) Calcium-induced folding and stabilization of the intrinsically
disordered RTX domain of the CyaA toxin. Biophys J 99, 3744–3753
[31] Zhang, Y., Tan, H., Lu, Y., Jia, Z., and Cheng, G. (2008) Ca(2+) dissociation from
the C-terminal EF-hand pair in calmodulin: a steered molecular dynamics study.
FEBS Lett 582, 1355–1361
[32] Zhang, M., Tanaka, T., and Ikura, M. (1995) Calcium-induced conformational transi-
tion revealed by the solution structure of apo calmodulin. Nat Struct Biol 2, 758–767
[33] Finn, B., Evenas, J., Drakenberg, T., Waltho, J., Thulin, E., and Forsen, S. (1995)
Calcium-induced structural changes and domain autonomy in calmodulin. Nat Struct
Biol 2, 777–783
[34] Glaser, P., Elmaoglou-Lazaridou, A., Krin, E., Ladant, D., B´arzu, O., and Danchin,
A. (1989) Identification of residues essential for catalysis and binding of calmodulin
in Bordetella pertussis adenylate cyclase by site-directed mutagenesis. EMBO J 8,
967–972
[35] Weinkam, P., Pons, J., and Sali, A. (2012) Structure-based model of allostery predicts
coupling between distant sites. PNAS 109, 4875–4880
[36] Weinkam, P., Chen, Y., Pons, J., and Sali, A. (2013) Impact of mutations on the
allosteric conformational equilibrium. J Mol Biol 425, 647–661
[37] Chennubhotla, C. and Bahar, I. (2007) Signal propagation in proteins and relation to
equilibrium fluctuations. PLoS Comput Biol 3, 1716–1726
[38] del Sol, A., Tsai, C., Ma, B., and Nussinov, R. (2009) The origin of allosteric func-
tional modulation: multiple pre-existing pathways. Structure 17, 1042–1050
[39] Dubay, K., Bothma, J., and Geissler, P. (2011) Long-range intra-protein communi-
cation can be transmitted by correlated side-chain fluctuations alone. PLoS Comput
Biol 7, e1002168
[40] Kuzu, G., Keskin, O., Gursoy, A., and Nussinov, R. (2012) Constructing structural
networks of signaling pathways on the proteome scale. Curr Opin Struct Biol 22,
367–377
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
16. Mutants of AC and AC/CaM interaction 15
[41] Cilia, E., Vuister, G., and Lenaerts, T. (2012) Accurate prediction of the dynamical
changes within the second PDZ domain of PTP1e. PLoS Comput Biol 8, e1002794
[42] Bakan, A. and Bahar, I. (2009) The intrinsic dynamics of enzymes plays a dominant
role in determining the structural changes induced upon inhibitor binding. Proc Natl
Acad Sci USA 106, 14349–14354
[43] Nussinov, R., Ma, B., Tsai, C., and Csermely, P. (2013) Allosteric conformational
barcodes direct signaling in the cell. Structure 21, 1509–1521
[44] Lockless, S. and Ranganathan, R. (1999) Evolutionarily conserved pathways of ener-
getic connectivity in protein families. Science 286, 295–299
[45] Dickson, R., Wahl, L., Fernandes, A., and Gloor, G. (2010) Identifying and seeing
beyond multiple sequence alignment errors using intra-molecular protein covariation.
PLoS One 5, e11082
[46] Reynolds, K., McLaughlin, R., and Ranganathan, R. (2011) Hot spots for allosteric
regulation on protein surfaces. Cell 147, 1564–1575
[47] Selvaratnam, R., Chowdhury, S., VanSchouwen, B., and Melacini, G. (2011) Mapping
allostery through the covariance analysis of NMR chemical shifts. Proc Natl Acad Sci
U S A 108, 6133–6138
[48] Lee, J., Natarajan, M., Nashine, V., Socolich, M., Vo, T., Russ, W., Benkovic, S.,
and Ranganathan, R. (2008) Surface sites for engineering allosteric control in proteins.
Science 322, 438–442
[49] Seifert, R. and Dove, S. (2012) Towards selective inhibitors of adenylyl cyclase toxin
from Bordetella pertussis. Trends Microbiol 20, 343–351
[50] Eswar, N., Eramian, D., Webb, B., Shen, M., and Sali, A. (2008) Protein structure
modeling with MODELLER. Methods Mol Biol 426, 145–159
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
17. Mutants of AC and AC/CaM interaction 16
FIGURE LEGENDS
Figure 1
a) X-ray crystallographic structure of the catalytic domain (AC) of adenyl cyclase
(CyaA, PDB entry 1YRT) drawn in cartoons. Helices F, G, and H colored in purple form
the SA region (residues 192–254). The loop 226–232 (Hom loop) colored in salmon at
the left extremity of SA colored in purple was missing from the X-ray crystallographic
structure and was modeled using Modeller9v4 [50]. The other protein regions are colored
in green (CA: residues 7–61, 187–197, 261–299, and 313–345), orange (CB: residues 62–
186), cyan (C-terminal tail/C tail: residues 346–364), and yellow (catalytic loop/C loop:
residues 300–312). The C-CaM lobe, which is colored in red, interacts with SA and the
C-terminal tail. Calcium ions are represented by silver beads. b) The modified residues,
i.e., Arg338, Asn347, and Asp360, located in CA and the C terminal tail, are indicated by
sticks. c) The LHL motif localized between the C-CaM/AC interface and the catalytic
loop is colored in brown.
Figure 2
Conformational drifts estimated based on the α carbon coordinates RMSD from the
starting conformations in the T1 (a-d) and T2 (e-h) series of simulations. (a, e) Drift cal-
culated based on the Cα carbons in the AC domain for ACm1A (black), ACm2A (green),
and ACm3A (red). (b–d,f–h) Drift calculated based on different regions of the AC domain,
which were analyzed for ACm1A (b, f), ACm2A (c, g), and ACm3A (d, h). The color
codes of the different protein regions are shown in panel (d). The AC regions are defined
as follows. 1) CA: residues 7–61, 187–197, 261–299, and 313–345. 2) Catalytic loop (C
Loop): residues 300–312. 3) C-terminal tail (C tail): residues 346–364. 4) CB: residues
62–186. 5) SA: residues 198–260. Helices H, F, G, and H’ correspond to residues 234–253,
198-210, 214-223, 256-260.
Figure 3
Fluctuations of the residues (RMSF: ˚A) observed in C-CaM based on the trajectories
recorded for: (a) wild-type and (b) modified C-CaM/AC complexes. The trajectory names
are shown in the legends. The WT2Ca trajectories were run on two Ca2+-loaded AC/C-
CaM complexes, whereas the WT0Ca trajectories were run on the AC/C-CaM complex
in the absence of calcium ions. The fluctuations were calculated based on the trajectories
after removing their first 10 ns.
Figure 4
C-CaM conformation extracted from ACm2A T2 and ACm3A T2, which are colored
according to the simulation times indicated. The N- and C-terminal ends are indicated,
as well as Asp-133, which is shown in black. The calcium ions are shown as gray spheres,
and the carboxyl oxygens of the Asp-133 sidechain are colored in red.
Figure 5
Correlation between geometric strains among the LHL residues, displayed for each
recorded trajectory. The time-correlation matrices were calculated between the variations
of the geometric strains of LHL residues and the first ten nanoseconds were discarded from
the analysis. In order to estimate the reliability of the prediction of correlation, the cal-
culation was repeated five times by selecting at each time, one data-point over five along
the analyzed time interval. The average values calculated for the LHL residues are shown
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18. Mutants of AC and AC/CaM interaction 17
in the figure. The intensity scale varies from 1.0 (pink) to –0.2 (dark green).
Figure 6
A. SDS-PAGE analysis of the purified AC variants, wild type AC, and CaM. The pro-
teins were separated by electrophoresis on a 4–12% SDS-polyacrylamide gel (Life Tech-
nologies). After migration, the gel was stained with PageBlue protein staining solution
(Thermo Fisher Scientific). B. Activation of modified ACs by CaM. The activity of the
purified wild-type AC and/or the variants were measured (as described in the Materials
and Methods) in the presence of the indicated CaM concentrations, and the results are
expressed as the percentage of the maximal activity (measured in the presence of 1µM
CaM). C. Catalytic properties of AC variants. The parameters were determined within
an error of ± 10%. ∆G is the calculated energy of association between CaM and AC.
Figure 7
A. SEC-TDA analysis of the oligomerization state of ACwt and ACm3A. Red curve:
right angle light scattering; blue curve: UV absorbance; green curve: molecular masses of
the eluted species. See the Materials and Methods for details. B. Synchrotron radiation
circular dichroism spectra of CaM and AC proteins in isolation or in a 1:1 complex. MRE:
mean residual ellipticity. See the Materials and Methods for details. C. Thermodynamic
stability of AC proteins following urea-induced denaturation. The ratio of the fluorescence
intensity at 360 and 320 nm (excitation wavelength = 295 nm) for the proteins as a func-
tion of the urea concentration was measured as described in the Materials and Methods.
D. Thermodynamics parameters of the urea-induced denaturation of AC proteins.
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19. Mutants of AC and AC/CaM interaction 18
Table I Details of the molecular systems simulated in molecular dynamics
(MD) trajectories.
Systems ACwt 2Ca ACwt 0Ca
Trajectories WT2Ca T1 WT0Ca T1
WT2Ca T2 WT0Ca T2
Number of Na+
counter-ions 14 18
Water box 92.6 x 106.9 91.3 x 106.9
dimensions x 103.3 ˚A3 x 106.4 ˚A3
Number of
water molecules 26455 27056
Total number
of atoms 85825 87630
Length (ns) 30 30
Table I
Systems ACm1A ACm2A ACm3A
Trajectories ACm1A T1 ACm2A T1 ACm3A T1
ACm1A T2 ACm2A T2 ACm3A T2
Number of Na+
counter-ions 14 18 14
Water box 109.6 x 82.8 108.1 x 82.8 109.6 x 82.8
dimensions x 111.7 ˚A3 x 111.7 ˚A3 x 111.7 ˚A3
Number of
water molecules 29003 29008 29008
Total number
of atoms 93465 93468 93464
Length (ns) 50 50 50
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20. Mutants of AC and AC/CaM interaction 19
Figure 1
a) C-CaM
C-tail
C-Loop
CA
CB
SAHom
loop
G
F
H
b) c)
L16
ASN-347
ARG-338
ASP-360
Figure 1
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21. Mutants of AC and AC/CaM interaction 20
Figure 2
Figure 2
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22. Mutants of AC and AC/CaM interaction 21
Figure 3
RMSF(A°)
79 84 89 94 99 105 111 117 123 129 135 141 147
0123
a)
Helix V Helix VI Helix VII Helix VIII
WT2Ca_T1
WT2Ca_T2
WT0Ca_T1
WT0Ca_T2
RMSF(A°)
79 84 89 94 99 104 110 116 122 128 134 140 146
0123
b)
Helix V Helix VI Helix VII Helix VIII
ACm1A_T1
ACm1A_T2
ACm2A_T1
ACm2A_T2
ACm3A_T1
ACm3A_T2
Residue number
RMSF(A°)RMSF(A°)
Figure 3 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
23. Mutants of AC and AC/CaM interaction 22
Figure 4
ACm2A_T2
Asp 133
COO-
C N ACm3A_T2 C
N
Asp 133
COO-
10 ns
20 ns
25 ns
start
Figure 4
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24. Mutants of AC and AC/CaM interaction 23
Figure 5
Residuenumber
345350355360
ACm1A_T1 ACm1A_T2Residuenumber
345350355360
ACm2A_T1 ACm2A_T2
Residuenumber
345350355360
ACm3A_T1 ACm3A_T2
Residuenumber
345350355360
WT2Ca_T1 WT2Ca_T2
Residue number
Residuenumber
340 345 350 355 360
345350355360
WT0Ca_T1
Residue number
Residue number
340 345 350 355 360
WT0Ca_T2
Residue number
−0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2
ResiduenumberResiduenumberResiduenumberResiduenumberResiduenumber
Figure 5
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25. Mutants of AC and AC/CaM interaction 24
Figure 6
A
170 -
130-
95-
72-
55-
43-
34-
26-
17-
10-
AC
ACm
3AACm
2AACm
1A
CaM
B
C kcat KATP
M KCaM
1/2 ∆G kcat/ KM
(s−1) (mM) (nM) (kcal.mol−1) 106 M−1s−1
ACwt 4600 0.60 0.11 13.8 7.6
ACm1A 2250 2.2 0.61 12.8 1.0
ACm2A 6000 1.5 0.66 12.7 4.0
ACm3A 650 3.0 26.7 10.5 0.2
Figure 6
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