HPRnase
•Download as PPT, PDF•
1 like•488 views
1. The document discusses molecular simulations comparing the human pancreatic ribonuclease (HP-RNase) to ribonuclease A (RNase A) to understand their differences in substrate binding and catalysis. 2. Experimental results show that HP-RNase preferentially cleaves substrates in an endonucleolytic manner, while RNase A shows more exo activity. Molecular dynamics simulations and free energy calculations of the two enzymes were performed. 3. Analysis of distances and free energy calculations revealed that the mutant RNase A had a higher free energy barrier for endonucleolytic cleavage compared to wild type HP-RNase, providing a potential explanation for their different activities.
Report
Share
Report
Share
![Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
Recommended
Quantitative In silico analysis of mammalian serine racemase activity
Serine racemase (SR) is a pyridoxal 5’-phosphate (PLP)-dependent enzyme catalyzing the racemization of S-serine to R-serine, and also oxidizes R-serine to pyruvate; however, the enzymatic racemization reaction is not fully understood. Therefore, quantitative in silico analysis of mammalian SR was performed followed byD-amino acid oxidase (DAO) analysis.The downloaded stereo structures of Rattus norvegicus (PBD ID: 3hmk) and mammalian (PDB ID: 3l6r and 3l6b) SR were optimized using molecular mechanic (MM2) calculation. Furthermore, the stereo structure of mammalian SR was constructed using 3hmk and the amino acid sequence data. The atomic partial charge (apc) of the target atoms was calculated using MOPAC-PM5. The atomic distances, bond angles, and apc of the mutants were used to study the enzyme reaction mechanism.The serine carboxyl group contacted lysine-56, where its amino group contacted the oxygen molecules of PLP aldehyde. The apc of C indicated that S-serine was selectively oxidized. Manganese located at another side of PLP is directly involved in the serine racemization by forming bonding with the hydroxyl group of serine. The enzyme racemization activity was quantitatively related to the bond angle of the substituted serine rather than to that of alanine. However, 316r and 316b lack several amino acid residues; therefore, the selective oxidation of S84 mutants was not clearly demonstrated.
Enzyme and enzyme inhibition
This document discusses enzymes and enzyme kinetics. It defines enzymes as biomolecules that catalyze chemical reactions and provides examples of enzyme units and the SI unit for enzyme activity, the katal. The document then summarizes Michaelis-Menten enzyme kinetics, including the key assumptions of the MM model. It describes parameters of the MM equation like Km, Vmax, kcat, and kcat/Km. Finally, it discusses enzyme inhibition, categorizing inhibitors as reversible or irreversible and describing different types of reversible and irreversible inhibition.
Enzyme kinetics
This document provides an overview of enzyme kinetics concepts including:
1) The relationship between reaction velocity and substrate concentration follows a hyperbolic curve known as Michaelis-Menten kinetics.
2) Enzymes can be inhibited through competitive, mixed, and allosteric inhibition mechanisms which impact the Michaelis-Menten curve.
3) Assays of enzyme activity can be used as diagnostic tools to detect tissue damage or disease based on abnormal levels of enzymes detected in blood serum.
Enzyme kinetics
This document discusses enzyme kinetics and the Michaelis-Menten model of enzyme kinetics. It defines key terms like reaction rate, elementary reactions, rate laws, and transition state theory. It then introduces the Michaelis-Menten equation, defines terms like Km, Vmax, and kcat. It discusses steady state kinetics and how the Michaelis-Menten equation was derived. It explains the meaning and uses of Km and Vmax and concludes by discussing the Lineweaver-Burk double reciprocal plot.
7.29.10 enzymes (kinetics) coloso
The document discusses enzyme kinetics and the Michaelis-Menten model. It explains that enzymes convert substrates to products over time in three phases: an initial rapid increase, then a steady state. The Michaelis-Menten model describes enzyme velocity as a function of substrate concentration using the constants KM and Vmax. KM represents the substrate concentration at half Vmax. Inhibitors are also discussed, including competitive and noncompetitive inhibition and how they affect the kinetic parameters.
Enzyme kinetics - Creative Enzymes
Enzyme kinetics is the study of the chemical reactions that are catalyzed by enzymes. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme's kinetics can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or an agonist might inhibit the enzyme. Creative Enzymes is a renowned service provider, supporting many industrial and academic researchers for kinetic studies. https://www.creative-enzymes.com/service/Enzyme-Kinetics_393.html
Kinetics of multi substrate enzyme catalyzed reaction
Enzyme kinetics is the study of enzyme-catalyzed chemical reactions. Enzymes lower the activation energy of reactions by binding substrates to their active sites. Multi-substrate reactions can follow sequential or non-sequential mechanisms. In sequential mechanisms, both substrates must bind before any product is released, while non-sequential mechanisms allow product release before all substrates bind. Ping-pong mechanisms are a type of non-sequential mechanism where the enzyme is temporarily modified between substrate bindings.
Kinetically Perfect Enzymes
A diffusion-limited enzyme catalyses a reaction so efficiently that the rate limiting step is that of substrate diffusion into the active site, or product diffusion out. This is also known as kinetic perfection or catalytic perfection. Since the rate of catalysis of such enzymes is set by the diffusion-controlled reaction, it therefore represents an intrinsic, physical constraint on evolution (a maximum peak height in the fitness landscape). Diffusion limited perfect enzymes are very rare. Most enzymes catalyse their reactions to a rate that is 1,000-10,000 times slower than this limit. This is due to both the chemical limitations of difficult reactions, and the evolutionary limitations that such high reaction rates do not confer any extra fitness.
Recommended
Quantitative In silico analysis of mammalian serine racemase activity
Serine racemase (SR) is a pyridoxal 5’-phosphate (PLP)-dependent enzyme catalyzing the racemization of S-serine to R-serine, and also oxidizes R-serine to pyruvate; however, the enzymatic racemization reaction is not fully understood. Therefore, quantitative in silico analysis of mammalian SR was performed followed byD-amino acid oxidase (DAO) analysis.The downloaded stereo structures of Rattus norvegicus (PBD ID: 3hmk) and mammalian (PDB ID: 3l6r and 3l6b) SR were optimized using molecular mechanic (MM2) calculation. Furthermore, the stereo structure of mammalian SR was constructed using 3hmk and the amino acid sequence data. The atomic partial charge (apc) of the target atoms was calculated using MOPAC-PM5. The atomic distances, bond angles, and apc of the mutants were used to study the enzyme reaction mechanism.The serine carboxyl group contacted lysine-56, where its amino group contacted the oxygen molecules of PLP aldehyde. The apc of C indicated that S-serine was selectively oxidized. Manganese located at another side of PLP is directly involved in the serine racemization by forming bonding with the hydroxyl group of serine. The enzyme racemization activity was quantitatively related to the bond angle of the substituted serine rather than to that of alanine. However, 316r and 316b lack several amino acid residues; therefore, the selective oxidation of S84 mutants was not clearly demonstrated.
Enzyme and enzyme inhibition
This document discusses enzymes and enzyme kinetics. It defines enzymes as biomolecules that catalyze chemical reactions and provides examples of enzyme units and the SI unit for enzyme activity, the katal. The document then summarizes Michaelis-Menten enzyme kinetics, including the key assumptions of the MM model. It describes parameters of the MM equation like Km, Vmax, kcat, and kcat/Km. Finally, it discusses enzyme inhibition, categorizing inhibitors as reversible or irreversible and describing different types of reversible and irreversible inhibition.
Enzyme kinetics
This document provides an overview of enzyme kinetics concepts including:
1) The relationship between reaction velocity and substrate concentration follows a hyperbolic curve known as Michaelis-Menten kinetics.
2) Enzymes can be inhibited through competitive, mixed, and allosteric inhibition mechanisms which impact the Michaelis-Menten curve.
3) Assays of enzyme activity can be used as diagnostic tools to detect tissue damage or disease based on abnormal levels of enzymes detected in blood serum.
Enzyme kinetics
This document discusses enzyme kinetics and the Michaelis-Menten model of enzyme kinetics. It defines key terms like reaction rate, elementary reactions, rate laws, and transition state theory. It then introduces the Michaelis-Menten equation, defines terms like Km, Vmax, and kcat. It discusses steady state kinetics and how the Michaelis-Menten equation was derived. It explains the meaning and uses of Km and Vmax and concludes by discussing the Lineweaver-Burk double reciprocal plot.
7.29.10 enzymes (kinetics) coloso
The document discusses enzyme kinetics and the Michaelis-Menten model. It explains that enzymes convert substrates to products over time in three phases: an initial rapid increase, then a steady state. The Michaelis-Menten model describes enzyme velocity as a function of substrate concentration using the constants KM and Vmax. KM represents the substrate concentration at half Vmax. Inhibitors are also discussed, including competitive and noncompetitive inhibition and how they affect the kinetic parameters.
Enzyme kinetics - Creative Enzymes
Enzyme kinetics is the study of the chemical reactions that are catalyzed by enzymes. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme's kinetics can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or an agonist might inhibit the enzyme. Creative Enzymes is a renowned service provider, supporting many industrial and academic researchers for kinetic studies. https://www.creative-enzymes.com/service/Enzyme-Kinetics_393.html
Kinetics of multi substrate enzyme catalyzed reaction
Enzyme kinetics is the study of enzyme-catalyzed chemical reactions. Enzymes lower the activation energy of reactions by binding substrates to their active sites. Multi-substrate reactions can follow sequential or non-sequential mechanisms. In sequential mechanisms, both substrates must bind before any product is released, while non-sequential mechanisms allow product release before all substrates bind. Ping-pong mechanisms are a type of non-sequential mechanism where the enzyme is temporarily modified between substrate bindings.
Kinetically Perfect Enzymes
A diffusion-limited enzyme catalyses a reaction so efficiently that the rate limiting step is that of substrate diffusion into the active site, or product diffusion out. This is also known as kinetic perfection or catalytic perfection. Since the rate of catalysis of such enzymes is set by the diffusion-controlled reaction, it therefore represents an intrinsic, physical constraint on evolution (a maximum peak height in the fitness landscape). Diffusion limited perfect enzymes are very rare. Most enzymes catalyse their reactions to a rate that is 1,000-10,000 times slower than this limit. This is due to both the chemical limitations of difficult reactions, and the evolutionary limitations that such high reaction rates do not confer any extra fitness.
Enzymology
This document provides an overview of enzymology and enzymes. It discusses how enzymes are biological catalysts that accelerate chemical reactions in living organisms. Each reaction is catalyzed by one or more specific enzymes, which are proteins that recognize substrate molecules and facilitate their transformation. Enzymes play a key role in coupling exergonic and endergonic reactions to allow biochemical processes to occur under the constraints of thermodynamics. The document covers basics of enzyme kinetics, cofactors, classification, factors influencing enzyme activity such as temperature and pH, inhibition, and measurement of enzymatic activity.
++Tihomir+Todorov_Interaction+between+red-type+Rubisco+and+the+unfoldase+ClpX
This study investigates the interaction between red-type Rubisco and the ATPase protein ClpX. Rubisco plays a key role in photosynthesis but can become inhibited, requiring activation by the protein Rubisco activase. The knowledge of how Rubisco activase works in red-type bacteria is limited. The researchers generated a version of Rubisco tagged with an ssrA tag, which allows for recognition and unfolding by ClpX. They aim to determine if the interaction between inhibited, tagged Rubisco and ClpX results in reactivation of Rubisco in order to gain insight into the mechanism of Rubisco activase. They purified the tagged Rubisco and found ClpX exhibited normal ATPase activity, laying the
Enzyme kinetics, factors and mechanism of enzyme activity
Enzyme kinetics involves studying the chemical reactions catalyzed by enzymes. There are two common kinetic processes: the Michaelis-Menten plot and Lineweaver-Burk plot. The Michaelis-Menten plot models the reaction between an enzyme, substrate, and product using an equation. It relates reaction rate to substrate concentration and determines values like Vmax and Km. The Lineweaver-Burk plot is a double reciprocal plot that modifies the Michaelis-Menten equation to allow determining Vmax and Km from the slope and y-intercept. Enzyme activity is affected by factors like concentration, temperature, pH, and activators. Mechanisms of enzyme action include the lock-and
Bisubstrate reactions enzyme kinetics
This document discusses two types of bisubstrate reactions: sequential or single-displacement reactions and ping-pong or double-displacement reactions. Sequential reactions involve both substrates binding to the enzyme before products are released, and can be ordered or random. Ping-pong reactions involve one substrate binding and being modified, then releasing one product before the second substrate binds and the second product is released, regenerating the original enzyme. Examples of each type of reaction are provided to illustrate the mechanisms.
Enzyme kinetics
Enzymes are proteins that catalyze biochemical reactions and lower their activation energy. Three factors affect the rate of enzyme reactions: temperature, pH, and substrate concentration. Temperature affects reaction rates because higher temperatures increase molecular collisions and velocities. Each enzyme works optimally within a certain temperature range, as extremes can denature the protein. pH also influences structure and activity, as enzymes have an optimal pH range where ionization of amino acids is not altered. Increasing substrate concentration increases reaction rates until the enzymes become saturated, while increasing enzyme concentration also boosts rates until another factor limits the reaction.
Enzymes crash course
Biocatalysts such as enzymes increase the rate of biochemical reactions. Enzymes are typically proteins but can also be RNA or artificial molecules called abzymes. Enzymes may require cofactors such as metal ions or organic coenzymes to be catalytically active. The document discusses enzyme kinetics including Michaelis-Menten kinetics, factors that affect reaction rate, kinetic parameters such as Km and Vmax, enzyme inhibition types including competitive, noncompetitive and irreversible inhibition, and regulation of enzyme activity through feedback, allosteric regulation and covalent modification.
Enzyme kinetics presentation
This document discusses enzyme kinetics and provides details about key concepts. It introduces enzymes and their role in catalyzing reactions. It then describes enzyme kinetics as the study of reaction rates of enzyme-catalyzed reactions under varying conditions. Several key aspects of enzyme kinetics are summarized, including parametric analysis of enzyme catalysis, enzyme specificity, the lock and key model, and the Michaelis-Menten kinetics model. This model describes how reaction rates increase with substrate concentration until reaching a maximum rate Vmax as the enzyme becomes saturated.
Enz Kinetics
This document discusses enzyme kinetics and mechanisms of enzyme action. It provides background on conditions necessary for life, how enzymes enhance chemical reaction rates, and binding energy contributions to catalysis. It then covers key concepts in enzyme kinetics including initial velocity, Michaelis-Menten kinetics, Lineweaver-Burke plots, and constants like Km and Kcat. Mechanisms of reversible and irreversible inhibition are described. Examples of specific enzymes like chymotrypsin and protein kinase A are also mentioned.
Enzkinetics 2014
1) Enzymes require cofactors like vitamins and metal ions to function properly and carry out reactions. Common coenzymes include NAD+, FAD, coenzyme A, biotin, and vitamin B12.
2) NAD+ acts as an electron acceptor in many oxidation reactions, FAD carries electrons and hydrogen atoms, and coenzyme A transfers acyl groups.
3) The cofactors help enzymes by participating directly in chemical transformations and bringing reactive groups close together to reduce the activation energy of reactions. Living systems rely on cofactors to drive essential metabolic pathways.
Enzyme kinetics
This presentation deals with basics of enzyme kinetics and introduction to various plots which aid in understanding the mechanism of inhibition of enzymes.
Bmm480 Enzymology lecture-3
This document discusses enzyme kinetics and the Michaelis-Menten model of enzyme kinetics. It provides details on several key aspects:
1) Substrate concentration affects the rate of enzyme-catalyzed reactions, with the initial rate (V0) increasing with substrate concentration ([S]) until reaching a maximum rate (Vmax) at high substrate levels.
2) The Michaelis-Menten model describes this relationship through kinetic parameters like Km (the substrate concentration when V0 is half of Vmax) and Vmax.
3) Various plots like Lineweaver-Burk, Eadie-Hofstee, and Hanes-Woolf plots can be used to
Sept 5 bt202
This document discusses enzyme kinetics and regulation. It begins by defining enzymes as proteins that catalyze chemical reactions in cells. Enzymes have specific active sites that bind substrates and use mechanisms like cofactors and induced fit to lower activation energy. Reaction rates follow Michaelis-Menten kinetics and can be regulated through feedback inhibition, allosteric modulation, covalent modification like phosphorylation, and proteolytic cleavage of zymogens. The document also describes different types of reversible and irreversible enzyme inhibition.
Enzyme kinetics
1) Chemical kinetics describes relationships between reaction rates and concentrations of reactants and products. Enzyme kinetics follows Michaelis-Menten kinetics which describes reaction rates at varying substrate concentrations.
2) The Michaelis-Menten equation models reaction rates as substrate concentration increases, with an initial linear increase until reaching the maximum reaction rate (Vmax) at substrate saturation.
3) The Michaelis constant KM represents the substrate concentration at half Vmax and indicates an enzyme's affinity for its substrate. Lower KM means higher affinity.
Enzyme kinetics
Enzyme kinetics can provide information about enzyme activity under different conditions. The Michaelis-Menten approach models enzyme-catalyzed reactions and describes reaction rates with the Michaelis-Menten constant (Km) and maximum reaction rate (Vmax). Enzymes can be inhibited reversibly or irreversibly by inhibitors that reduce reaction rates. Different types of reversible inhibition include competitive, uncompetitive, and mixed inhibition. Temperature, pH, and allosteric effectors can regulate enzymatic activity through various mechanisms.
Enzyme kinetics
This document discusses enzyme kinetics and the Michaelis-Menten model. It explains that the rate of enzyme-catalyzed reactions depends on substrate concentration and is characterized by rate constants. The initial rate of product formation is measured at various substrate concentrations to obtain a rate vs. substrate concentration plot. This plot typically follows Michaelis-Menten kinetics which can be described by the Michaelis constant Km and maximum velocity Vmax. Km represents the substrate concentration needed for half the maximum velocity and provides information about enzyme-substrate binding.
2.order of reaction & mm equ
1) The document discusses key concepts related to enzyme kinetics including Michaelis-Menten kinetics, reaction orders, and kinetic parameters.
2) It derives the Michaelis-Menten equation based on the assumptions that the enzyme-substrate complex is in steady state and the rate limiting step is breakdown of this complex.
3) Important kinetic parameters discussed include Km, Vmax, Kcat, and Kcat/Km, which provide information about enzyme-substrate affinity and catalytic efficiency.
4) Limitations of the Michaelis-Menten model for enzymes exhibiting cooperative binding or more complex reaction mechanisms are also addressed.
Enzyme kinetics
Enzyme kinetics is the study of enzyme-catalyzed reaction rates. The Michaelis-Menten equation relates reaction velocity to substrate concentration and kinetic parameters. It describes the hyperbolic relationship between velocity and substrate concentration. The equation can be linearized into the Lineweaver-Burk plot for easier analysis. Enzyme inhibition studies help understand reaction mechanisms and are important for drug development, as most drugs function by inhibiting specific enzymes.
Enzyme kinetics
This document provides an overview of enzyme kinetics. It defines important terms like rate constant, substrate concentration, enzyme unit, and Michaelis constant. It describes models used to study enzyme kinetics like the Michaelis-Menten equations and Lineweaver-Burk, Hanes-Woolf, and Eadie-Hofstee plots. It discusses factors that affect reaction rates like pH, temperature, and inhibitors. The document also covers cooperative enzyme systems and multireactant reactions.
Enzymes
The document summarizes key concepts in cell biology related to enzymes. It defines important terms like metabolism, enzyme, substrate, and coenzyme. It describes the roles of enzymes in biochemical reactions and factors that affect their activity, such as pH, temperature, substrate concentration, and inhibitors. Lastly, it discusses experimental design and the scientific method.
NAPP-DR6 poster
This study used computational methods to identify peptide inhibitors of the interaction between the death receptor DR6 and the N-terminal fragment of amyloid precursor protein (NAPP), which is implicated in Alzheimer's disease (AD). A focused peptide library was virtually screened and peptides were docked and scored against the NAPP binding site. Several tetrapeptides were predicted to bind strongly to NAPP, particularly Pro-Lys-Trp-Trp, which was predicted to inhibit the DR6-NAPP interaction through hydrogen bonding with key NAPP residues. Future work will include synthesizing and testing the top peptides to validate the computational predictions.
Final_Khoi_Urop
A molecular dynamics simulation investigated the ability of an artificial amino acid called δ-ornithine (δOrn) to stabilize beta-hairpin structures. The simulation showed that a cyclic peptide containing two δOrn turns folded into a well-defined beta-hairpin at low temperatures (<276K), demonstrating δOrn is an effective turn motif. However, at higher temperatures the δOrn turns became more flexible and extended, preventing beta-hairpin formation. Thus, δOrn effectively promotes beta-hairpins only at lower temperatures by adopting a compact conformation.
Final Presentation
This document summarizes an experiment aiming to identify the RNA-binding domain of the human LARP6 protein. The researcher expressed and purified constructs of LARP6 containing residues 70-300 and 70-313. While purification of the SUMO tag was successful, the LARP6 portions degraded. As a control, the SUMO tag alone showed non-specific binding to test RNAs. Future work will optimize expression and purification conditions to prevent degradation and characterize RNA binding of intact LARP6 constructs.
More Related Content
What's hot
Enzymology
This document provides an overview of enzymology and enzymes. It discusses how enzymes are biological catalysts that accelerate chemical reactions in living organisms. Each reaction is catalyzed by one or more specific enzymes, which are proteins that recognize substrate molecules and facilitate their transformation. Enzymes play a key role in coupling exergonic and endergonic reactions to allow biochemical processes to occur under the constraints of thermodynamics. The document covers basics of enzyme kinetics, cofactors, classification, factors influencing enzyme activity such as temperature and pH, inhibition, and measurement of enzymatic activity.
++Tihomir+Todorov_Interaction+between+red-type+Rubisco+and+the+unfoldase+ClpX
This study investigates the interaction between red-type Rubisco and the ATPase protein ClpX. Rubisco plays a key role in photosynthesis but can become inhibited, requiring activation by the protein Rubisco activase. The knowledge of how Rubisco activase works in red-type bacteria is limited. The researchers generated a version of Rubisco tagged with an ssrA tag, which allows for recognition and unfolding by ClpX. They aim to determine if the interaction between inhibited, tagged Rubisco and ClpX results in reactivation of Rubisco in order to gain insight into the mechanism of Rubisco activase. They purified the tagged Rubisco and found ClpX exhibited normal ATPase activity, laying the
Enzyme kinetics, factors and mechanism of enzyme activity
Enzyme kinetics involves studying the chemical reactions catalyzed by enzymes. There are two common kinetic processes: the Michaelis-Menten plot and Lineweaver-Burk plot. The Michaelis-Menten plot models the reaction between an enzyme, substrate, and product using an equation. It relates reaction rate to substrate concentration and determines values like Vmax and Km. The Lineweaver-Burk plot is a double reciprocal plot that modifies the Michaelis-Menten equation to allow determining Vmax and Km from the slope and y-intercept. Enzyme activity is affected by factors like concentration, temperature, pH, and activators. Mechanisms of enzyme action include the lock-and
Bisubstrate reactions enzyme kinetics
This document discusses two types of bisubstrate reactions: sequential or single-displacement reactions and ping-pong or double-displacement reactions. Sequential reactions involve both substrates binding to the enzyme before products are released, and can be ordered or random. Ping-pong reactions involve one substrate binding and being modified, then releasing one product before the second substrate binds and the second product is released, regenerating the original enzyme. Examples of each type of reaction are provided to illustrate the mechanisms.
Enzyme kinetics
Enzymes are proteins that catalyze biochemical reactions and lower their activation energy. Three factors affect the rate of enzyme reactions: temperature, pH, and substrate concentration. Temperature affects reaction rates because higher temperatures increase molecular collisions and velocities. Each enzyme works optimally within a certain temperature range, as extremes can denature the protein. pH also influences structure and activity, as enzymes have an optimal pH range where ionization of amino acids is not altered. Increasing substrate concentration increases reaction rates until the enzymes become saturated, while increasing enzyme concentration also boosts rates until another factor limits the reaction.
Enzymes crash course
Biocatalysts such as enzymes increase the rate of biochemical reactions. Enzymes are typically proteins but can also be RNA or artificial molecules called abzymes. Enzymes may require cofactors such as metal ions or organic coenzymes to be catalytically active. The document discusses enzyme kinetics including Michaelis-Menten kinetics, factors that affect reaction rate, kinetic parameters such as Km and Vmax, enzyme inhibition types including competitive, noncompetitive and irreversible inhibition, and regulation of enzyme activity through feedback, allosteric regulation and covalent modification.
Enzyme kinetics presentation
This document discusses enzyme kinetics and provides details about key concepts. It introduces enzymes and their role in catalyzing reactions. It then describes enzyme kinetics as the study of reaction rates of enzyme-catalyzed reactions under varying conditions. Several key aspects of enzyme kinetics are summarized, including parametric analysis of enzyme catalysis, enzyme specificity, the lock and key model, and the Michaelis-Menten kinetics model. This model describes how reaction rates increase with substrate concentration until reaching a maximum rate Vmax as the enzyme becomes saturated.
Enz Kinetics
This document discusses enzyme kinetics and mechanisms of enzyme action. It provides background on conditions necessary for life, how enzymes enhance chemical reaction rates, and binding energy contributions to catalysis. It then covers key concepts in enzyme kinetics including initial velocity, Michaelis-Menten kinetics, Lineweaver-Burke plots, and constants like Km and Kcat. Mechanisms of reversible and irreversible inhibition are described. Examples of specific enzymes like chymotrypsin and protein kinase A are also mentioned.
Enzkinetics 2014
1) Enzymes require cofactors like vitamins and metal ions to function properly and carry out reactions. Common coenzymes include NAD+, FAD, coenzyme A, biotin, and vitamin B12.
2) NAD+ acts as an electron acceptor in many oxidation reactions, FAD carries electrons and hydrogen atoms, and coenzyme A transfers acyl groups.
3) The cofactors help enzymes by participating directly in chemical transformations and bringing reactive groups close together to reduce the activation energy of reactions. Living systems rely on cofactors to drive essential metabolic pathways.
Enzyme kinetics
This presentation deals with basics of enzyme kinetics and introduction to various plots which aid in understanding the mechanism of inhibition of enzymes.
Bmm480 Enzymology lecture-3
This document discusses enzyme kinetics and the Michaelis-Menten model of enzyme kinetics. It provides details on several key aspects:
1) Substrate concentration affects the rate of enzyme-catalyzed reactions, with the initial rate (V0) increasing with substrate concentration ([S]) until reaching a maximum rate (Vmax) at high substrate levels.
2) The Michaelis-Menten model describes this relationship through kinetic parameters like Km (the substrate concentration when V0 is half of Vmax) and Vmax.
3) Various plots like Lineweaver-Burk, Eadie-Hofstee, and Hanes-Woolf plots can be used to
Sept 5 bt202
This document discusses enzyme kinetics and regulation. It begins by defining enzymes as proteins that catalyze chemical reactions in cells. Enzymes have specific active sites that bind substrates and use mechanisms like cofactors and induced fit to lower activation energy. Reaction rates follow Michaelis-Menten kinetics and can be regulated through feedback inhibition, allosteric modulation, covalent modification like phosphorylation, and proteolytic cleavage of zymogens. The document also describes different types of reversible and irreversible enzyme inhibition.
Enzyme kinetics
1) Chemical kinetics describes relationships between reaction rates and concentrations of reactants and products. Enzyme kinetics follows Michaelis-Menten kinetics which describes reaction rates at varying substrate concentrations.
2) The Michaelis-Menten equation models reaction rates as substrate concentration increases, with an initial linear increase until reaching the maximum reaction rate (Vmax) at substrate saturation.
3) The Michaelis constant KM represents the substrate concentration at half Vmax and indicates an enzyme's affinity for its substrate. Lower KM means higher affinity.
Enzyme kinetics
Enzyme kinetics can provide information about enzyme activity under different conditions. The Michaelis-Menten approach models enzyme-catalyzed reactions and describes reaction rates with the Michaelis-Menten constant (Km) and maximum reaction rate (Vmax). Enzymes can be inhibited reversibly or irreversibly by inhibitors that reduce reaction rates. Different types of reversible inhibition include competitive, uncompetitive, and mixed inhibition. Temperature, pH, and allosteric effectors can regulate enzymatic activity through various mechanisms.
Enzyme kinetics
This document discusses enzyme kinetics and the Michaelis-Menten model. It explains that the rate of enzyme-catalyzed reactions depends on substrate concentration and is characterized by rate constants. The initial rate of product formation is measured at various substrate concentrations to obtain a rate vs. substrate concentration plot. This plot typically follows Michaelis-Menten kinetics which can be described by the Michaelis constant Km and maximum velocity Vmax. Km represents the substrate concentration needed for half the maximum velocity and provides information about enzyme-substrate binding.
2.order of reaction & mm equ
1) The document discusses key concepts related to enzyme kinetics including Michaelis-Menten kinetics, reaction orders, and kinetic parameters.
2) It derives the Michaelis-Menten equation based on the assumptions that the enzyme-substrate complex is in steady state and the rate limiting step is breakdown of this complex.
3) Important kinetic parameters discussed include Km, Vmax, Kcat, and Kcat/Km, which provide information about enzyme-substrate affinity and catalytic efficiency.
4) Limitations of the Michaelis-Menten model for enzymes exhibiting cooperative binding or more complex reaction mechanisms are also addressed.
Enzyme kinetics
Enzyme kinetics is the study of enzyme-catalyzed reaction rates. The Michaelis-Menten equation relates reaction velocity to substrate concentration and kinetic parameters. It describes the hyperbolic relationship between velocity and substrate concentration. The equation can be linearized into the Lineweaver-Burk plot for easier analysis. Enzyme inhibition studies help understand reaction mechanisms and are important for drug development, as most drugs function by inhibiting specific enzymes.
Enzyme kinetics
This document provides an overview of enzyme kinetics. It defines important terms like rate constant, substrate concentration, enzyme unit, and Michaelis constant. It describes models used to study enzyme kinetics like the Michaelis-Menten equations and Lineweaver-Burk, Hanes-Woolf, and Eadie-Hofstee plots. It discusses factors that affect reaction rates like pH, temperature, and inhibitors. The document also covers cooperative enzyme systems and multireactant reactions.
Enzymes
The document summarizes key concepts in cell biology related to enzymes. It defines important terms like metabolism, enzyme, substrate, and coenzyme. It describes the roles of enzymes in biochemical reactions and factors that affect their activity, such as pH, temperature, substrate concentration, and inhibitors. Lastly, it discusses experimental design and the scientific method.
What's hot (19)
++Tihomir+Todorov_Interaction+between+red-type+Rubisco+and+the+unfoldase+ClpX
++Tihomir+Todorov_Interaction+between+red-type+Rubisco+and+the+unfoldase+ClpX
Enzyme kinetics, factors and mechanism of enzyme activity
Enzyme kinetics, factors and mechanism of enzyme activity
Similar to HPRnase
NAPP-DR6 poster
This study used computational methods to identify peptide inhibitors of the interaction between the death receptor DR6 and the N-terminal fragment of amyloid precursor protein (NAPP), which is implicated in Alzheimer's disease (AD). A focused peptide library was virtually screened and peptides were docked and scored against the NAPP binding site. Several tetrapeptides were predicted to bind strongly to NAPP, particularly Pro-Lys-Trp-Trp, which was predicted to inhibit the DR6-NAPP interaction through hydrogen bonding with key NAPP residues. Future work will include synthesizing and testing the top peptides to validate the computational predictions.
Final_Khoi_Urop
A molecular dynamics simulation investigated the ability of an artificial amino acid called δ-ornithine (δOrn) to stabilize beta-hairpin structures. The simulation showed that a cyclic peptide containing two δOrn turns folded into a well-defined beta-hairpin at low temperatures (<276K), demonstrating δOrn is an effective turn motif. However, at higher temperatures the δOrn turns became more flexible and extended, preventing beta-hairpin formation. Thus, δOrn effectively promotes beta-hairpins only at lower temperatures by adopting a compact conformation.
Final Presentation
This document summarizes an experiment aiming to identify the RNA-binding domain of the human LARP6 protein. The researcher expressed and purified constructs of LARP6 containing residues 70-300 and 70-313. While purification of the SUMO tag was successful, the LARP6 portions degraded. As a control, the SUMO tag alone showed non-specific binding to test RNAs. Future work will optimize expression and purification conditions to prevent degradation and characterize RNA binding of intact LARP6 constructs.
AR_ResearchProspectus
1. The author proposes using selective 2'-OH acylation analyzed by primer extension (SHAPE) chemistry to study RNA structure, including the bI5 intron and exon splice enhancers (ESEs) involved in spinal muscular atrophy (SMA).
2. Preliminary results on the bI5 intron show SHAPE is capable of analyzing over 400 nucleotides but signal decays with length. Interpreting reactivity data to constrain structure prediction is challenging.
3. SHAPE validates a predicted tertiary interaction in bI5 and computer modeling suggests a single nucleotide polymorphism in an ESE involved in SMA causes structural changes that could lead to incorrect splicing.
NMR method development for large proteins presented at ENC 2005
Protein/Protein and Protein/Ligand interactions in large and dynamically disordered systems studied by NMR in solution
bradykinin receptor antagonist and thrombin inhibitors
1) Bradykinin receptor antagonists and thrombin inhibitors were presented. Bradykinin is a 9-amino acid peptide that promotes inflammation by binding to B1 and B2 G protein-coupled receptors.
2) Conformationally constrained bradykinin antagonist peptides were designed to probe the receptor binding site. NMR studies showed the peptides adopt a beta-turn structure when binding.
3) Receptor binding experiments on cloned human receptors showed similar binding affinities, providing insights into antagonist interactions with bradykinin receptors.
Randomizing genome-scale metabolic networks
The document proposes a new Markov Chain Monte Carlo (MCMC) based method to generate randomized metabolic networks that impose biochemical and functional constraints. The method successively constrains the networks by (1) fixing the number of reactions, (2) fixing the number of metabolites, (3) excluding blocked reactions, and (4) requiring growth on a specified environment. Imposing these constraints causes the randomized networks to more closely match properties of real metabolic networks like E. coli. The approach generates an ensemble of diverse yet meaningful randomized networks to help identify design principles in metabolic networks.
Bachelor Thesis Presentation
The document summarizes research on RNA splicing and A-to-I RNA editing. Key findings include:
- JetPEI performed better than PEI as a transfection reagent with lower toxicity at low concentrations.
- Co-transfection with ADAR1 showed no changes in editing levels between three Azin1 constructs.
- The three Gria2 constructs showed that longer splicing duration was positively correlated with higher editing frequency.
- Producing new Gria2 constructs with single mutations in the pyrimidine rich tract could provide better insight into the coupling of splicing and editing.
LSSC2011 Optimization of intermolecular interaction potential energy paramete...
Optimization of intermolecular interaction potential energy parameters for Monte-Carlo and Molecular dynamics simulations using Genetic Algorithms (GA)
QSAR : Activity Relationships Quantitative Structure
A QSAR is a mathematical relationship between a biological activity of a molecular system and its geometric and chemical characteristics.
QSAR attempts to find consistent relationship between biological activity and molecular properties, so that these “rules” can be used to evaluate the activity of new compounds.
Protein structure
This document provides an overview of protein structure from primary to quaternary levels. It discusses the building blocks of proteins including amino acids and peptide bonds. Secondary structures like alpha helices and beta sheets are explained. Tertiary structure refers to the global folding of the protein chain. Quaternary structure involves the assembly of multiple protein subunits. Examples are given of protein complexes demonstrating tertiary and quaternary levels of structure. The document also outlines different classes of proteins based on function, structure, and cellular localization.
Poster_RosanaLopez_SULI_Summer2011_aug8_final_2
This document describes the expression and purification of the DNARR1 protein, which is involved in DNA double-strand break repair. Researchers cloned the DNARR1 gene with and without a FLAG tag into an expression vector and expressed the recombinant proteins in E. coli. They found that DNARR1 expression was highest at 37°C. Purification using nickel affinity chromatography and anti-FLAG affinity gel yielded purified DNARR1 protein. Future studies will use this purified protein to investigate its specific role in double-strand break repair through biochemical assays.
Gutell 112.j.phys.chem.b.2010.114.13497
Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures.
The Journal of Physical Chemistry B, 114(42):13497-13506.
Beyond transcription: RNA-binding proteins as emerging regulator of plant res...
This document provides an overview of RNA-binding proteins (RBPs) and their functions in plants, particularly in response to environmental stresses. It begins with an introduction to RBPs, describing the different types of RNA-binding domains and how RBPs bind to RNA. It then discusses the diverse functions of RBPs in processes like alternative splicing, RNA modification, polyadenylation, and mRNA localization, transport, stability, and translation. A major section explores the role of RBPs in responding to environmental stresses like temperature, osmotic stress, drought, and flooding. It presents examples of specific RBPs that are regulated under stress conditions. The document concludes with discussing future research perspectives on further characterizing plant
DNA,RNA and PROTEIN Overview.Just know about the genetics
This document provides an overview of DNA, RNA, and proteins. It discusses the components of DNA and RNA, including the four bases, nucleotides, and base pairing. It also covers mutations, the genetic code, amino acids, and protein structure. Protein structure is discussed from the primary level up to the tertiary level, including alpha helices, beta sheets, and interactions that determine three-dimensional folding. Common questions about genomes and proteomes are also listed.
Critical Assessment of Function Annotation, 2005
A talk I gave at the Automated Function Prediction meeting, 2005. Highlights different challenges in running a competition between protein function prediction servers. Talks of the use of semantic similarity in Gene Ontology as a metric for assessment, the problems in determining a "Gold Standard" and more
ABRCMS Poster2012
This study tested the hypothesis that a base-pairing interaction between nucleotide A79 in the Hepatitis Delta Virus (HDV) ribozyme and nucleotide U(-1) in its substrate is necessary for catalytic activity. Mutant ribozymes and substrates with variations at these positions were created and their kinetic activity analyzed. While mutation of A79 significantly reduced activity, further experiments found the hypothesis was incorrect. Additional nucleotides like A78 may interact with the substrate and warrant further investigation.
Molecular_bilogy_lab_report_2
This laboratory report summarizes an experiment exploring RNA splicing in Drosophila melanogaster. Genomic DNA and total RNA were extracted from fruit flies and used to study the rngo gene. PCR and RT-PCR were performed on the genomic DNA and cDNA samples. The genomic PCR product was cloned and sequenced. Bioinformatics analysis showed the genomic sequence was longer, containing introns absent from the cDNA, indicating splicing of the rngo pre-mRNA. Future work could investigate other splicing sites and homology to human genes.
Docking
Docking is used to predict the binding of two molecules and evaluate their interaction energy. It involves representing molecules, exploring possible configurations, and ranking them by binding energy using a scoring system. There are two main categories: protein-protein docking treats both molecules as rigid, while protein-ligand docking allows flexibility in the ligand. AutoDock software is commonly used for docking via genetic algorithms and other search methods to minimize energy between a protein and ligand. Docking preparation involves adding hydrogens, assigning charges and merging atoms for both molecules. The results can provide insight into protein interactions and rational drug design.
Quantative Structure-Activity Relationships (QSAR)
This document discusses quantitative structure-activity relationship (QSAR) modeling and 3D-QSAR techniques. It explains that QSAR aims to find consistent relationships between biological activity and molecular properties in order to predict activity of new compounds. It also describes several common 3D-QSAR software programs and techniques, including CoMFA, VolSurf, Catalyst, and DOCK, and provides examples of their applications to modeling various cytochrome P450 enzymes.
Similar to HPRnase (20)
NMR method development for large proteins presented at ENC 2005
NMR method development for large proteins presented at ENC 2005
bradykinin receptor antagonist and thrombin inhibitors
bradykinin receptor antagonist and thrombin inhibitors
LSSC2011 Optimization of intermolecular interaction potential energy paramete...
LSSC2011 Optimization of intermolecular interaction potential energy paramete...
QSAR : Activity Relationships Quantitative Structure
QSAR : Activity Relationships Quantitative Structure
Beyond transcription: RNA-binding proteins as emerging regulator of plant res...
Beyond transcription: RNA-binding proteins as emerging regulator of plant res...
DNA,RNA and PROTEIN Overview.Just know about the genetics
DNA,RNA and PROTEIN Overview.Just know about the genetics
Quantative Structure-Activity Relationships (QSAR)
Quantative Structure-Activity Relationships (QSAR)
More from University of Minnesota Rochester
Chemistry Gamification - Edulearn 2014
Introductory chemistry and other undergraduate first-year science courses involve some topics that need first to be mastered before students can address higher-order thinking problems. One could say that students need to first learn the language of that scientific discipline before they can express themselves in that language. In chemistry, for example, it is necessary to master low-order skills such as chemistry nomenclature, common oxidation states, memorizing the amino acids or identify the strength of common acids and bases before one can solve some higher-order problems. These kind of low-order skills are typically repetitive and students have a hard time being engaged and achieve the desired mastery level. A solution to this problem is imple gamification, that is, to design more engaging game-like activities to achieve the desired goal.
We are presenting a set of web-based game-like activities developed by students themselves. Game-like activities can be thought as the perfect active learning activity since they show clear goals, give immediate feedback and, if designed well and aligned with the course learning objectives, are engaging and improve retention.
Some of our students who had already taken the introductory chemistry course or who were taking it concurrently, took a semester to learn some basics of Javascript and web design to develop their own game-like activities. Having students designing the activities has resulted in a win-win situation for both instructors and students. The instructors have engaging game-like tools to be used in forthcoming courses and students learn some programming and find it rewarding to create from scratch their own games that other students may use.
We will also report how we developed an open repository of chemistry data to be used both for low-order skills such as the online games mentioned above, but also for higher-order thinking and self-regulated learning. The same set of molecules and molecular properties are used for both purposes and it is open access to everyone available at http://chemdata.r.umn.edu.
ChemEd X Data - BCCE 2014
This document summarizes a presentation about ChemEd X Data, an open web platform containing chemical data to support student learning. The platform contains unstructured data on elements, compounds, and reactions that students can explore to discover trends. It aims to move beyond static pre-cooked data by allowing students to choose data, identify patterns, and find exceptions. The document describes how the data is organized and can be visualized. It also discusses early findings that show the platform improves students' abilities to design experiments, draw conclusions from evidence, and identify exceptions. The overall goal is to enhance higher-order thinking skills.
Chile 2015 - Chemistry learning and technology (Spanish) - UNAB
La disponibilidad de grandes cantidades de información en internet y la proliferación de herramientas pedagógicas en computadora ha multiplicado las posibilidades para mejorar el aprendizaje en química y a su vez ha incrementado los peligros que el mal uso de estas pueden acarrear.
En esta charla vamos a considerar qué conceptos y aptitudes en el temario de cursos introductorios de química pueden beneficiarse de las herramientas online. Primero vamos a describir qué herramientas interactivas pueden ayudar a entender y predecir la estructura molecular (http://chemdata.r.umn.edu/jmol/). También describiremos plataformas web para comprender el carácter dinámico del mundo molecular. Estas simulaciones se pueden usar tanto como demostración en clase, actividades para laboratorio virtual o como tarea fuera de clase.
En la segunda parte de la charla nos preguntaremos si la presencia de internet ha cambiado los fundamentos del aprendizaje en química. En particular, cuando la información abunda y su acceso es instantáneo, la memorización es menos importante y los estudiantes tienen que saber navegar grandes cantidades de datos, encontrar pautas y excepciones por si solos (J. Chem. Educ., 2014, 91 (9), pp 1501–1504).
Por ejemplo, se ha dicho que la esencia del saber química es juzgar entre influencias en conflicto ya que rara vez una única propiedad decide el resultado de un cambio físico o químico. Ejemplos en química general donde hay conflicto de influencias son la periodicidad de elementos químicos, factores que afectan el punto de ebullición de compuestos o incluso la predicción de la configuración electrónica de elementos. En todos estos ejemplos, los alumnos pueden explorar resultados experimentales y encontrar por si solos cuales son los factores más relevantes en cada caso. Los alumnos también descubren excepciones y entienden que es igual de importante entender el poder predictivo de una ley científica como los límites de esta.
El saber reconocer un experimento controlado e identificar evidencias sin prejuicio alguno es una aptitud que trasciende el ámbito de la química y tiene relevancia para toda persona que aspire a ser un ciudadano activo en una sociedad participativa.
Chile 2015 - Active learning and technology (Spanish) - UNAB
Está ya todo inventado en las metodologías de la enseñanza?
Entre las estrategias más conservadoras dónde el alumno es pasivo durante la lección y las posiciones más rompedoras donde el alumno marca el ritmo y contenido de la clase hay un gran abanico de posibilidades. Ni todo lo que se ha hecho hasta ahora está mal, ni todo lo nuevo es mejor. Lo que está claro es que la presencia de internet y su abundancia de información y herramientas no puede dejar a nadie indiferente y cabe preguntarse qué lugar debe ocupar la tecnología informática en la educación.
En este taller daremos una visión rápida y generalizada a las diferentes estrategias para involucrar al alumno durante el tiempo de clase sin que se tenga que sacrificar ni el nivel del curso ni los objetivos de contenido. Vamos a poner especial énfasis en métodos tecnológicos “open source” o gratuitos que pueden ayudar al alumno para que venga más preparado a clase, participe más en clase y practique más fuera de ella. A su vez, también, hablaremos de herramientas de análisis para que el profesor sepa en todo momento el rendimiento de sus alumnos o pueda llevar a cabo estudios longitudinales donde se analizan datos a lo largo de varios cursos o de todo un grado.
UMR - My ongoing projects with Technology - Rochester - 2015
In this talk I will summarize my several attempts to introduce to students the basics of computer programming in a degree in Health Science. While the curriculum at the BSHS does not align very well with computer science content, the learning of a computer language addresses some essential higher-order thinking skills that bring cognitive benefits to the student as well as practical skills for their professional careers.
In the second half of the talk I will navigate four years of student data in General Chemistry with our in-house developed learning analytics tool BoSCO (Browser of Student and Course Objects). Rather than an intensive statistical analysis tool, BoSCO allows an “intentional browsing” of student data and it can be understood as a hypothesis generating tool that creates questions rather than giving a definitive answer or evidence. In particular, we will look at student performance in different types of assignments of the General Chemistry curriculum throughout the years filtered by different demographics criteria. More specifically, we will use the SLICE approach (Showing Longitudinal Interactions of Course Events) to bundle grades from different assignments or courses to quantify the learning of a specific skill.
Elearning Summit 2015 - BoSCO - Minneapolis
The disconnect between data collection and analysis across sectors of academic institutions makes it challenging to incorporate data into curricular design. Understanding the factors related to student persistence and success is unlikely to occur by focusing only on one sector at a time. Facilitating evidence-based course design might begin with the creation of a tool that allows real-time exploration of data across sectors for integration into the traditional course/curricular design. Our paper describes how data from institutional, learning, and what we call “developmental” analytics can be incorporated into course and curricular design by using a purposefully built analysis tool that permits the exploration of student and course objects. This Browser of Student and Course Objects (BoSCO) is being built in a faculty driven-process and can be used as a bridge between the analytics space and the course/curriculum design environments.
Xavier Prat-Resina has a PhD in Physical Chemistry. He is a faculty member at the “Center for Learning Innovation” in the UofM Rochester campus. His interests are the design of web materials to enhance student learning and to analyze student and course data to optimize the academic curriculum.
-It takes institutional, learning and developmental data to assess a curriculum.
-BoSCO is an agile tool that may encourage teachers to use analytics for course and curricular design.
-Evidence-based course design requires the involvement of many sectors of the academic institution.
Ecrice - ChemEd X Data - Barcelona - 2016 talk
In the General Chemistry curriculum there are several instances in which students are asked to judge between conflicting factors to decide an outcome. In fact, some have identified “the skill to judge between conflicting influences” as the essence of chemistry that all chemistry students should learn. To that aim I wrote the ChemEd X Data web interface1 (http://chemdata.r.umn.edu/chemedXdata/). The main pedagogical objective of the website is to allow students to navigate, select and graphically represent data such as boiling and melting points, enthalpies of combustion and heat capacities for hundreds of molecules. By doing so, students can independently identify correlations between magnitudes, laws, and outliers. One of the merits of this tool is that it may help students recognize situations when conflicting influences play a role (e.g. molecular weight, shape and dipole effect on boiling point). Identifying conflicting influences empowers students with analytical skills that will lead them to higher-order thinking and self-regulated learning.
Talk Jan05
The document summarizes a study of the reaction mechanism of mandelate racemase using quantum mechanics/molecular mechanics (QM/MM) modeling. It finds that the enzyme stabilizes the transition state of the reaction relative to reactants through electrostatic interactions with active site residues such as Lys166 and His297. This stabilization lowers the reaction's energy barrier compared to the uncatalyzed reaction in water.
Water Sept05
1. The document discusses using SCCdftb/MM (self-consistent charge density functional tight binding/molecular mechanics) hybrid quantum mechanics/molecular mechanics simulations to model water and solvated proton, hydroxide, and neutral water systems.
2. It evaluates different SCCdftb methods for modeling the diffusion of solvated proton, hydroxide, and neutral water and compares the results to experimental values.
3. The document also discusses dynamically switching water molecules between the quantum mechanics and molecular mechanics regions in the simulations.
Cytochrome c Oxidase Jan06
The document summarizes research on the reaction mechanism of cytochrome c oxidase (CcO).
1) It describes simulations conducted to analyze the role of Glu242 and surrounding waters in proton transport and pumping. Calculations show Glu242's pK is higher in the ND98 mutant, explaining its impaired pumping.
2) Calculations were also conducted to determine His291's pK, though more work is needed to accurately model the copper site and quantify changes in pK under different ligation states.
3) Overall the research aims to better understand proton transport and coupling between chemical and physical sites in CcO through quantitative simulations and pK calculations.
More from University of Minnesota Rochester (10)
Chile 2015 - Chemistry learning and technology (Spanish) - UNAB
Chile 2015 - Chemistry learning and technology (Spanish) - UNAB
Chile 2015 - Active learning and technology (Spanish) - UNAB
Chile 2015 - Active learning and technology (Spanish) - UNAB
UMR - My ongoing projects with Technology - Rochester - 2015
UMR - My ongoing projects with Technology - Rochester - 2015
Recently uploaded
Chapter 4 - Islamic Financial Institutions in Malaysia.pptx
Chapter 4 - Islamic Financial Institutions in Malaysia.pptxMohd Adib Abd Muin, Senior Lecturer at Universiti Utara Malaysia
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
Chapter wise All Notes of First year Basic Civil Engineering.pptx
Chapter wise All Notes of First year Basic Civil Engineering
Syllabus
Chapter-1
Introduction to objective, scope and outcome the subject
Chapter 2
Introduction: Scope and Specialization of Civil Engineering, Role of civil Engineer in Society, Impact of infrastructural development on economy of country.
Chapter 3
Surveying: Object Principles & Types of Surveying; Site Plans, Plans & Maps; Scales & Unit of different Measurements.
Linear Measurements: Instruments used. Linear Measurement by Tape, Ranging out Survey Lines and overcoming Obstructions; Measurements on sloping ground; Tape corrections, conventional symbols. Angular Measurements: Instruments used; Introduction to Compass Surveying, Bearings and Longitude & Latitude of a Line, Introduction to total station.
Levelling: Instrument used Object of levelling, Methods of levelling in brief, and Contour maps.
Chapter 4
Buildings: Selection of site for Buildings, Layout of Building Plan, Types of buildings, Plinth area, carpet area, floor space index, Introduction to building byelaws, concept of sun light & ventilation. Components of Buildings & their functions, Basic concept of R.C.C., Introduction to types of foundation
Chapter 5
Transportation: Introduction to Transportation Engineering; Traffic and Road Safety: Types and Characteristics of Various Modes of Transportation; Various Road Traffic Signs, Causes of Accidents and Road Safety Measures.
Chapter 6
Environmental Engineering: Environmental Pollution, Environmental Acts and Regulations, Functional Concepts of Ecology, Basics of Species, Biodiversity, Ecosystem, Hydrological Cycle; Chemical Cycles: Carbon, Nitrogen & Phosphorus; Energy Flow in Ecosystems.
Water Pollution: Water Quality standards, Introduction to Treatment & Disposal of Waste Water. Reuse and Saving of Water, Rain Water Harvesting. Solid Waste Management: Classification of Solid Waste, Collection, Transportation and Disposal of Solid. Recycling of Solid Waste: Energy Recovery, Sanitary Landfill, On-Site Sanitation. Air & Noise Pollution: Primary and Secondary air pollutants, Harmful effects of Air Pollution, Control of Air Pollution. . Noise Pollution Harmful Effects of noise pollution, control of noise pollution, Global warming & Climate Change, Ozone depletion, Greenhouse effect
Text Books:
1. Palancharmy, Basic Civil Engineering, McGraw Hill publishers.
2. Satheesh Gopi, Basic Civil Engineering, Pearson Publishers.
3. Ketki Rangwala Dalal, Essentials of Civil Engineering, Charotar Publishing House.
4. BCP, Surveying volume 1
ANATOMY AND BIOMECHANICS OF HIP JOINT.pdf
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
Pengantar Penggunaan Flutter - Dart programming language1.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptx
Hindi varnamala | hindi alphabet PPT.pdf
हिंदी वर्णमाला पीपीटी, hindi alphabet PPT presentation, hindi varnamala PPT, Hindi Varnamala pdf, हिंदी स्वर, हिंदी व्यंजन, sikhiye hindi varnmala, dr. mulla adam ali, hindi language and literature, hindi alphabet with drawing, hindi alphabet pdf, hindi varnamala for childrens, hindi language, hindi varnamala practice for kids, https://www.drmullaadamali.com
Reimagining Your Library Space: How to Increase the Vibes in Your Library No ...
Librarians are leading the way in creating future-ready citizens – now we need to update our spaces to match. In this session, attendees will get inspiration for transforming their library spaces. You’ll learn how to survey students and patrons, create a focus group, and use design thinking to brainstorm ideas for your space. We’ll discuss budget friendly ways to change your space as well as how to find funding. No matter where you’re at, you’ll find ideas for reimagining your space in this session.
BÀI TẬP BỔ TRỢ TIẾNG ANH LỚP 9 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2024-2025 - ...
BÀI TẬP BỔ TRỢ TIẾNG ANH LỚP 9 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2024-2025 - ...Nguyen Thanh Tu Collection
https://app.box.com/s/tacvl9ekroe9hqupdnjruiypvm9rdaneNatural birth techniques - Mrs.Akanksha Trivedi Rama University
Natural birth techniques - Mrs.Akanksha Trivedi Rama UniversityAkanksha trivedi rama nursing college kanpur.
Natural birth techniques are various type such as/ water birth , alexender method, hypnosis, bradley method, lamaze method etcBBR 2024 Summer Sessions Interview Training
Qualitative research interview training by Professor Katrina Pritchard and Dr Helen Williams
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Aberdeen
Pollock and Snow "DEIA in the Scholarly Landscape, Session One: Setting Expec...
Pollock and Snow "DEIA in the Scholarly Landscape, Session One: Setting Expec...National Information Standards Organization (NISO)
This presentation was provided by Steph Pollock of The American Psychological Association’s Journals Program, and Damita Snow, of The American Society of Civil Engineers (ASCE), for the initial session of NISO's 2024 Training Series "DEIA in the Scholarly Landscape." Session One: 'Setting Expectations: a DEIA Primer,' was held June 6, 2024.Walmart Business+ and Spark Good for Nonprofits.pdf
"Learn about all the ways Walmart supports nonprofit organizations.
You will hear from Liz Willett, the Head of Nonprofits, and hear about what Walmart is doing to help nonprofits, including Walmart Business and Spark Good. Walmart Business+ is a new offer for nonprofits that offers discounts and also streamlines nonprofits order and expense tracking, saving time and money.
The webinar may also give some examples on how nonprofits can best leverage Walmart Business+.
The event will cover the following::
Walmart Business + (https://business.walmart.com/plus) is a new shopping experience for nonprofits, schools, and local business customers that connects an exclusive online shopping experience to stores. Benefits include free delivery and shipping, a 'Spend Analytics” feature, special discounts, deals and tax-exempt shopping.
Special TechSoup offer for a free 180 days membership, and up to $150 in discounts on eligible orders.
Spark Good (walmart.com/sparkgood) is a charitable platform that enables nonprofits to receive donations directly from customers and associates.
Answers about how you can do more with Walmart!"
Wound healing PPT
This document provides an overview of wound healing, its functions, stages, mechanisms, factors affecting it, and complications.
A wound is a break in the integrity of the skin or tissues, which may be associated with disruption of the structure and function.
Healing is the body’s response to injury in an attempt to restore normal structure and functions.
Healing can occur in two ways: Regeneration and Repair
There are 4 phases of wound healing: hemostasis, inflammation, proliferation, and remodeling. This document also describes the mechanism of wound healing. Factors that affect healing include infection, uncontrolled diabetes, poor nutrition, age, anemia, the presence of foreign bodies, etc.
Complications of wound healing like infection, hyperpigmentation of scar, contractures, and keloid formation.
Recently uploaded (20)
Chapter 4 - Islamic Financial Institutions in Malaysia.pptx
Chapter 4 - Islamic Financial Institutions in Malaysia.pptx
Chapter wise All Notes of First year Basic Civil Engineering.pptx
Chapter wise All Notes of First year Basic Civil Engineering.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptx
NEWSPAPERS - QUESTION 1 - REVISION POWERPOINT.pptx
NEWSPAPERS - QUESTION 1 - REVISION POWERPOINT.pptx
Reimagining Your Library Space: How to Increase the Vibes in Your Library No ...
Reimagining Your Library Space: How to Increase the Vibes in Your Library No ...
Digital Artefact 1 - Tiny Home Environmental Design
Digital Artefact 1 - Tiny Home Environmental Design
BÀI TẬP BỔ TRỢ TIẾNG ANH LỚP 9 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2024-2025 - ...
BÀI TẬP BỔ TRỢ TIẾNG ANH LỚP 9 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2024-2025 - ...
Natural birth techniques - Mrs.Akanksha Trivedi Rama University
Natural birth techniques - Mrs.Akanksha Trivedi Rama University
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
Pollock and Snow "DEIA in the Scholarly Landscape, Session One: Setting Expec...
Pollock and Snow "DEIA in the Scholarly Landscape, Session One: Setting Expec...
Walmart Business+ and Spark Good for Nonprofits.pdf
Walmart Business+ and Spark Good for Nonprofits.pdf
HPRnase
- 1. Human Pancreatic Ribonuclease Molecular Simulations to compare it with Ribonuclease A Group Meeting Xavier Prat-Resina April 20 th 2007
- 4. 1. Introduction: Struct. & React. Structure: HP-RNase with tetra-nucleotide (4 cytidine) in endo coordination The difference between HP-Rnase and Rnase A is that the former has 2 more positively charged residues at the N-terminal: Lys6 and Arg4
- 5. 1. Introduction: Struct. & React. Enzymatic reaction The substrate for our simulations: tetra-cytidilic acid with a cyclic phosphate
- 6. 1. Introduction: Struct. & React. Active site and binding sites in Exo coordination 4-Cytidine with cyclic phosphate Endo/Exo P3/P2 P2/P1 P1/P0 P2/P-1 Exo product Endo Product
- 10. 3. Setup for Simulations Homology modelling (Alex Gomez-Garrido): Initial structures: RNAse A bovine 1RCN and HP-RNase mutant 1DZA with 4 DNA nucleosides (ATAA) The structure are all very similar
- 13. Analysis of important distances We want to see the role of different residues Differences between exo/endo and wild type and mutant 4. Struct. Analysis of MD Lys1 Arg4 Lys7 Arg10 Lys6
- 14. Arg4-P2 endo exo Arg4-P3 4. Struct. Analysis of MD Analysis of important distances
- 15. Lys6-P2 endo exo Lys6-P3 4. Struct. Analysis of MD Analysis of important distances
- 17. D Gtot(Wild type) > D Gtot(mutant) ? The ratio between exo and endonucleolytic product is 1.35 in HP-RNase and 2.15 for the mutant. D Gtot ? Endo Exo 5. Free Energy Calculations D G1 D G2 D Gtot= D G 1 + D G2 Alchemical pathway
- 18. Alchemical Free Energy 5. Free Energy Calculations We run Molecular Dynamics and collect the energy difference between reactant ”a” and product ”b” To converge the calculation we alchemically transform ”a” into ”b” scaling the two structures. We define a system as a combination of reactants ”a” and products ”b” We run several ”windows” at different values of l and combine them (100 ps/window)
- 19. 5. Free Energy Calculations D G1 D G2 Wild Type Mutant Free Energy (Kcal/mol) Lambda (0-1)
- 20. D G 1=202.54 D G 2=-199.17 D G tot= 202.54 -199.17 =3.37 kcal/mol Wild Type Endo Exo 5. Free Energy Calculations D G tot= 198.90-189.27 =8.63 kcal/mol D G 1=198.90 D G 2=-189.27 Mutant