The document describes an experiment measuring the static light scattering of concentrated protein solutions as a function of concentration. Specifically, it measured bovine serum albumin, ovalbumin, ovomucoid, and mixtures of these proteins up to 125 g/L, as well as chymotrypsin A at different pH levels up to 70 g/L. The measured scattering was quantitatively accounted for by an effective hard particle model, in which each protein is represented as a hard sphere and interactions are treated as hard particle repulsions and association equilibria.
Spectroscopic and ITC studies of binding of Ferulic acid with BSADr Himanshu Ojha
This document summarizes a journal article that studied the binding interaction between ferulic acid (FA) and bovine serum albumin (BSA) using fluorescence, circular dichroism, and isothermal titration calorimetry techniques. The fluorescence data determined one class of binding site with a binding constant of 40.14 × 104 M−1 at 298 K. Circular dichroism data showed changes in BSA secondary structure upon binding with FA, indicating non-covalent interactions and increased thermal stability of BSA. Isothermal titration calorimetry suggested FA binds to BSA at two sites with high affinity through electrostatic and hydrogen bonding forces, and binding caused conformational changes in BSA.
1. Five hydroxamate small molecule inhibitors and three quinoline inhibitors were evaluated for their ability to inhibit Botulinum neurotoxin type A (BoNT-A) using an in vitro LC/MSMS assay. The hydroxamates exhibited high potency inhibition at 1 μM, while the quinolines showed much weaker inhibition and did not fully inhibit even at 400 μM.
2. A 66-mer peptide substrate containing the BoNT-A cleavage site was characterized and its N-terminal cleavage product was identified. Using this longer substrate requires less BoNT-A light chain protease for experiments, reducing costs.
3. Two cyclic peptides previously shown to inhibit BoNT-A were characterized in
Protein purification techniques can be categorized into those based on molecular size, solubility, and electric charge. Size-based techniques include dialysis, ultrafiltration, and size-exclusion chromatography which separate proteins based on their ability to pass through semi-permeable membranes or porous beads. Solubility-based techniques include isoelectric precipitation and salting out which alter a protein's solubility by adjusting pH or salt concentration. Charge-based techniques such as ion-exchange and electrophoresis separate proteins using their net electric charge in an applied electric field or ion-exchange column.
This document summarizes an experiment studying the kinetics of the tyrosinase enzyme using L-dopa as a substrate. Sodium benzoate was used as an inhibitor at 0.1 mM and 0.2 mM concentrations. The optimal tyrosinase concentration was determined to be 6.8 units/ml. For uninhibited tyrosinase, the Km was 490.35 μM and Vmax was 500 μM/s. With inhibition, Km and Vmax values changed, indicating mixed inhibition with an emphasis on uncompetitive inhibition. Experimental conditions influenced results.
A New Lupan type Triterpene Butilinol from Viburnum grandiflorumIOSR Journals
The isolation and structural studies on the chemical constituents of Viburnum grandiflorum are described. The medicinal properties of the plant are also described. The mentholic extract was subjected to the preparative thin layer chromatography (PTLC) test experiments to investigate the isolation pattern. Based on the PTLC test experiments, the extract was subjected to the silica gel column chromatography. The column was eluted with increasing polarities of organic solvents. This afforded several fractions. The fractions were re-chromatographed on silica gel column to afford a new lupan type triterpene butilinol (1) with several known compounds i. e. oleanolic acid (2), ursolic acid (3), β-sitosterol (4), butilinic acid (5), butilin (6), α-amyrin (7) and germanicol (8). The compound (6) was not reported previously from the genus Viburnum. This therefore represents its first report from Viburnum grandiflorum. The compounds (2) and (4) have been previously reported from Viburnum pronifolium while the compounds (3) and (8) from Viburnum opulus and Viburnum erubescens, respectively. This represents the first report of the presence of these compounds in Viburnum grandiflorum. The structures of the above compounds were identified on the basis of spectral data (UV, IR, Mass, 1NMR, 13C-NMR) and literature evidences. The hexane and ethyl acetate soluble portions of the methanolic extract showed significant antifungal activity, while the chloroform soluble portion and the remaining methanol extract showed moderate activity.
This document summarizes the isolation and characterization of opioid peptides (exorphins) derived from food proteins wheat gluten and casein. The key points are:
1) Peptides with opioid activity were isolated from pepsin digests of wheat gluten and casein and shown to inhibit adenylate cyclase and electrically stimulated mouse vas deferens contractions in a naloxone-reversible manner, indicating opioid activity.
2) The wheat gluten exorphin was purified 10,000 times and casein exorphin purified through multiple chromatography steps.
3) Both exorphins competed for binding to rat brain opioid receptors, demonstrating their ability to bind at opioid receptor sites.
This document provides information about an upcoming exam on protein purification techniques and related topics. It outlines the skills and concepts students should have learned, including using pipettes, spectrophotometers, organizing protocols, and preparing reports. It notes an upcoming protein purification lab experiment and encourages students to pay attention to details and properly label all samples to avoid issues. Finally, it provides an overview of the protein purification strategy and techniques to be used, including ammonium sulfate precipitation, dialysis, and column chromatography.
This document summarizes research exploring the structure and function of HMG-CoA reductase (HMGR) in Burkholderia cenocepacia. Key findings include:
1) B. cenocepacia HMGR (BcHMGR) exhibits properties of a morpheein, meaning it can exist in multiple quaternary structure states that influence enzymatic activity.
2) The equilibrium between BcHMGR structure states is affected by factors like ligand concentration, enzyme concentration, and pH.
3) BcHMGR preferentially catalyzes the oxidation of mevalonate to HMG-CoA, unlike most HMGRs which catalyze the reverse reaction.
Spectroscopic and ITC studies of binding of Ferulic acid with BSADr Himanshu Ojha
This document summarizes a journal article that studied the binding interaction between ferulic acid (FA) and bovine serum albumin (BSA) using fluorescence, circular dichroism, and isothermal titration calorimetry techniques. The fluorescence data determined one class of binding site with a binding constant of 40.14 × 104 M−1 at 298 K. Circular dichroism data showed changes in BSA secondary structure upon binding with FA, indicating non-covalent interactions and increased thermal stability of BSA. Isothermal titration calorimetry suggested FA binds to BSA at two sites with high affinity through electrostatic and hydrogen bonding forces, and binding caused conformational changes in BSA.
1. Five hydroxamate small molecule inhibitors and three quinoline inhibitors were evaluated for their ability to inhibit Botulinum neurotoxin type A (BoNT-A) using an in vitro LC/MSMS assay. The hydroxamates exhibited high potency inhibition at 1 μM, while the quinolines showed much weaker inhibition and did not fully inhibit even at 400 μM.
2. A 66-mer peptide substrate containing the BoNT-A cleavage site was characterized and its N-terminal cleavage product was identified. Using this longer substrate requires less BoNT-A light chain protease for experiments, reducing costs.
3. Two cyclic peptides previously shown to inhibit BoNT-A were characterized in
Protein purification techniques can be categorized into those based on molecular size, solubility, and electric charge. Size-based techniques include dialysis, ultrafiltration, and size-exclusion chromatography which separate proteins based on their ability to pass through semi-permeable membranes or porous beads. Solubility-based techniques include isoelectric precipitation and salting out which alter a protein's solubility by adjusting pH or salt concentration. Charge-based techniques such as ion-exchange and electrophoresis separate proteins using their net electric charge in an applied electric field or ion-exchange column.
This document summarizes an experiment studying the kinetics of the tyrosinase enzyme using L-dopa as a substrate. Sodium benzoate was used as an inhibitor at 0.1 mM and 0.2 mM concentrations. The optimal tyrosinase concentration was determined to be 6.8 units/ml. For uninhibited tyrosinase, the Km was 490.35 μM and Vmax was 500 μM/s. With inhibition, Km and Vmax values changed, indicating mixed inhibition with an emphasis on uncompetitive inhibition. Experimental conditions influenced results.
A New Lupan type Triterpene Butilinol from Viburnum grandiflorumIOSR Journals
The isolation and structural studies on the chemical constituents of Viburnum grandiflorum are described. The medicinal properties of the plant are also described. The mentholic extract was subjected to the preparative thin layer chromatography (PTLC) test experiments to investigate the isolation pattern. Based on the PTLC test experiments, the extract was subjected to the silica gel column chromatography. The column was eluted with increasing polarities of organic solvents. This afforded several fractions. The fractions were re-chromatographed on silica gel column to afford a new lupan type triterpene butilinol (1) with several known compounds i. e. oleanolic acid (2), ursolic acid (3), β-sitosterol (4), butilinic acid (5), butilin (6), α-amyrin (7) and germanicol (8). The compound (6) was not reported previously from the genus Viburnum. This therefore represents its first report from Viburnum grandiflorum. The compounds (2) and (4) have been previously reported from Viburnum pronifolium while the compounds (3) and (8) from Viburnum opulus and Viburnum erubescens, respectively. This represents the first report of the presence of these compounds in Viburnum grandiflorum. The structures of the above compounds were identified on the basis of spectral data (UV, IR, Mass, 1NMR, 13C-NMR) and literature evidences. The hexane and ethyl acetate soluble portions of the methanolic extract showed significant antifungal activity, while the chloroform soluble portion and the remaining methanol extract showed moderate activity.
This document summarizes the isolation and characterization of opioid peptides (exorphins) derived from food proteins wheat gluten and casein. The key points are:
1) Peptides with opioid activity were isolated from pepsin digests of wheat gluten and casein and shown to inhibit adenylate cyclase and electrically stimulated mouse vas deferens contractions in a naloxone-reversible manner, indicating opioid activity.
2) The wheat gluten exorphin was purified 10,000 times and casein exorphin purified through multiple chromatography steps.
3) Both exorphins competed for binding to rat brain opioid receptors, demonstrating their ability to bind at opioid receptor sites.
This document provides information about an upcoming exam on protein purification techniques and related topics. It outlines the skills and concepts students should have learned, including using pipettes, spectrophotometers, organizing protocols, and preparing reports. It notes an upcoming protein purification lab experiment and encourages students to pay attention to details and properly label all samples to avoid issues. Finally, it provides an overview of the protein purification strategy and techniques to be used, including ammonium sulfate precipitation, dialysis, and column chromatography.
This document summarizes research exploring the structure and function of HMG-CoA reductase (HMGR) in Burkholderia cenocepacia. Key findings include:
1) B. cenocepacia HMGR (BcHMGR) exhibits properties of a morpheein, meaning it can exist in multiple quaternary structure states that influence enzymatic activity.
2) The equilibrium between BcHMGR structure states is affected by factors like ligand concentration, enzyme concentration, and pH.
3) BcHMGR preferentially catalyzes the oxidation of mevalonate to HMG-CoA, unlike most HMGRs which catalyze the reverse reaction.
Protein microarrays, ICAT, and HPLC protein purificationRaul Soto
The document discusses the Isotope-Coded Affinity Tag (ICAT) method for protein quantification and identification. ICAT uses chemical labeling reagents that specifically label cysteine residues. There are 4 main steps: 1) Lyse and label protein samples from two states with light and heavy ICAT tags, 2) Mix and proteolyze samples to generate peptide fragments, some tagged, 3) Isolate tagged fragments using avidin affinity chromatography, 4) Analyze isolated peptides using mass spectrometry to identify and quantify proteins between the two states. ICAT allows accurate quantification of complex protein mixtures.
This document summarizes a study that explored using RNA nucleosides as chiral sensing agents in NMR spectroscopy. Adenosine, guanosine, uridine, and cytidine were used as chiral derivatizing agents to differentiate between chiral primary amines. A three-component protocol was adopted to form complexes between the nucleosides and amines. The chiral differentiation ability of the nucleosides was examined using the 1H NMR chemical shift differences (ΔδR,S) between diastereomers formed from R- and S-amines. Adenosine and guanosine showed large chiral differentiation due to their purine rings. The measured diastereomeric excess using adenos
1. Immunoprecipitation is a technique used to isolate a protein of interest along with any interacting proteins from a mixture. It involves using an antibody against the target protein to form an immune complex, which is then isolated using a secondary antibody or protein A/G.
2. Immunogold labeling localizes proteins in cells and tissues using antibodies tagged with gold particles and visualized with electron microscopy. It was used in one study to quantify serotonin receptor subtypes in post-mortem brain samples from suicide victims versus controls.
3. Western blotting separates proteins by gel electrophoresis then transfers them to a membrane where antibodies are used to detect specific proteins. It allows visualization and quantification of proteins.
Proteome-wide covalent ligand discovery in native biological systemsMegha Majumder
The document describes a new method for finding drug candidates that bind to specific proteins called isoTOP-ABPP. It involves applying small molecule fragments that covalently bind to cysteine amino acids on proteins. This allows researchers to detect which proteins the fragments bind to. They tested a library of these fragments on cancer cell proteins and found they bound to over 750 cysteines on more than 600 proteins, including some previously considered undruggable. Further experiments showed some fragments could selectively target and inhibit certain proteins like IDH1/2 and label inactive pro-forms of proteins like caspase-8, but not the active forms.
Antibacterial Activity of Schiff Bases Derived from OrthoDiaminocyclohexane, ...inventionjournals
Schiff bases (SBs) are known to possess many biological activities. In this paper we will be interested in nine SBs derived from ortho-diaminocyclohexane, meta-phenylenediamine, 1,6-diaminohexane and benzaldehydes variously substituted by nitro group. We had synthesized, characterized and tested these molecules for their antibacterial properties. Herein our study focuses in particular on the determination of quantum descriptors on which observed antibacterial activity depends, in order to be able to predict biological activities in analogue molecule series. Using quantum chemistry methods at B3LYP / 6-31G (d, p) level, we determined for each molecules, theoretical antibacterial potentials that we correlated to the experimental ones. Calculation results showed that, the energy of the Highest Occupied Molecular Orbital (EHOMO), electronegativity (χ) and electronic energy (E), are the best quantum descriptors related to the antibacterial activity values of studied molecules. The correlation coefficient R 2 indicates that 92.1% of the molecular descriptors defining this model are taken into account with a standard deviation of 0.152.The model significance is reflected by Fischer coefficient F = 7.721: Correlation coefficient of cross-validation = 0.88. This model is acceptable with . The values of the pCE50theo/pCE50exp values of the validation set tend to unity
Introduction
Proteins
Function Of Protein And Their Properties
Protein Isolation And Purification
Methods Of Cell Lysis
Steps Of Protein Characterisation:
Determination Of Protein Concentration
Biuret Reaction
Lowry (Folin-Lowry) Method
UV- Spectroscopy
Assessment Of Protein Purity
SDS -Phage
Immunoblot
Surface Charge Analysis
Isoelectro Focusing
Ion Exchange Chromatography
Size, Shape And Conformation Analysis
2d-Electrophorasis
X-Ray Crytalliography
Protein Structure and Sequence Analysis
Edman Sequencing
Conclusion
References
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.
TOTAL POLYPHENOLS AND DPPH FREE RADICALS SCAVENGING ACTIVITY IN SIX LEAFY VEG...Md. Kamaruzzaman
TOTAL POLYPHENOLS AND DPPH FREE RADICALS SCAVENGING ACTIVITY IN SIX LEAFY VEGETABLES OF BANGLADESH
Harun-Ar-Rashid, Sheikh Julfikar Hossain, Sk. Amir Hossain, Md Mahfuzur Rahman, Md. Kamaruzzaman
This document provides an overview of the schedule and topics for a course on metabolic networks. The course covers various topics related to metabolism, including enzyme assays, mass spectrometry techniques, primary metabolism, glycogen metabolism, metabolic networks in humans, flux analysis, and biochemical databases. Homework discussions are scheduled every other Friday. Guest lecturers will discuss biochemical databases and tools for modeling metabolism on the last two class meetings. The course includes no class on Veteran's Day and Thanksgiving.
This document provides information on several common methods used to measure antioxidant capacity in biological samples and foods. It describes the principles, procedures, and key measurements of assays such as ORAC, DPPH, ABTS, Folin-Ciocalteu, FRAP, CAA, HPLC, UPLC, and ELISA. These assays utilize different chemical reactions and detection methods to quantify a sample's ability to inhibit oxidation initiated by free radicals.
This document discusses various chromatography techniques used to purify biomolecules, including affinity chromatography, ion exchange chromatography, size exclusion chromatography, and reversed phase chromatography. It provides details on how each technique separates molecules based on specific properties, such as biological recognition (affinity chromatography), charge (ion exchange chromatography), size (size exclusion chromatography), and hydrophobicity (reversed phase chromatography).
This document discusses various enzymatic analytical methods used for food analysis, including substrate determination, enzyme activity determination, enzyme immunoassay, and polymerase chain reaction. Specifically, it covers:
1) Substrate determination methods like end-point assays that use coupled enzyme reactions to measure food constituents.
2) Determining enzyme activity in food to evaluate quality and optimize processes by measuring reaction rates under controlled conditions.
3) Enzyme immunoassays like ELISA that use antibody-antigen reactions and enzyme-labeled antigens to detect food compounds.
4) Polymerase chain reaction (PCR) which amplifies DNA for sensitive species identification and detecting genetically modified foods. PCR allows analysis of heat-treated foods where proteins
The document discusses various techniques for protein purification and characterization, including:
1. Detergents solubilize transmembrane proteins by having affinity for hydrophobic groups and water.
2. Centrifugation separates particles of different masses or densities, with denser particles pelleted first.
3. Electrophoresis separates charged particles in an electrical field depending on their charge and size.
4. Chromatography techniques separate proteins based on properties like size, charge, or binding affinity.
The document summarizes different methods for protein analysis, including qualitative and quantitative techniques. It discusses the history of protein analysis and introduces various methods such as the Biuret test, spectroscopy, chromatography, and electrophoresis. Specific techniques are described in detail, such as ion exchange chromatography, affinity chromatography, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The document concludes by discussing size exclusion chromatography and provides references on the topic of protein analysis.
The document provides information on protein purification techniques including:
1) Primary techniques involve breaking open cells, fractionating proteins based on size or charge, and salting out using ammonium sulfate.
2) Chromatography techniques separate proteins based on properties like binding interactions, charge, size, and isoelectric point using columns.
3) The final purity required depends on the application, with 95-99% purity needed for assays and over 99% for therapeutic use. Analytical techniques confirm identity and purity of the purified protein.
This document summarizes an experiment on isolating and characterizing the enzyme alkaline phosphatase (AP) from E. coli bacteria. Key steps included purifying AP using dialysis, salting-in/salting-out, and DEAE cellulose chromatography. SDS-PAGE was used to analyze purity and molecular weight. Kinetic experiments at varying pH levels used the substrate PNPP and spectrophotometry to generate Michaelis-Menten and Lineweaver-Burk plots, allowing determination of kinetic parameters like Vmax and Km. The goal was to understand AP enzymatic activity and affinity for substrate under different conditions.
1) Molecular simulations were used to analyze the mode of inhibition of three pesticides (baygon, metacrate, and velpar) on firefly luciferase. The simulations revealed that the pesticides share the same binding site in the luciferin pocket of luciferase.
2) Experiments were conducted to determine the toxicities of the three individual pesticides and 15 binary mixtures on firefly luciferase bioluminescence. Concentration addition modeling was able to predict the toxicities of the mixtures based on the molecular simulation results.
3) There was a linear relationship found between the calculated binding free energy of the mixtures from the individual pesticide components, and the median effective concentrations of the mixtures in experiments.
This research aims to synthesize heterocyclic compounds containing a 3,5-dimethylisoxazole motif to inhibit bromodomains for potential cancer treatment. Existing inhibitors use this motif along with an acetyl-lysine mimetic and additional groups to bind bromodomain pockets. The researchers synthesized analogs of UMB-32, one of their most potent compounds, to explore how changes to the fused-bicyclic scaffold affect biochemical and pharmacological properties. They developed compounds with low nanomolar potency and improved pharmacokinetics profiles.
This document describes a new method called multiple products monitoring (MpM) for quantifying target peptides using liquid chromatography-mass spectrometry (LC-MS). MpM monitors multiple product ions from the MS2 spectra of target peptides, rather than selecting a single product ion as in selected/multiple reaction monitoring. It uses a scoring system based on the intensities of matching product ions between the target and reference MS2 spectra. The authors demonstrate that MpM improves sensitivity and selectivity for peptide quantification compared to conventional approaches.
Protein purification chp-5-bioc-361-version-oct-2012Jody Haddow
very simple view of protein purification which is a small component of the course here (chem 361). Mostly from Campbell 6th ed. with a small bit added on 2D gels.
Online: the rise and rise. How Web 2.0 is changing construction PR and marketingpwcom.co.uk Ltd
Slides used at Be2camp Brum (12 August 2009). Opening presentation gave an overview of the range of social media tools available for use in corporate PR and marketing (not solely for construction organisations - but that was the main focus of the event)
The document presents a business plan for "Udyog Farming Agency", an agricultural services agency that aims to provide farmers in Uttar Pradesh, India with equipment, seeds, fertilizers, and consultancy services to improve productivity and incomes. It outlines the company mission and objectives, market analysis, products and services, operational costs, financial projections, and strategies for promotion. The agency seeks to become the leading farming services provider in the country through the use of modern technology and services to large numbers of farmers.
Protein microarrays, ICAT, and HPLC protein purificationRaul Soto
The document discusses the Isotope-Coded Affinity Tag (ICAT) method for protein quantification and identification. ICAT uses chemical labeling reagents that specifically label cysteine residues. There are 4 main steps: 1) Lyse and label protein samples from two states with light and heavy ICAT tags, 2) Mix and proteolyze samples to generate peptide fragments, some tagged, 3) Isolate tagged fragments using avidin affinity chromatography, 4) Analyze isolated peptides using mass spectrometry to identify and quantify proteins between the two states. ICAT allows accurate quantification of complex protein mixtures.
This document summarizes a study that explored using RNA nucleosides as chiral sensing agents in NMR spectroscopy. Adenosine, guanosine, uridine, and cytidine were used as chiral derivatizing agents to differentiate between chiral primary amines. A three-component protocol was adopted to form complexes between the nucleosides and amines. The chiral differentiation ability of the nucleosides was examined using the 1H NMR chemical shift differences (ΔδR,S) between diastereomers formed from R- and S-amines. Adenosine and guanosine showed large chiral differentiation due to their purine rings. The measured diastereomeric excess using adenos
1. Immunoprecipitation is a technique used to isolate a protein of interest along with any interacting proteins from a mixture. It involves using an antibody against the target protein to form an immune complex, which is then isolated using a secondary antibody or protein A/G.
2. Immunogold labeling localizes proteins in cells and tissues using antibodies tagged with gold particles and visualized with electron microscopy. It was used in one study to quantify serotonin receptor subtypes in post-mortem brain samples from suicide victims versus controls.
3. Western blotting separates proteins by gel electrophoresis then transfers them to a membrane where antibodies are used to detect specific proteins. It allows visualization and quantification of proteins.
Proteome-wide covalent ligand discovery in native biological systemsMegha Majumder
The document describes a new method for finding drug candidates that bind to specific proteins called isoTOP-ABPP. It involves applying small molecule fragments that covalently bind to cysteine amino acids on proteins. This allows researchers to detect which proteins the fragments bind to. They tested a library of these fragments on cancer cell proteins and found they bound to over 750 cysteines on more than 600 proteins, including some previously considered undruggable. Further experiments showed some fragments could selectively target and inhibit certain proteins like IDH1/2 and label inactive pro-forms of proteins like caspase-8, but not the active forms.
Antibacterial Activity of Schiff Bases Derived from OrthoDiaminocyclohexane, ...inventionjournals
Schiff bases (SBs) are known to possess many biological activities. In this paper we will be interested in nine SBs derived from ortho-diaminocyclohexane, meta-phenylenediamine, 1,6-diaminohexane and benzaldehydes variously substituted by nitro group. We had synthesized, characterized and tested these molecules for their antibacterial properties. Herein our study focuses in particular on the determination of quantum descriptors on which observed antibacterial activity depends, in order to be able to predict biological activities in analogue molecule series. Using quantum chemistry methods at B3LYP / 6-31G (d, p) level, we determined for each molecules, theoretical antibacterial potentials that we correlated to the experimental ones. Calculation results showed that, the energy of the Highest Occupied Molecular Orbital (EHOMO), electronegativity (χ) and electronic energy (E), are the best quantum descriptors related to the antibacterial activity values of studied molecules. The correlation coefficient R 2 indicates that 92.1% of the molecular descriptors defining this model are taken into account with a standard deviation of 0.152.The model significance is reflected by Fischer coefficient F = 7.721: Correlation coefficient of cross-validation = 0.88. This model is acceptable with . The values of the pCE50theo/pCE50exp values of the validation set tend to unity
Introduction
Proteins
Function Of Protein And Their Properties
Protein Isolation And Purification
Methods Of Cell Lysis
Steps Of Protein Characterisation:
Determination Of Protein Concentration
Biuret Reaction
Lowry (Folin-Lowry) Method
UV- Spectroscopy
Assessment Of Protein Purity
SDS -Phage
Immunoblot
Surface Charge Analysis
Isoelectro Focusing
Ion Exchange Chromatography
Size, Shape And Conformation Analysis
2d-Electrophorasis
X-Ray Crytalliography
Protein Structure and Sequence Analysis
Edman Sequencing
Conclusion
References
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.
TOTAL POLYPHENOLS AND DPPH FREE RADICALS SCAVENGING ACTIVITY IN SIX LEAFY VEG...Md. Kamaruzzaman
TOTAL POLYPHENOLS AND DPPH FREE RADICALS SCAVENGING ACTIVITY IN SIX LEAFY VEGETABLES OF BANGLADESH
Harun-Ar-Rashid, Sheikh Julfikar Hossain, Sk. Amir Hossain, Md Mahfuzur Rahman, Md. Kamaruzzaman
This document provides an overview of the schedule and topics for a course on metabolic networks. The course covers various topics related to metabolism, including enzyme assays, mass spectrometry techniques, primary metabolism, glycogen metabolism, metabolic networks in humans, flux analysis, and biochemical databases. Homework discussions are scheduled every other Friday. Guest lecturers will discuss biochemical databases and tools for modeling metabolism on the last two class meetings. The course includes no class on Veteran's Day and Thanksgiving.
This document provides information on several common methods used to measure antioxidant capacity in biological samples and foods. It describes the principles, procedures, and key measurements of assays such as ORAC, DPPH, ABTS, Folin-Ciocalteu, FRAP, CAA, HPLC, UPLC, and ELISA. These assays utilize different chemical reactions and detection methods to quantify a sample's ability to inhibit oxidation initiated by free radicals.
This document discusses various chromatography techniques used to purify biomolecules, including affinity chromatography, ion exchange chromatography, size exclusion chromatography, and reversed phase chromatography. It provides details on how each technique separates molecules based on specific properties, such as biological recognition (affinity chromatography), charge (ion exchange chromatography), size (size exclusion chromatography), and hydrophobicity (reversed phase chromatography).
This document discusses various enzymatic analytical methods used for food analysis, including substrate determination, enzyme activity determination, enzyme immunoassay, and polymerase chain reaction. Specifically, it covers:
1) Substrate determination methods like end-point assays that use coupled enzyme reactions to measure food constituents.
2) Determining enzyme activity in food to evaluate quality and optimize processes by measuring reaction rates under controlled conditions.
3) Enzyme immunoassays like ELISA that use antibody-antigen reactions and enzyme-labeled antigens to detect food compounds.
4) Polymerase chain reaction (PCR) which amplifies DNA for sensitive species identification and detecting genetically modified foods. PCR allows analysis of heat-treated foods where proteins
The document discusses various techniques for protein purification and characterization, including:
1. Detergents solubilize transmembrane proteins by having affinity for hydrophobic groups and water.
2. Centrifugation separates particles of different masses or densities, with denser particles pelleted first.
3. Electrophoresis separates charged particles in an electrical field depending on their charge and size.
4. Chromatography techniques separate proteins based on properties like size, charge, or binding affinity.
The document summarizes different methods for protein analysis, including qualitative and quantitative techniques. It discusses the history of protein analysis and introduces various methods such as the Biuret test, spectroscopy, chromatography, and electrophoresis. Specific techniques are described in detail, such as ion exchange chromatography, affinity chromatography, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The document concludes by discussing size exclusion chromatography and provides references on the topic of protein analysis.
The document provides information on protein purification techniques including:
1) Primary techniques involve breaking open cells, fractionating proteins based on size or charge, and salting out using ammonium sulfate.
2) Chromatography techniques separate proteins based on properties like binding interactions, charge, size, and isoelectric point using columns.
3) The final purity required depends on the application, with 95-99% purity needed for assays and over 99% for therapeutic use. Analytical techniques confirm identity and purity of the purified protein.
This document summarizes an experiment on isolating and characterizing the enzyme alkaline phosphatase (AP) from E. coli bacteria. Key steps included purifying AP using dialysis, salting-in/salting-out, and DEAE cellulose chromatography. SDS-PAGE was used to analyze purity and molecular weight. Kinetic experiments at varying pH levels used the substrate PNPP and spectrophotometry to generate Michaelis-Menten and Lineweaver-Burk plots, allowing determination of kinetic parameters like Vmax and Km. The goal was to understand AP enzymatic activity and affinity for substrate under different conditions.
1) Molecular simulations were used to analyze the mode of inhibition of three pesticides (baygon, metacrate, and velpar) on firefly luciferase. The simulations revealed that the pesticides share the same binding site in the luciferin pocket of luciferase.
2) Experiments were conducted to determine the toxicities of the three individual pesticides and 15 binary mixtures on firefly luciferase bioluminescence. Concentration addition modeling was able to predict the toxicities of the mixtures based on the molecular simulation results.
3) There was a linear relationship found between the calculated binding free energy of the mixtures from the individual pesticide components, and the median effective concentrations of the mixtures in experiments.
This research aims to synthesize heterocyclic compounds containing a 3,5-dimethylisoxazole motif to inhibit bromodomains for potential cancer treatment. Existing inhibitors use this motif along with an acetyl-lysine mimetic and additional groups to bind bromodomain pockets. The researchers synthesized analogs of UMB-32, one of their most potent compounds, to explore how changes to the fused-bicyclic scaffold affect biochemical and pharmacological properties. They developed compounds with low nanomolar potency and improved pharmacokinetics profiles.
This document describes a new method called multiple products monitoring (MpM) for quantifying target peptides using liquid chromatography-mass spectrometry (LC-MS). MpM monitors multiple product ions from the MS2 spectra of target peptides, rather than selecting a single product ion as in selected/multiple reaction monitoring. It uses a scoring system based on the intensities of matching product ions between the target and reference MS2 spectra. The authors demonstrate that MpM improves sensitivity and selectivity for peptide quantification compared to conventional approaches.
Protein purification chp-5-bioc-361-version-oct-2012Jody Haddow
very simple view of protein purification which is a small component of the course here (chem 361). Mostly from Campbell 6th ed. with a small bit added on 2D gels.
Online: the rise and rise. How Web 2.0 is changing construction PR and marketingpwcom.co.uk Ltd
Slides used at Be2camp Brum (12 August 2009). Opening presentation gave an overview of the range of social media tools available for use in corporate PR and marketing (not solely for construction organisations - but that was the main focus of the event)
The document presents a business plan for "Udyog Farming Agency", an agricultural services agency that aims to provide farmers in Uttar Pradesh, India with equipment, seeds, fertilizers, and consultancy services to improve productivity and incomes. It outlines the company mission and objectives, market analysis, products and services, operational costs, financial projections, and strategies for promotion. The agency seeks to become the leading farming services provider in the country through the use of modern technology and services to large numbers of farmers.
11 20-09 mbsb single molecule techniques.pptmganguly123
This document contains over 100 images from various scientific sources related to topics in optics, microscopy, fluorescence, plasmonics, and single molecule techniques. The images depict experimental setups, microscopy images, diagrams, graphs, and other figures illustrating different scientific phenomena and techniques. Captions provide brief descriptions and citations for the source of each image.
This slideshow was developed by PRECE students to show the history, programs, methodology and success of PRECE. PRECE stands for the Educational Program using Cooperative Cells and works to empower individuals and communities. PRECE is located in the northeastern part of Brazil, in the state of Ceara. For more information about PRECE or to support PRECE please email Kacy Brubaker at kacyleighbrubaker@gmail.com.
Vikram Jain's curriculum vitae provides information about his education and qualifications. He is currently pursuing an MBA from PCTE-Ludhiana with a specialization in finance and has a Bachelor of Commerce degree from G.G.N Khalsa College Ludhiana. He has core competencies in financial exposure, strong academics, interpersonal skills, and hands-on experience. His objective is to make best use of his acquired knowledge and keep learning new things.
In the last 18 months, the rise of the real-time Web has created many interesting business opportunities but is this only the tip of the
iceberg? Is the real-time Web hiding a bigger, more strategic opportunity? Is the temporal Web the next big revolution after “location”? Sebastien Provencher will present his latest thoughts on
the subject.
This document summarizes a study that investigated how different salts screen charge interactions in proteins. Specifically, it examined the effects of NaCl, guanidinium chloride, and guanidinium thiocyanate on the stability of wild-type E. coli thioredoxin and a variant. The results suggest that more denaturing salts like guanidinium chloride are more efficient at screening charge interactions than NaCl. This efficiency correlates with the salts' position in the Hofmeister series and ability to accumulate on protein surfaces. An electrostatic model was used to estimate contributions of charge interactions to stability.
The document contains survey results from people who reviewed the film "A Walk Among the Tombstones" including: percentages showing there were more male than female respondents; 80% had seen the trailer beforehand; ratings were mostly in the 5-9 range indicating most thought it was good; 80% didn't see it specifically for Liam Neeson; and a majority said they would see a sequel and recommend it to others.
Analytical affinity chromatography was used to measure the binding of the inhaled anesthetic halothane to isolated proteins. Zonal elution experiments showed halothane binding to immobilized bovine serum albumin (BSA) but not to myoglobin or cytochrome C, indicating specific rather than nonspecific binding. Continuous elution experiments derived quantitative binding parameters for BSA-halothane binding, showing low affinity and multisite binding. Manipulations known to alter halothane binding to free BSA, such as low pH and denaturants, produced similar effects on immobilized BSA, demonstrating the technique can characterize ligand binding to isolated proteins.
Analysis of bioreactor parameters online and offlinevikash_94
The document discusses various online and offline methods for monitoring cell properties in bioreactors. Online methods discussed include spectrophotometry, fluorometry, and culture fluorescence intensity. Offline analytical methods discussed include measuring medium properties, analyzing cell population composition, analyzing proteins and RNA, and flow cytometry. In situ fluorometry is highlighted as the only continuous monitoring strategy that provides information on the biochemical or metabolic state of cells.
Applications of mass spectrometry.seminar.pptxAsif Shaikh
The document discusses various applications of mass spectrometry including molecular mass determination, identification of elements through isotopic ratios, isotopic abundance determination, isotopic dilution methods, distinguishing between cis and trans isomers, evaluation of heat sublimation, environmental analysis, forensic analysis, clinical research applications like drug screening and disease biomarker detection, protein identification, protein sequencing, determination of ionization potential and bond dissociation energies, and impurity detection. Mass spectrometry is widely used across many fields due to its high sensitivity and selectivity.
Exploring Proteins and Proteomes. Stryer,CHAPTER 3 pptkhair ullah
Methods in Protein Chemistry
This chapter discusses several methods used to isolate, purify, detect, degrade, analyze, and synthesize proteins. It describes techniques such as centrifugation, solubility, dialysis, gel filtration, affinity chromatography, HPLC, electrophoresis, and mass spectrometry. It also covers determining a protein's amino acid sequence through methods like Edman degradation, solid phase synthesis, chemical and enzymatic cleavage, and the use of DNA sequencing. The goal of these methods is to obtain a protein's amino acid sequence and gain functional information about proteins and proteomes.
VALIDATED LIQUID CHROMATOGRAPHY/TANDEM MASS SPECTROMETRY METHOD FOR DETERMINA...Manik Ghosh
A simple, highly sensitive and rapid LC-MS/MS method has been developed and validated for the quantification of metolazone in rat plasma using irbesartan as internal standard (IS). After simple protein precipitation extraction by acetonitrile, the analyte and IS were extracted from 50 μL plasma sample on an Agilent Poroshell 120, EC- C18 (50 mm × 4.6 mm, i.d., 2.7 μm) column using 5μL injection volume with a total run time of 2 min. Acidified methanol/water mixture was used as a mobile phase. The parent/product ion transitions for metolazone (m/z 366.1/258.9) and IS (m/z 429.2/207.0) were monitored on a triple quadrupole mass spectrometer, operating in the multiple reaction monitoring and positive ion mode. The method was found to be linear in the range of 0.05 – 200 metolazone. The method was validated with respect to selectivity, linearity, accuracy, precision, recovery and stability according to accepted regulatory guidelines. The described method was successfully applied to preclinical pharmacokinetic studies of analytes after an oral administration of metolazone (1 mg/kg) in rats.
This document summarizes a study examining the anti-proliferative effects of Arisaema intermedium lectin (AIL) on human colon cancer cells. AIL was purified from Arisaema intermedium tubers and its effects were tested on HCT-15 colon cancer cells. MTT assays showed AIL inhibited the growth of HCT-15 cells in a dose-dependent manner, with 53% inhibition at 100 μg/mL AIL. Further experiments found AIL treatment led to DNA fragmentation, changes in nucleic acid content, cell morphology changes, and decreased cell viability, indicating AIL induces apoptosis in HCT-15 cells. The results suggest AIL has anti-cancer properties and works through an apoptotic
We investigated the gas‐phase fragmentation reactions of a series of 2‐aroylbenzofuran derivatives
by electrospray ionization tandem mass spectrometry (ESI‐MS/MS). The most intense fragment
ions were the acylium ions m/z 105 and [M+H–C6H6]+, which originated directly from the
precursor ion as a result of 2 competitive hydrogen rearrangements. Eliminations of CO and CO2
from [M+H–C6H6]+ were also common fragmentation processes to all the analyzed compounds.
In addition, eliminations of the radicals •Br and •Cl were diagnostic for halogen atoms at aromatic
ring A, whereas eliminations of •CH3 and CH2O were useful to identify the methoxyl group
attached to this same ring. We used thermochemical data, obtained at the B3LYP/6‐31+G(d) level
of theory, to rationalize the fragmentation pathways and to elucidate the formation of E, which
involved simultaneous elimination of 2 CO molecules from B.
A visual chip-based coimmunoprecipitation technique for analysis of protein–p...Qing Chen
This document describes a visual chip-based coimmunoprecipitation (vChip-coIP) technique for analyzing protein-protein interactions. Key points:
1. The technique combines advantages of antibody microarrays, traditional coIP, and silver enhancement detection. Antibodies are spotted onto slides to capture interacting protein pairs from cell lysates.
2. Interactions are detected using a biotinylated antibody, colloidal gold-labeled streptavidin, and silver enhancement. This makes interaction signals visible without further processing.
3. The technique is shown to be simple, cost-effective, and efficient for comprehensive study of protein-protein interactions using small amounts of crude cell lysate.
The document discusses protein quantification methods. Spectroscopic methods like UV-Vis spectroscopy are commonly used to quantify protein concentrations. Classical assays include Biuret, Bradford, and Lowry tests. The Biuret test quantifies total protein content and is the focus. An experiment is described that uses the Biuret test to determine the protein concentration of an unknown food sample, finding it to be approximately 44 μg/ml.
Histochemical methods identify chemicals in cells and tissues through staining reactions. Proteins can be separated based on properties like charge, size, and binding affinity through techniques like gel electrophoresis, centrifugation, and chromatography. Mass spectrometry identifies proteins by measuring peptide masses after digestion. Assays then detect and quantify isolated proteins through methods such as staining, autoradiography, antibodies, and crystallography.
This study investigated the binding targets of the inhaled anesthetic halothane in rat brain. The researchers used quantitative photoaffinity labeling and electrophoresis to analyze rat cerebellar homogenates exposed to [14C]halothane. They found that halothane incorporated into many soluble and membrane-bound proteins, with stoichiometry values ranging from 0 to 4 and apparent IC50 values from 0.2 to 2.0 mM. Competition experiments showed that unlabeled halothane, chloroform, and isoflurane inhibited halothane labeling to varying degrees, while a non-anesthetic compound inhibited the least. These results suggest that halothane binding motifs can be found in a wide variety of proteins in the brain
Voss et al. - 2006 - Identification and characterization of riproximin,Cristina Voss
1. Researchers purified and characterized a new type II ribosome-inactivating protein called riproximin from the plant Ximenia americana.
2. Riproximin was found to potently inhibit protein synthesis and cancer cell growth in vitro with picomolar IC50 values, and inhibit tumor growth in vivo after intraperitoneal or oral administration in a rat model.
3. The researchers identified the riproximin protein through mass spectrometry and cDNA sequencing. Molecular modeling showed riproximin has structural similarity to other toxic type II ribosome-inactivating proteins and an active site for its RNA N-glycosidase activity.
This document describes new methods for using size-exclusion chromatography coupled with light scattering, refractive index, and UV detection to determine the degree of polymer conjugation to proteins and protein association states. It presents techniques to determine the degree of polyethylene glycol conjugation to RNase A and BDNF, and the association states of these molecules, without requiring calibration curves. The methods are also applied to determining the degree of erythropoietin glycosylation.
Siavosh Naji-Talakar
[email protected]
TITLE: Enzyme Kinetics
INTRODUCTION
Alkaline phosphatases are enzymes that are typically membrane-bound glycoproteins that catalyze the hydrolytic cleavage of monoesters at basic pH levels2. This enzyme is found in most advanced level eukaryotes and prokaryotes. When the hydrolysis of the monophosphate ester takes place at the basic pH levels an inorganic phosphate is released2. The enzyme can remove phosphate groups from several different types of molecules such as alkaloids, proteins, or nucleotides. In humans’ alkaline phosphatases play critical roles in the growth and development of teeth and bones, however, it can be found it other parts of the body such as in the liver and kidneys3. The phosphatases are essential for mineralization in humans to allow calcium and phosphorus to be deposited in bones and teeth3. The enzyme was reacted with 4-nitrophenyl phosphate as the substrate1. 4-nitrophenyl phosphate does not resemble a protein and is a non-specific substrate commonly used to assay alkaline phosphatases4. When the alkaline phosphatase performs hydrolysis on 4-nitrophenyl phosphate a highly colored phosphate free product is given1,4. This reaction releases the phosphate group on 4-nitrophenyl phosphate to give the product 4-nitrophenolate which has a molar absorptivity at 405nm under basic conditions with an extinction co-efficient of 18.8x103 M-1cm-1 1,4.
To experiment the effects of inhibition on the enzyme the inhibitor phenylalanine at 75mM and Na2HPO4 at 15mM was also used. Inhibition of enzymes may be carried out via irreversible pathways that work through covalent bonds or through reversible pathways. Reversible pathways include a competitive inhibition where the inhibitor binds to the active site of the enzyme or through a noncompetitive pathway where the enzyme binds to a side other than the active site, which may subsequently change the shape or conformation of the active site6. When a phosphate group PO43- is removed by hydrolysis from an organic compound it is referred to as dephosphorylation. This is the reaction in which the phosphatases operate. The reaction is important in a physiological setting because it enables the activation or deactivation of enzymes by removal of phosphoric esters; a prime example is the conversation of adenosine triphosphate to adenosine diphosphate through phosphorylation7.
The Michaelis-Menten kinetics model is used in biochemistry as a model for enzyme kinetics. The model uses an equation to explain the rate of the enzymatic reactions that occur . It does this by relating the reaction rate, Velocity or Vmax, to the substrate concentration, [S]. Vmax describes the constant values for each enzyme-substrate complex with the theoretical maximum velocity of the enzyme to turn over products at maximum saturation of the substrate concentration6. The Km value, known as the Michaelis constant, is the dissociation constant of the enzyme-substrate complex and.
The document discusses methods for preparing tissue or cell extracts for protein separation and analysis. It describes various cell lysis buffers and their uses depending on the protein location. It also discusses steps to inhibit protein degradation during extraction, such as using protease inhibitors and reducing agents. The document compares the Lowry and Bradford methods for estimating protein concentration, noting the principles, advantages, and disadvantages of each. It also discusses the importance of trichloroacetic acid precipitation to separate proteins from interfering substances.
Evaluation of Metabolic Stability of Kinsenoside, an Antidiabetic Candidate, ...Cây thuốc Việt
This study evaluated the metabolic stability of kinsenoside, a potential antidiabetic drug candidate, in rat and human liver microsomes. Kinsenoside was found to be stable in buffer and showed little non-enzymatic degradation over 8 hours. When incubated with liver microsomes, 74-78% of kinsenoside remained after 2 hours, indicating good metabolic stability. These results suggest kinsenoside would exert its pharmacological effects as the parent compound rather than as metabolites, and provide useful information for further pharmacokinetic studies.
Evaluation of metabolic stability of kinsenoside, an antidiabetic candidate,Cây thuốc Việt
Kinsenoside is a principle bioactive compound of Anoectochilus formosanus. It exhibits various pharmacological
effects such as antihyperglycemic, antioxidant, anti-inflammatory, immunostimulating, and hepatoprotective activities and has recently been developed as an antidiabetic drug candidate. In this study, as part of an in vitro pharmacokinetic study, the stability of kinsenoside in rat and human liver microsomes was evaluated. Kinsenoside was found to have good metabolic stability in both rat and human liver microsomes. These results will provide useful information for further in vivo pharmacokinetic and metabolism studies.
This study aims to investigate how the charge distribution on protein surfaces affects protein-polymer interactions. The researchers will:
1. Express GFP proteins with varying charge distributions through site-directed mutagenesis.
2. Synthesize model polymers using RAFT polymerization and conjugate them to the GFP proteins.
3. Use techniques like turbidity measurements and DLS to analyze how the proteins interact with cationic, anionic, and neutral polymers depending on the proteins' charge distributions.
Preliminary results showed the proteins were successfully expressed and conjugated to polymers while maintaining structure. Turbidity data also indicated how charge affects protein aggregation with polyelectrolytes. Overall, this work could help understand how
1) Polymeric excipients like PEG can stabilize proteins against denaturation during freezing by increasing the transfer free energy of the protein. However, these same polymers can induce phase separation in aqueous solutions.
2) During lyophilization, the concentrating effects of freezing can cause formulations to enter the two-phase region, resulting in liquid/liquid phase separation. This subjects the protein to potential partitioning between phases with different compositions.
3) Experimental studies on hemoglobin lyophilized in PEG/dextran mixtures provide evidence that phase separation during lyophilization can damage protein structure in the dried state.
This document is the user manual for the VP-DSC MicroCalorimeter. It provides specifications for the instrument, safety information, and instructions for operation. Key details include:
- The VP-DSC allows for high sensitivity measurement of heat capacity, binding thermodynamics, and kinetics.
- Safety precautions must be followed when using hazardous or volatile solutions in the tantalum cells.
- VPViewer software interfaces with Origin for instrument control and real-time data display.
- Sections provide tutorials for common experiments, calibration procedures, troubleshooting tips, and maintenance instructions.
1. The study characterized the aggregation of recombinant human Interleukin-1 receptor type II (rhuIL-1RII) using differential scanning calorimetry (DSC) and size exclusion chromatography (SEC).
2. A scan-rate dependence in the DSC experiment and a break from linearity in initial aggregation rates near the melting temperature (Tm) suggested that protein unfolding significantly contributes to the aggregation reaction pathway.
3. A mechanistic model was developed to extract meaningful thermodynamic and kinetic parameters from the irreversibly denatured aggregation process by simulating how unfolding properties could predict aggregation rates at different temperatures above and below the Tm.
This document reviews lyophilization (freeze-drying) as a method for developing solid protein pharmaceuticals. Lyophilization generates stresses that can denature proteins, including low temperature stress, freezing stresses from increased concentration and ice formation, and drying stress from removing the hydration shell. Several studies are discussed that demonstrate denaturation of specific proteins from these stresses during lyophilization and storage. The review discusses excipient protection of proteins, lyophilization cycle design, and formulation strategies to increase stability of solid protein pharmaceuticals and overcome instability issues.
This document summarizes the calculation of translational friction and intrinsic viscosity for four globular proteins (ribonuclease A, lysozyme, myoglobin, and chymotrypsinogen A) using their detailed atomic structures. The inclusion of a 0.9 Angstrom thick hydration shell around each protein allows the calculated translational friction and intrinsic viscosity to match experimental measurements. This hydration shell thickness corresponds to a hydration level of 0.3-0.4 grams of water per gram of protein, consistent with measurements from other techniques. Using detailed protein structures thus allows hydrodynamic measurements to support a unified picture of protein hydration, in contrast to earlier models that treated proteins as ellipsoids and found widely varying hydr
Proton euilibria in minor groove of dnamganguly123
1) The document describes an experiment testing the prediction that regions of increased hydrogen ion density exist in the grooves of DNA. Probes with variable linker lengths and a proton-sensitive carboxyl group were attached to DNA in the minor groove.
2) The apparent pKa values of the carboxyl groups were higher than in free solution, increasing with shorter linker lengths. This agrees with calculations showing higher hydrogen ion density in the grooves.
3) The experiment provides experimental evidence supporting the theoretical prediction of acidic domains with elevated hydrogen ion density in the DNA minor groove.
This document summarizes a study that investigated the effects of two disaccharides (trehalose and sucrose) and trimethylamine N-oxide (TMAO) on amyloid-beta (Aβ) aggregation and interaction with lipid membranes. The key findings were:
1) In the absence of lipid vesicles, trehalose and sucrose delayed Aβ aggregation as measured by Thioflavin T fluorescence, but TMAO did not affect aggregation.
2) In the presence of lipid vesicles, all three osmolytes (trehalose, sucrose, TMAO) significantly attenuated dye leakage from the vesicles induced by Aβ aggregates.
3) Hydrogen exchange mass spectrometry (HX-MS) and
1) The study examines how long- and short-range electrostatic interactions affect the rheology and protein-protein interactions (PPI) of highly concentrated monoclonal antibody (mAb) solutions.
2) At high concentrations, both long- and short-range interactions contribute significantly to PPI, whereas at low concentrations only long-range interactions are important.
3) The study uses high frequency rheology, dynamic light scattering, circular dichroism, and zeta potential measurements to characterize PPI over a range of pH and ionic strengths, and develops a 3D computer model of the mAb to study charge distribution.
This chapter reviews the oxidation of methionine residues in model peptides. It discusses how neighboring amino acids can influence the oxidation pattern of methionine. For example, when a hydroxyl radical attacks Thr-Met, the neighboring threonine residue is cleaved. It also notes that the oxidation of peptides and proteins is a complex process that depends on the nature of the oxidizing species and the peptide/protein sequence and structure. Oxidation can lead to chain reactions as oxidation products themselves can initiate further oxidation remote from the initial attack site.
The document discusses several phase diagrams generated using different experimental data visualization techniques including:
1) A phase diagram of ricin toxin A-chain created using fluorescence and circular dichroism spectroscopic data showing four protein states.
2) An empirical phase diagram of the respiratory syncytial virus determined from multiple biophysical measurements across a pH range.
3) Phase diagrams of various non-viral gene delivery vehicles and proteins mapped against pH and temperature.
Basic fibroblast growth factor (bFGF) is being investigated for its ability to accelerate wound healing. Sulfated compounds like heparin enhance the stability of bFGF against thermal denaturation. To assess the effect on bFGF shelf life, formulations containing these excipients were incubated and analyzed. In the presence of sulfated compounds, precipitates formed that dissociated back to multimers with native structure, whereas without them precipitates were unfolded protein. Disulfide-linked multimers also increased in solution with sulfated compounds. Heparin stabilized bFGF structure and prevented rearrangement of disulfide bonds, indirectly promoting multimerization. However, loss of soluble bFGF monomer still
This document summarizes the use of differential scanning calorimetry (DSC) to optimize an antibody manufacturing process. DSC was used to screen conditions for a viral inactivation step and identify increased pH storage conditions for maximum stability. Low pH treatment reduced thermal stability, indicating structure loss. DSC provided insights into instability causes and process improvements, demonstrating its role in biotherapeutic development.
This document describes a study on controlled intracranial delivery of antibodies in rats. The researchers developed polymer matrices and microspheres for long-term antibody release directly in the brain. They implanted polymer discs containing IgG antibodies in rat brains and measured IgG concentrations at the implantation site and other brain regions over 28 days, finding highest levels with the polymer implants. The polymer provided sustained antibody levels beyond what was achieved with direct injection.
This document summarizes a study that measured the enthalpy change (ΔH) associated with the α-helix to random coil transition of an alanine peptide in water using calorimetry. The researchers synthesized a 50-residue peptide containing primarily alanine residues and determined its ΔH to be between 0.9-1.3 kcal/mol per residue, providing a basic parameter for predicting thermal unfolding of peptide helices. Circular dichroism spectra and melting curves confirmed the peptide adopted an α-helical structure at low temperatures and underwent a reversible helix-coil transition. The ΔH value suggests the peptide backbone, rather than side chains, makes the dominant contribution to helix stability.
1) Aspartame degradation kinetics depend on factors like pH, temperature, buffer type and concentration, and water activity. Higher temperatures, pH, buffer concentrations and water activities increase degradation rates.
2) The activation energies for aspartame degradation decrease with increasing pH or moisture content. Phosphate buffer significantly enhances degradation more than citrate buffer.
3) In solid systems, degradation rates increase with higher initial buffer concentrations and water activities. However, the glass transition temperature does not influence degradation rates as much as water activity.
This chapter discusses the application of light scattering techniques to analyze the solution behavior of protein pharmaceuticals. It provides examples of using light scattering to characterize proteins and protein complexes, detect soluble aggregate formation, and elucidate protein-ligand interactions. The chapter also describes the theoretical background and instrumentation for light scattering measurements and analysis. It presents applications of light scattering including analyzing self-associating protein systems, selecting optimal solvent conditions, and studying the kinetics of molecular interactions.
Ion water interaction biophysical journalmganguly123
The document discusses how the charge density of ions affects their strength of hydration and interactions in biological structures. It finds that small, highly charged ions (kosmotropes) strongly bind water molecules, while large monovalent ions of low charge density (chaotropes) weakly bind water. Crystalline salts dissolve exothermically only when one ion is a kosmotrope and the other is a chaotrope. This suggests kosmotropes and chaotropes preferentially form ion pairs in solution. The major intracellular ions—phosphate and carboxylate anions and potassium/arginine cations—behave as kosmotropes and chaotropes, respectively, allowing them
This document presents a study using differential scanning calorimetry (DSC) to examine the thermal stability of S-protein and its complexes with S-peptide at pH 7.0. DSC measurements showed that S-protein denatures through a reversible two-state transition with a denaturation temperature between 38.5-40.0°C and enthalpy of 165-180 kJ/mol, demonstrating its lower stability without S-peptide. A two-dimensional nonlinear regression analysis of excess heat capacity curves at varying temperatures and S-peptide concentrations was used to determine the binding thermodynamic parameters, yielding values of Kb = 1.10 × 106 M-1, ΔbH = -185 kJ
The document summarizes the origin of photosensitivity in a monoclonal immunoglobulin G (IgG). UV irradiation of the monoclonal IgG causes a 70% decrease in intrinsic fluorescence and the appearance of new fluorescence, suggesting photooxidation of one or two tryptophan residues. This leads to extensive quenching of the protein's fluorescence through nonradiative energy transfer, even though few residues are directly oxidized. The photooxidation products, N-formylkynurenine and kynurenine, absorb light above 300 nm and contribute to changes in the UV-visible absorption spectrum with irradiation.
This study examines the effect of the antimicrobial peptide gramicidin S (GS) on the thermotropic phase behavior of lipid bilayer membranes composed of dimyristoylphosphatidylcholine (DMPC), dimyristoylphosphatidylethanolamine (DMPE), and dimyristoylphosphatidylglycerol (DMPG) using differential scanning calorimetry. The results show that GS interacts more strongly with anionic DMPG bilayers than with zwitterionic DMPC or DMPE bilayers, reducing the temperature and cooperativity of DMPG's phase transition to a greater degree. In contrast, GS has little effect on DMP
1. 1992 Biophysical Journal Volume 96 March 2009 1992–1998
Static Light Scattering From Concentrated Protein Solutions II:
Experimental Test of Theory for Protein Mixtures and Weakly
Self-Associating Proteins
´
Cristina Fernandez and Allen P. Minton*
Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S.
Department of Health and Human Services, Bethesda Maryland
´
ABSTRACT Using an experimental technique recently developed in this laboratory (Fernandez C. and A. P. Minton. 2008.
Anal. Biochem. 381:254–257), the Rayleigh light scattering of solutions of bovine serum albumin, hen egg white ovalbumin,
hen egg white ovomucoid, and binary mixtures of these three proteins was measured as a function of concentration at concen-
trations up to 125 g/L. The measured concentration dependence of scattering of both pure proteins and binary mixtures is
accounted for nearly quantitatively by an effective hard particle model (Minton A. P. 2007. Biophys. J. 93:1321–1328) in which
each protein species is represented by an equivalent hard sphere, the size of which is determined by the nature of repulsive
interactions between like molecules under a given set of experimental conditions. The light scattering of solutions of chymo-
trypsin A was measured as a function of concentration at concentrations up to 70 g/L at pH 4.1, 5.4, and 7.2. At each pH, the
measured concentration dependence is accounted for quantitatively by an effective hard particle model, according to which
monomeric protein may self-associate to form an equilibrium dimer and, depending upon pH, an equilibrium pentamer or
hexamer.
INTRODUCTION
Interest in the physical properties of highly concentrated rium associations. The effective hard particle model has
protein solutions has increased significantly in recent years, been shown to account quantitatively for the concentration
as it has become more widely recognized that an under- dependence of thermodynamically-based solution properties
standing of those properties is prerequisite to an understanding (e.g. sedimentation equilibrium, osmotic pressure, and static
of chemical equilibria and rate processes in biological fluids light scattering) of individual proteins over a broad range of
(1,2) and in biopharmaceutical formulations (3). Weakly concentrations (6–11).
attractive and repulsive interactions between protein mole- Concurrently, we have also developed an efficient exper-
cules that are undetectable at the low protein concentrations imental method for measuring the concentration dependence
ordinarily encountered in a biophysical experiment (typ- of the static light scattering of protein solutions over a broad
ically <5 g/L) exert an ever-greater influence upon solution range of concentrations(12). In this study, we employed the
properties as protein concentrations approach the saturation newly developed experimental methodology to measure the
limit, which, depending upon experimental conditions, may concentration dependence of light scattering of three glob-
be as large as several hundred g/L. With few exceptions, ular proteins (bovine serum albumin, hen egg ovalbumin,
one cannot reliably predict the behavior of a protein at a and hen egg ovomucoid) and mixtures of these proteins,
high concentration on the basis of knowledge obtained from and compared the observed results with predictions of the
experiments carried out at low concentrations. Quantitative approximate theory. We additionally measured the concen-
characterization of the concentration-dependent behavior of tration and pH dependence of light scattering of a protein,
protein solutions in the high concentration regime (>50 g/L), chymotrypsin A, that is known to self-associate with an
therefore, presents both experimental and theoretical chal- affinity that changes with pH (13–15), and interpreted the
lenges to the investigator. results in the context of models for self-association and
We have recently presented an approximate theory for the nonspecific repulsive interaction.
interpretation of the light scattering of multiple species of
proteins at arbitrary concentrations (5), in which each species
is treated as an effective hard convex particle, the size of MATERIALS AND METHODS
which reflects not only steric repulsion but also short-ranged Materials
‘‘soft’’ electrostatic repulsion between macromolecules.
Monomeric bovine serum albumin (BSA) was obtained from Sigma-Aldrich
Attractive intermolecular interactions are treated as equilib- (St. Louis, MO) (A1900). Albumin (chicken egg white), ovomucoid (Trypsin
inhibitor) and inactivated chymotrypsin A were obtained from Worthington
Biochemical Corporation (Lakewood, NJ) (LS003048, LS003087, and
Submitted August 28, 2008, and accepted for publication November 25,
LS001434, respectively). All proteins elute from a size exclusion chromatog-
2008.
raphy column with an on line light scattering detector as a single peak corre-
*Correspondence: minton@helix.nih.gov sponding to the monomer, except for BSA, which shows a small additional
Editor: Kathleen B. Hall.
Ó 2009 by the biophysical society
0006-3495/09/03/1992/7 $2.00 doi: 10.1016/j.bpj.2008.11.054
2. Concentrated Protein Light Scattering 1993
peak (<3% of total protein) corresponding to the covalent dimer. Before use, where Mi denotes the molar mass of the ith scattering species and <Dci Dcj>
BSA, ovalbumin and ovomucoid were dialyzed against phosphate buffer, denotes the mean product of the fluctuations of the molar concentrations of
0.05 M phosphate, 0.15 M NaCl at pH 7.2. Chymotrypsin A was dialyzed the ith and the jth scattering species about their respective equilibrium
against phosphate buffer, 0.05 M phosphate, 0.20 M NaCl at pH 5.4 and values, henceforth referred to as the average cofluctuation of the two species.
pH 7.2, and citric acid 0.05 M, 0.20 M NaCl at pH 4.1. Dialysis for buffer It has been pointed out that in principle, salt-protein interactions can under
exchange was performed against excess solvent overnight using Pierce certain conditions contribute significantly to the dependence of solution light
10000 MWCO Slide-A-Lyzer Dialysis cassettes. To prepare concentrated scattering on protein concentration (22,23). However, in solutions of
protein solutions, proteins were dissolved at low concentrations (<30 g/L), moderate ionic strength where approximations underlying the effective
dialyzed, and then concentrated using Centricon filter devices (Ultracel hard particle model are expected to be realistic (24), we assume that the
YM-10 membrane – 10,000 NMWL; Millipore, Billerica, MA) to different influence of salt-protein interactions is taken into account implicitly as
final concentrations. Final concentrations were determined from the absor- a factor affecting protein-protein interactions, and thus the size of the effec-
bance at 280 nm using the following standard values for absorbance in optical tive hard particle best representing a particular protein species. Accordingly,
density units per centimeter pathlength for 1 g/L solution: BSA, 0.65 (16); the summation indicated in Eq. 3 is carried out only over protein species.
ovalbumin, 0.75 (16); ovomucoid, 0.41 (17); and chymotrypsin A, 2.04 Justification for this simplification is presented below.
(13). The buffer and protein were prefiltered through 0.02-mm Whatman Expressions for average self- and hetero-cofluctuations in mixtures of up
Anotop filters (Whatman, Florham Park, NJ). Immediately before measure- to three scattering species are presented by Minton (5) as functions of the
ments of light scattering were taken, protein solutions were centrifuged at molar concentrations of each species, ci, and partial derivatives of the loga-
80000 g for 30 min to remove residual particulates and microscopic bubbles. rithm of the thermodynamic activity coefficient of each species with respect
to the concentrations of all species, v ln gi/vcj. The derivatives are evaluated
Experimental Procedures as a function of the concentrations of all protein species using the scaled
particle theory of hard convex particle mixtures (25,26) as described in Min-
Measurements were carried out via automated sequential dilution as ton (5).
described in Fernandez and Minton (12). Briefly, a MiniDAWN Tristar light
´ In the model presented previously (5), attractive interactions are treated as
scattering detector (Wyatt Technology, Santa Barbara, CA) was modified by association equilibria. Whereas such treatment may be formally derived
the addition of a Variomag Mini cuvette stirrer (Variomag-USA, Daytona from any attractive potential (27), it is most realistic and useful when the
Beach, FL) mounted in the base of the MiniDawn read head, and the light range of attractive interactions is short relative to the size of the interacting
scattering flow cell was replaced by a square cuvette holder. A square fluo- molecules (24). According to this picture, an oligomeric species is defined or
rescence cuvette containing 2 ml of protein solution and a small magnetic designated on the basis of stoichiometry and propinquity, and does not
stirring bar was inserted into the cuvette holder. The gradient of protein necessarily possess a well-defined structure. It follows that oligomeric
concentration was created by successive dilutions of the initially concen- species whose presence is deduced from analysis of data within the context
trated solution using a programmable dual-syringe pump to add buffer and of this model, particularly those characterized by very low equilibrium
remove solution. Although the light scattering apparatus used lacked means
for controlling the temperature of the sample, sample temperature was moni-
tored continuously and found to remain constant to within 2 C over the
approximately one hour time course of a dilution experiment. Depending
upon the ambient temperature in the laboratory during a particular experi-
ment (which varied with the season), average sample temperatures measured
during a dilution experiment varied between 26 C and 31 C. However,
replicate experiments conducted at different times showed no significant
dependence of the measured scattering intensity upon temperature within
this limited range of temperatures.
As previously described (18), the baseline-subtracted intensity of light
scattered at 90 was converted to the Rayleigh ratio expressed in units of
the optical constant K, defined by
2
4p~2 ðd~=dwÞ
n n
K ¼ ; (1)
l4 NA
0
where n denotes the refractive index of solution, lo is the wavelength of inci-
˜
dent light in vacuum (690 nm), and NA is Avogadro’s number. The refractive
increment dn/dw is equal to 0.185 cm3/g for all proteins studied here (19). It
˜
follows that the refractive index of a solution containing multiple species of
protein may be expressed as
À Á
~ ¼ ~0 þ d~=dw wtot ;
n n n (2) FIGURE 1 Dependence of normalized scattering intensity upon total
molar concentration of BSA, ovalbumin, and binary mixtures. Experimental
where no denotes the refractive index of solvent (phosphate buffered
˜ data: circles, squares, triangles, pentagrams and diamonds are results from
saline, 1.335) and wtot denotes the total weight/volume concentration of protein. solutions containing BSA mole fraction 1 (pure BSA), 0.8, 0.5, 0.2, and 0
(pure ovalbumin), respectively. Solid curves for the pure proteins were
Analysis calculated using the effective hard sphere model for a single species with
best-fit parameter values given in Table 1. Dashed curves for the mixtures
According to the fluctuation theory of light scattering, the static light scat-
were calculated using the effective hard sphere model for two species and
tering of a solution of multiple solutes is given by (20,21)
mole fractions constrained to the values given above. Solid curves for the
R X mixtures were calculated using the effective hard sphere model for two
¼ Mi Mj Dci Dcj ; (3) species with adjustable mole fraction of BSA using the following best fit
K i; j
values: 0.84, 0.55, and 0.24 respectively.
Biophysical Journal 96(5) 1992–1998
3. 1994 ´
Fernandez and Minton
FIGURE 3 Dependence of normalized scattering intensity upon total
FIGURE 2 Dependence of normalized scattering intensity upon total molar concentration of ovalbumin, ovomucoid, and an equimolar mixture.
molar concentration of BSA, ovomucoid, and an equimolar mixture. Exper- Experimental data: circles, squares, and triangles are results from solutions
imental data: circles, squares, and triangles, are results from solutions containing ovalbumin mole fraction 1, 0.5, and 0, respectively. Solid curves
containing BSA mole fraction 1, 0.5, and 0, respectively. Solid curves for for the pure proteins were calculated as described above. The dashed curve
the pure proteins were calculated as described above. Dashed curve for for the equimolar mixture was calculated using the effective hard sphere
the equimolar mixture was calculated using the effective hard sphere model model for two species and ovalbumin mole fraction constrained to 0.5.
for two species and BSA mole fraction constrained to 0.5. The solid curve The solid curve for the equimolar mixture was calculated using the effective
for the equimolar mixture was calculated using the effective hard sphere hard sphere model for two species with adjustable mole fraction of oval-
model for two species with adjustable mole fraction of BSA using a best bumin using a best fit value of 0.55.
fit value of 0.58.
association constants, may include weakly associated clusters arising from
specific volumes of the particles representing each protein
nonspecific attractions in addition to well-structured oligomers resulting vary slightly from those reported earlier due to correction
from specific interactions (28). of a minor error in the calculation of normalized scattering
Within the context of the effective hard particle model, the dependence of intensity).
Rayleigh scattering intensity upon the composition of a solution containing The effective specific volume of BSA, 1.77 cm3/g, is in
multiple macromolecular scattering species is thus specified by the
following parameters: the size or specific volume and shape of the equivalent
semiquantitative agreement with values obtained from prior
hard particle representing each scattering species, and, if necessary, one or measurements of light scattering, osmotic pressure and sedi-
more association constants governing equilibrium relations between the mentation equilibrium conducted under similar conditions of
concentrations of monomeric and oligomeric scattering species as functions pH and ionic strength (summarized in (6)).
of the total specified concentration of each component. The method of Given the best-fit values of molar mass and specific
numerical calculation of scattering is described in Minton (5).
volume corresponding to each protein, Eqs.1–8 and 25–27
of (5) were used to compute the concentration dependence
RESULTS AND DISCUSSION of scattering for binary nonassociating mixtures of the
proteins containing specified mole fractions of each species.
Nonassociating proteins and protein mixtures The results are plotted as dashed curves in Figs. 1–3. Finally,
The normalized scattering intensity of pure BSA, ovalbumin, the mole fraction of each species in a mixture was allowed to
and ovomucoid and binary mixtures of each pair of proteins vary to achieve a best-fit of the model to the experimental
is plotted as a function of total molar concentration in Figs. data. The best-fit value of mole fraction corresponding to
1–3 The results presented for each preparation represent all each mixture is presented in the corresponding figure legend.
of the data obtained from two to five replicate experiments, It is evident upon inspection that without any adjustment the
thus providing a measure of experimental precision.
The concentration dependence of scattering intensity of TABLE 1 Best-fit values of effective hard-sphere parameters
characterizing globular proteins at high concentration
each individual globular protein was presented recently
(12) as a validation of the utility of the experimental method Protein MW veff (cm3/g)
used in this study. As reported earlier, all three data sets may BSA 68700 Æ 1600 1.77 Æ 0.06
be well-described by a non-self-associating equivalent hard ovalbumin 45500 Æ 1000 1.64 Æ 0.05
sphere model, with best-fit molecular weights and specific ovomucoid 28000 Æ 820 1.61 Æ 0.07
volumes presented in Table 1. (The best-fit values of the Indicated uncertainties correspond to 1 standard error of estimate.
Biophysical Journal 96(5) 1992–1998
4. Concentrated Protein Light Scattering 1995
A B C FIGURE 4 Concentration dependence of normalized
scattering intensity of chymotrypsin A solutions at pH
4.1 (A), pH 5.4 (B), and pH 7.2 (C). Circles: Experimental
data; thick solid curve: best fit of the three species effective
hard sphere model with allowance for formation of equilib-
rium dimer and one higher oligomer, using the best-fit
parameter values indicated in Table 2. Best fit curves calcu-
lated from the monomer-dimer-pentamer and monomer-
dimer-hexamer models at pH 5.4 are indistinguishable.
Also plotted in each panel are reference curves calculated
according to the one-species effective hard sphere model
for hypothetical nonassociating monomer (thin solid line),
dimer (dashed), pentamer (dotted) and hexamer (dot-
dashed).
effective hard particle model provides a nearly quantitative tering over the entire range of concentrations to within exper-
description of the concentration-dependent scattering of imental precision. Models incorporating monomer, equilib-
these three mixtures up to total protein concentrations of rium dimer, and one equilibrium higher-order oligomer of
100 g/L. The agreement between model prediction and varying stoichiometry were then tried. It was found that to
data is improved even further by allowing the designated fit the experimental data to within experimental precision
mole fraction of proteins in each mixture to vary by a few over the entire range of concentrations, it was necessary to
percent from the nominal value, which is probably within postulate at least three significant species: monomer, dimer
the uncertainty to which molecular weights, and hence molar and, depending upon pH, either pentamer (pH 4.1 and 5.4)
concentrations, can be determined experimentally by means or hexamer (pH 5.4 and 7.2). The dependence of scattering
of static light scattering. upon concentration calculated at each pH according to the
best-fit model or models with the best-fit parameter values
Self-associating protein (chymotrypsin A) presented in Table 2 is plotted together with the data in
Fig. 4 A–C. In addition, the concentration dependent scat-
The concentration dependence of the static light scattering of
tering calculated at each pH value for pure hard spherical
solutions of chymotrypsin A was measured at three pH
monomer, dimer, pentamer and hexamer using the appro-
values, and the data were plotted as a function of w/v concen-
priate molar mass and the best-fit value of veff are plotted
tration in Fig. 4 A–C. Since prior studies of the equilibrium
in the respective figures for comparison with the concentra-
self-association of chymotrypsin A performed at low protein
tion dependence calculated according to the best-fit equilib-
concentrations (13–15) have established that the protein
rium scheme.
could form an equilibrium dimer, the data obtained in this
study was modeled by expressions for the concentration
dependence of light scattering by a mixture of monomer,
DISCUSSION
equilibrium dimer, and possibly a third larger species in
equilibrium with the monomer in a nonideal solution. Each The effect of thermodynamic nonideality upon the light scat-
of the species is represented within the model by an effective tering intensity of interacting protein mixtures has previously
hard spherical particle having a mass corresponding to the been considered by Bajaj et al (29) and Alford et al (30).
stoichiometry of the assumed oligomer and a single specific These prior treatments are subject to the following limita-
volume common to all species. It was quickly established tions. a), only first order deviations from thermodynamic
that a two-species (monomer-dimer) model could not ideality (two-body interactions or so-called second virial
account for the observed concentration dependence of scat- coefficient effects) are taken into account. b), only two
TABLE 2 Best-fit values of model parameters assuming various association schemes
pH Self-association scheme log K2 (MÀ1) log Kn (M-nþ1) veff (cm3/g)
7.2 Monomer-dimer- hexamer (n ¼ 6) 3.45 (À0.15, þ0.15) 16.67 (À0.29, þ0.33) 0.86 (À0.10, þ0.10)
5.4 Monomer-dimer- hexamer (n ¼ 6) 3.76 (À0.17, þ0.18) 16.49 (À0.37, þ0.44) 1.58 (À0.20, þ0.18)
or 3.44 (À0.15, þ0.14) 12.36 (À0.36, þ0.24) 1.00 (À0.36, þ0.20)
Monomer-dimer-pentamer (n ¼ 5)
4.1 Monomer-dimer- pentamer (n ¼ 5) 4.47 (À0.15, þ0.17) 14.94 (À0.31, þ0.34) 1.50 (À0.18, þ0.14)
M1 was fixed at a value of 23000 on the basis of results obtained from experiments carried out at low total concentration. Indicated uncertainties correspond to 1
standard error of estimate.
Biophysical Journal 96(5) 1992–1998
5. 1996 ´
Fernandez and Minton
A B C
FIGURE 5 Fractional abundance of species plotted as
a function of the logarithm of total protein concentration
at pH 4.1 (A), 5.4 (B), and 7.2 (C), calculated as described
in Minton et al (5) using the best-fit parameter values given
in Table 2. Species abundance at pH 5.4 is calculated
according to the best-fit monomer-dimer-hexamer model
(solid curves) and the best-fit monomer-dimer-pentamer
model (dashed curves).
scattering species (monomer and equilibrium dimmer) are The finding that an equilibrium between monomer and at
treated. The formalism of the treatments is such that exten- least one oligomeric species larger than dimer must be
sion to more complex interacting systems and more highly invoked to account for the concentration dependence of light
nonideal solutions (higher total protein concentration) would scattering of chymotrypsin A at high concentration is not
be prohibitively difficult. In contrast, the thermodynamic surprising in view of earlier findings that other proteins not
model used to interpret the data presented here (5) may be generally recognized as self-associating proteins, such as
applied in a straightforward and parsimonious fashion to aldolase (28), ribonuclease A (31) and immunoglobulin
mixtures of an arbitrary number of interacting scattering G (32), may self-associate weakly at sufficiently high
species at arbitrarily high concentration. concentrations. The existence of a monomer-n-mer equilib-
The finding that the effective hard spherical particle model rium with n ¼ 6 Æ 1 in low concentration, low ionic strength
can fairly accurately predict the concentration dependence of solutions of chymotrypsin A at pH 8 has been deduced
light scattering of mixtures of noninteracting proteins at high from the concentration dependence of the weight-average
total protein concentration reinforces the recent observation sedimentation velocity (33) and the shape of trailing zonal
that the effective hard particle model provides a quantitative boundaries in analytical gel filtration (34). The study pre-
description of the concentration dependence of the osmotic sented here indicates that a significant mass fraction of
pressure of an equimolar mixture of bovine serum albumin a similar if not identical oligomeric species may exist in equi-
and ovalbumin over a range of concentration up to several librium with monomer and dimer even in solutions of
hundred g/L (7). This finding also provides support for the substantially greater ionic strength and lower pH provided
validity of the greatly simplifying approximation, introduced that the total protein concentration is sufficiently great.
above, that in solutions of moderate ionic strength, the effect According to the effective hard particle model, the extent
of salt-protein interactions upon scattering may be treated to which the effective specific volume of a protein species
implicitly as modulating protein-protein interaction instead exceeds the partial specific volume is a measure of the
of through attempting to explicitly evaluate the contribution
of salt-protein cofluctuations to the summation indicated in
Eq. 3.
The mass fraction of each significant association state of
chymotrypsin, calculated using the best-fit model(s) with
the best-fit parameter values presented in Table 2, is plotted
as a function of the logarithm of total protein concentration at
each pH value in Fig. 5 A–C Inspection of these figures
reveals that an equilibrium monomer-dimer model should
suffice to account for the concentration dependence of scat-
tering at total protein concentrations below ~10 g/L, but
would be increasingly inadequate at higher concentrations
where the equilibrium mass fraction of pentamer and/or
hexamer becomes significant. It is noteworthy that the
best-fit values of the monomer-dimer equilibrium association
constant obtained from analysis of the present data at the two
lower pH values are in good agreement with prior estimates
of the pH dependence of the monomer-dimer equilibrium
FIGURE 6 Comparison of values of the pH-dependent monomer-dimer
constant obtained from studies of chymotrypsin A at low equilibrium constant presented in Table 2 (þ symbols) with values previ-
concentration by sedimentation equilibrium (13,14) and ously reported for chymotrypsin A in the literature (all other symbols as indi-
static light scattering (15), as shown in Fig. 6 cated in the caption to Fig. 4 B of reference 15).
Biophysical Journal 96(5) 1992–1998
6. Concentrated Protein Light Scattering 1997
magnitude of soft repulsive interactions between like mole- concentrated solutions of bovine serum albumin and other nonassociat-
ing proteins. J. Pharm. Sci. 96:3466–3469.
cules, and generally increases with the net charge of the
7. Minton, A. P. 2008. Effective hard particle model for the osmotic pres-
macromolecule under a given set of conditions (11,8). Ac- sure of highly concentrated binary protein solutions. Biophys. J.
cording to the present analysis, the effective specific volume 94:L57–L59.
of chymotrypsin A increases with decreasing pH. This is 8. Minton, A. P., and H. Edelhoch. 1982. Light scattering of bovine serum
attributed to increasing net positive charge as solution pH albumin solutions: extension of the hard particle model to allow for
electrostatic repulsion. Biopolymers. 21:451–458.
decreases below 8.8, the isoelectric point of the protein (35).
9. Rivas, G., J. A. Fernandez, and A. P. Minton. 1999. Direct observation
The success of the effective hard particle model in of the self-association of dilute proteins in the presence of inert macro-
accounting for the concentration dependent light scattering molecules at high concentration via tracer sedimentation equilibrium:
of mixtures of BSA, ovalbumin, and ovomucoid indicates theory, experiment, and biological significance. Biochemistry.
38:9379–9388.
that repulsive interactions between like and unlike protein
10. Ross, P. D., R. W. Briehl, and A. P. Minton. 1978. Temperature depen-
molecules in these solutions are approximately additive. dence of nonideality in concentrated solutions of hemoglobin. Biopoly-
Note that this finding is not equivalent to the statement that mers. 17:2285–2288.
the model for scattering is additive in the scattering of indi- 11. Minton, A. P. 1995. A molecular model for the dependence of the
vidual species, which is shown by the data presented in osmotic pressure of bovine serum albumin upon concentration and
pH. Biophys. Chem. 57:65–70.
Fig. 1–3 to be clearly untrue at high total concentration.
12. Fernandez, C., and A. P. Minton. 2008. Automated measurement of the
´
In the language of this model, the distance between the static light scattering of macromolecular solutions over a broad range of
centers of effective spheres representing species i and j at concentrations. Anal. Biochem. 381:254–257.
close contact, denoted by rij, may be approximated by 13. Morimoto, K., and G. Kegeles. 1967. Dimerization and activity of
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rij z rii þ rjj =2: (4) 14. Aune, K., and S. N. Timasheff. 1971. Dimerization of alpha-
chymotrypsin I. pH dependence in the acid region. Biochemistry.
The validity of this approximation is attributed to the fact 10:1609–1617.
that all three proteins have isoelectric points between 4.4 15. Kameyama, K., and A. P. Minton. 2006. Rapid quantitative character-
and 4.8 (35,36), and thus bear net negative charges at the ization of protein interactions by composition gradient static light scat-
tering. Biophys. J. 90:2164–2169.
pH of measurement. At present it is unclear whether the
16. Kirschenbaum, D. M. 1976. Molar absorptivity and A1 cm1% values for
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