Research Interests: Neuroscience, Biology, Neurotransmission, Enzyme Inhibitors, Biological Chemistry, and 15 moreMedicine, Biological Sciences, Hippocampus, Humans, Mice, Animals, Biological, Dendrites, Synaptic Transmission, Neurons, CHEMICAL SCIENCES, Synaptophysin, Hippocampal formation, Excitatory Postsynaptic Potentials, and Medical and Health Sciences
Research Interests: Thermodynamics, Chemistry, Kinetics, Biological Chemistry, Medicine, and 14 moreBiological Sciences, Lysozyme, Temperature, CHEMICAL SCIENCES, Protein Conformation, Guanidines, Ambroxol Hydrochloride, Protein Binding, Drug Stability, Protein Denaturation, Oligosaccharides, N-acetylglucosamine, binding sites, and Medical and Health Sciences
Research Interests: Biophysics, Chemistry, Protein Folding, Kinetics, Biological Chemistry, and 13 moreStability, Medicine, Biological Sciences, Biological, Temperature, Urea, CHEMICAL SCIENCES, Protein Conformation, Mechanism in Biology, Hydrogen-Ion Concentration, Thallophyta, ribonuclease, and Medical and Health Sciences
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Research Interests: Chemistry, Biology, Medicine, Gene expression, Streptomyces, and 12 moreEscherichia coli, Protein expression and purification, Isoenzymes, Protein Expression, Amino Acid Sequence, Recombinant Proteins, Biochemistry and cell biology, Isoelectric point, Ribonucleases, Molecular Sequence Data, culture medium, and absorption coefficient
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On the basis of studies of Asn to Ala mutants, the gain in stability from burying amide groups that are hydrogen bonded to peptide groups is 80 cal/(mol A(3)). On the basis of similar studies of Leu to Ala and Ile to Val mutants, the gain... more
On the basis of studies of Asn to Ala mutants, the gain in stability from burying amide groups that are hydrogen bonded to peptide groups is 80 cal/(mol A(3)). On the basis of similar studies of Leu to Ala and Ile to Val mutants, the gain in stability from burying -CH(2)- groups is 50 cal/(mol A(3)). Thus, the burial of an amide group contributes more to protein stability than the burial of an equivalent volume of -CH(2)- groups. Applying these results to folded proteins leads to the surprising conclusion that peptide group burial makes a larger contribution to protein stability than nonpolar side chain burial. Several studies have shown that the desolvation penalty for burying peptide groups is considerably smaller than generally thought. This suggests that the hydrogen bonding and van der Waals interactions of peptide groups in the tightly packed interior of folded protein are more favorable than similar interactions with water in the unfolded protein.
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Research Interests: Biochemistry, Computer Science, Thermodynamics, Chemistry, Medicine, and 12 moreProtein Stability, Animals, Horses, Myoglobin, Protein Conformation, Guanidines, Ambroxol Hydrochloride, Structure activity Relationship, Drug Stability, Protein Denaturation, Biochemistry and cell biology, and Medical biochemistry and metabolomics
Research Interests: Biochemistry, Chemistry, Crystallography, Hydrogen, Protein Folding, and 13 moreKinetics, NMR Spectroscopy, Magnetic Resonance Spectroscopy, Medicine, Deuterium, Hydrogen Bond, Amides, Hydrogen Deuterium Exchange, Molecule, Biochemistry and cell biology, Nuclear Magnetic Resonance Spectroscopy, Folding Intermediate, and Medical biochemistry and metabolomics
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Proteins carry out the most important and difficult tasks in all living organisms. To do so, they must often interact specifically with other small and large molecules. This requires that they fold to a globular conformation with a unique... more
Proteins carry out the most important and difficult tasks in all living organisms. To do so, they must often interact specifically with other small and large molecules. This requires that they fold to a globular conformation with a unique active site that is used for the specific interaction. Consequently, protein folding can be regarded as the “secret of life”. Biochemists and chemists have a great interest in elucidating the mechanism by which proteins fold and in predicting the folded conformation and its stability given just the amino acid sequence. This challenge is sometimes called the “protein folding problem”. The ability to construct proteins differing in sequence by one or more amino acids and to analyze their three‐dimensional structures by X‐ray crystallography and NMR spectroscopy is a powerful tool for investigating the conformational stability and folding of proteins. Several proteins are now under intensive study by this approach. One of these is ribonuclease T1.
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Research Interests: Chemistry, Kinetics, Biology, Biological Chemistry, Medicine, and 15 moreAspergillus, Biological Sciences, Mutation, Escherichia coli, Biological, CHEMICAL SCIENCES, Cysteine, Protein Conformation, Hydrolysis, Drug Stability, Protein Denaturation, Gene Expression Regulation, ribonuclease, Aspergillus oryzae, and Medical and Health Sciences
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The stability of globular proteins is important in medicine, proteomics, and basic research. The conformational stability of the folded state can be determined experimentally by analyzing urea, guanidinium chloride, and thermal... more
The stability of globular proteins is important in medicine, proteomics, and basic research. The conformational stability of the folded state can be determined experimentally by analyzing urea, guanidinium chloride, and thermal denaturation curves. Solvent denaturation curves in particular may give useful information about a protein such as the existence of domains or the presence of stable folding intermediates. The linear extrapolation method (LEM) for analyzing solvent denaturation curves gives the parameter m, which is a measure of the dependence of ΔG on denaturant concentration. There is much recent interest in the m value as it relates to the change in accessible surface area of a protein when it unfolds and what it may reveal about the denatured states of proteins.
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The energetics of thermal denaturation of two isoforms of ribonuclease T1 (Gln25 and Lys25) in various solvents have been studied by differential scanning calorimetry. It has been shown that the thermal transition of both forms of RNase... more
The energetics of thermal denaturation of two isoforms of ribonuclease T1 (Gln25 and Lys25) in various solvents have been studied by differential scanning calorimetry. It has been shown that the thermal transition of both forms of RNase T1 is strongly affected by slow kinetics, which cause an apparent deviation of the transition from a simple two-state model. By decreasing the heating rate or increasing the transition temperature, the denaturation of RNase approaches an equilibrium two-state transition. This permits determination of the thermodynamic parameters characterizing unfolding of the native structure. These thermodynamic parameters were correlated with the structural features of protein. Analysis of different contributions to the stability of RNase T1 shows that van der Waals interactions and hydrogen bonding are the major contributors to the conformational stability of the protein.
Research Interests: Biochemistry, Thermodynamics, Chemistry, Physical Chemistry, Kinetics, and 12 moreMedicine, Differential scanning calorimetry, Escherichia coli, Energetics, RNAse P, Hydrogen Bonding, Recombinant Proteins, Protein Denaturation, Biochemistry and cell biology, ribonuclease, Aspergillus oryzae, and Medical biochemistry and metabolomics
Research Interests: Biochemistry, Thermodynamics, Chemistry, Protein Folding, Magnetic Resonance Spectroscopy, and 15 moreMedicine, RNAse P, Hydrogen Bond, Amides, Isoenzymes, Protein Conformation, Solvent, Protein Denaturation, Protons, Sodium Chloride, Static Electricity, Biochemistry and cell biology, Ribonucleases, ribonuclease, and Medical biochemistry and metabolomics
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Research Interests: Chemistry, Catalysis, Kinetics, Protein Science, Protein, and 15 moreMedicine, Differential scanning calorimetry, Stereochemistry, RNAse P, Active site, Glutamine, Substrate Specificity, Isoenzymes, Arginine, Recombinant Proteins, Glutamic Acid, Histidine, Biochemistry and cell biology, Ribonucleases, and ribonuclease
Originally published in: Protein Folding Handbook. Part I. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley-VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3-527-30784-2 Introduction How Urea Denatures Proteins... more
Originally published in: Protein Folding Handbook. Part I. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley-VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3-527-30784-2 Introduction How Urea Denatures Proteins Linear Extrapolation Method ΔG(H2O) m-Values Conclusions Practical Considerations How to Choose the Best Denaturant for your Study How to Prepare Denaturant Solutions Preparation of a urea stock solution How to Determine Solvent Denaturation Curves Determining a Urea or GdmCl Denaturation Curve How to Analyze Urea or GdmCl Denaturant Curves Determining Differences in Stability Acknowledgments Keywords: urea; guanidinium; protein unfolding; conformational stability; denaturation curve
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The primary goal of this study was to gain a better understanding of the effect of environment and ionic strength on the pK values of histidine residues in proteins. The salt-dependence of pK values for two histidine residues in... more
The primary goal of this study was to gain a better understanding of the effect of environment and ionic strength on the pK values of histidine residues in proteins. The salt-dependence of pK values for two histidine residues in ribonuclease Sa (RNase Sa) (pI=3.5) and a variant in which five acidic amino acids have been changed to lysine (5K) (pI=10.2) was measured and compared to pK values of model histidine-containing peptides. The pK of His53 is elevated by two pH units (pK=8.61) in RNase Sa and by nearly one pH unit (pK=7.39) in 5K at low salt relative to the pK of histidine in the model peptides (pK=6.6). The pK for His53 remains elevated in 1.5M NaCl (pK=7.89). The elevated pK for His53 is a result of screenable electrostatic interactions, particularly with Glu74, and a non-screenable hydrogen bond interaction with water. The pK of His85 in RNase Sa and 5K is slightly below the model pK at low salt and merges with this value at 1.5M NaCl. The pK of His85 reflects mainly effects of long-range Coulombic interactions that are screenable by salt. The tautomeric states of the neutral histidine residues are changed by charge reversal. The histidine pK values in RNase Sa are always higher than the pK values in the 5K variant. These results emphasize that the net charge of the protein influences the pK values of the histidine residues. Structure-based pK calculations capture the salt-dependence relatively well but are unable to predict absolute histidine pK values.
Research Interests: Chemistry, Molecular Biology, Kinetics, Medicine, Molecular, and 15 moreEscherichia coli, Long Range, Hydrogen Bond, Hydrogen Bonding, Lysine, Isoenzymes, Finite Difference, Protein Conformation, Electrostatic Interactions, Ionic Strength, Poisson Boltzmann, Histidine, Biochemistry and cell biology, Isoelectric point, and Electrostatic interaction
The pK values of the titratable groups in ribonuclease Sa (RNase Sa) (pI=3.5), and a charge-reversed variant with five carboxyl to lysine substitutions, 5K RNase Sa (pI=10.2), have been determined by NMR at 20 degrees C in 0.1M NaCl. In... more
The pK values of the titratable groups in ribonuclease Sa (RNase Sa) (pI=3.5), and a charge-reversed variant with five carboxyl to lysine substitutions, 5K RNase Sa (pI=10.2), have been determined by NMR at 20 degrees C in 0.1M NaCl. In RNase Sa, 18 pK values and in 5K, 11 pK values were measured. The carboxyl group of Asp33, which is buried and forms three intramolecular hydrogen bonds in RNase Sa, has the lowest pK (2.4), whereas Asp79, which is also buried but does not form hydrogen bonds, has the most elevated pK (7.4). These results highlight the importance of desolvation and charge-dipole interactions in perturbing pK values of buried groups. Alkaline titration revealed that the terminal amine of RNase Sa and all eight tyrosine residues have significantly increased pK values relative to model compounds.A primary objective in this study was to investigate the influence of charge-charge interactions on the pK values by comparing results from RNase Sa with those from the 5K variant. The solution structures of the two proteins are very similar as revealed by NMR and other spectroscopic data, with only small changes at the N terminus and in the alpha-helix. Consequently, the ionizable groups will have similar environments in the two variants and desolvation and charge-dipole interactions will have comparable effects on the pK values of both. Their pK differences, therefore, are expected to be chiefly due to the different charge-charge interactions. As anticipated from its higher net charge, all measured pK values in 5K RNase are lowered relative to wild-type RNase Sa, with the largest decrease being 2.2 pH units for Glu14. The pK differences (pK(Sa)-pK(5K)) calculated using a simple model based on Coulomb's Law and a dielectric constant of 45 agree well with the experimental values. This demonstrates that the pK differences between wild-type and 5K RNase Sa are mainly due to changes in the electrostatic interactions between the ionizable groups. pK values calculated using Coulomb's Law also showed a good correlation (R=0.83) with experimental values. The more complex model based on a finite-difference solution to the Poisson-Boltzmann equation, which considers desolvation and charge-dipole interactions in addition to charge-charge interactions, was also used to calculate pK values. Surprisingly, these values are more poorly correlated (R=0.65) with the values from experiment. Taken together, the results are evidence that charge-charge interactions are the chief perturbant of the pK values of ionizable groups on the protein surface, which is where the majority of the ionizable groups are positioned in proteins.
Research Interests: Chemistry, Molecular Biology, Medicine, Molecular, Pi, and 15 moreHydrogen Bond, Hydrogen Bonding, Lysine, Dielectric Constant, Isoenzymes, Finite Difference, Isotope effect, Protein Conformation, Electrostatic Interactions, Poisson Boltzmann, Protein Denaturation, Glutamic Acid, Biochemistry and cell biology, Isoelectric point, and Electrostatic interaction
To investigate the pH dependence of the conformational stability of barnase, urea denaturation curves were determined over the pH range 2-10. The maximum conformational stability of barnase is 9 kcal mol-1 and occurs between pH 5 and 6.... more
To investigate the pH dependence of the conformational stability of barnase, urea denaturation curves were determined over the pH range 2-10. The maximum conformational stability of barnase is 9 kcal mol-1 and occurs between pH 5 and 6. The dependence of delta G on urea concentration increases from 1850 cal mol-1 M-1 at high pH to about 3000 cal mol-1 M-1 near pH 3. This suggests that the unfolded conformations of barnase become more accessible to urea as the net charge on the molecule increases. Previous studies suggested that in 8 M urea barnase unfolds more completely than ribonuclease T1, even with the disulfide bonds broken [Pace, C.N., Laurents, D. V., & Thomson, J.A. (1990) Biochemistry 29, 2564-2572]. In support of this, solvent perturbation difference spectroscopy showed that in 8 M urea the Trp and Tyr residues in barnase are more accessible to perturbation by dimethyl sulfoxide than in ribonuclease T1 with the disulfide bonds broken.
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To investigate the pH dependence of the conformational stability of ribonucleases A and T1, urea and guanidine hydrochloride denaturation curves have been determined over the pH range 2-10. The maximum conformational stability of both... more
To investigate the pH dependence of the conformational stability of ribonucleases A and T1, urea and guanidine hydrochloride denaturation curves have been determined over the pH range 2-10. The maximum conformational stability of both proteins is about 9 kcal/mol and occurs near pH 4.5 for ribonuclease T1 and between pH 7 and 9 for ribonuclease A. The pH dependence suggests that electrostatic interactions among the charged groups make a relatively small contribution to the conformational stability of these proteins. The dependence of delta G on urea concentration increases from about 1200 cal mol-1 M-1 at high pH to about 2400 cal mol-1 M-1 at low pH for ribonuclease A. This suggests that the unfolded conformations of RNase A become more accessible to urea as the net charge on the molecule increases. For RNase T1, the dependence of delta G on urea concentration is minimal near pH 6 and increases at both higher and lower pH. An analysis of information of this type for several proteins in terms of a model developed by Tanford [Tanford, C. (1964) J. Am. Chem. Soc. 86, 2050-2059] suggests that the unfolded states of proteins in urea and GdnHCl solutions may differ significantly in the extent of their interaction with denaturants. Thus, the conformations assumed by unfolded proteins may depend to at least some extent on the amino acid sequence of the protein.
Research Interests: Biochemistry, Thermodynamics, Chemistry, Crystallography, Medicine, and 11 moreUrea, RNAse P, Protein Conformation, Guanidines, Ambroxol Hydrochloride, Hydrogen-Ion Concentration, Protein Denaturation, Biochemistry and cell biology, ribonuclease, Aspergillus oryzae, and Medical biochemistry and metabolomics
In order to use results from calorimetry or thermal unfolding curves to estimate the free energy change for protein unfolding at 25 degrees C, it is necessary to know the change in heat capacity for unfolding, delta Cp. We describe a new... more
In order to use results from calorimetry or thermal unfolding curves to estimate the free energy change for protein unfolding at 25 degrees C, it is necessary to know the change in heat capacity for unfolding, delta Cp. We describe a new method for measuring delta Cp which is based on results from urea and thermal unfolding curves but does not require a calorimeter. We find that delta Cp = 1650 +/- 200 cal/(deg.mol) for the unfolding of ribonuclease T1 and that delta Cp = 2200 +/- 300 cal/(deg.mol) for the unfolding of ribonuclease A.
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Research Interests: Mathematics, Chemistry, Kinetics, Biological Chemistry, Medicine, and 15 moreBiological Sciences, Pregnancy, Lysozyme, Female, Animals, Goats, CHEMICAL SCIENCES, Protein Conformation, Calorimetry, Guanidines, Protein Binding, Optical Rotation, Chymotrypsin, binding sites, and Medical and Health Sciences
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We have used NMR methods to characterize the structure and dynamics of ribonuclease Sa in solution. The solution structure of RNase Sa was obtained using the distance constraints provided by 2,276 NOEs and the C6-C96 disulfide bond. The... more
We have used NMR methods to characterize the structure and dynamics of ribonuclease Sa in solution. The solution structure of RNase Sa was obtained using the distance constraints provided by 2,276 NOEs and the C6-C96 disulfide bond. The 40 resulting structures are well determined; their mean pairwise RMSD is 0.76 A (backbone) and 1.26 A (heavy atoms). The solution structures are similar to previously determined crystal structures, especially in the secondary structure, but exhibit new features: the loop composed of Pro 45 to Ser 48 adopts distinct conformations and the rings of tyrosines 51, 52, and 55 have reduced flipping rates. Amide protons with greatly reduced exchange rates are found predominantly in interior beta-strands and the alpha-helix, but also in the external 3/10 helix and edge beta-strand linked by the disulfide bond. Analysis of (15)N relaxation experiments (R1, R2, and NOE) at 600 MHz revealed five segments, consisting of residues 1-5, 28-31, 46-50, 60-65, 74-77, retaining flexibility in solution. The change in conformation entropy for RNase SA folding is smaller than previously believed, since the native protein is more flexible in solution than in a crystal.
Research Interests: Chemistry, Crystallography, Protein Folding, Protein Science, Magnetic Resonance Spectroscopy, and 15 moreMedicine, Entropy, Biological Sciences, Crystal structure, Mathematical Sciences, Protein structure, Proteins, RNAse P, Hydrogen Bonding, Isoenzymes, Protein Conformation, Recombinant Proteins, Solution Structure, Ribonucleases, and ribonuclease
Our goal was to gain a better understanding of how protein stability can be increased by improving beta-turns. We studied 22 beta-turns in nine proteins with 66-370 residues by replacing other residues with proline and glycine and... more
Our goal was to gain a better understanding of how protein stability can be increased by improving beta-turns. We studied 22 beta-turns in nine proteins with 66-370 residues by replacing other residues with proline and glycine and measuring the stability. These two residues are statistically preferred in some beta-turn positions. We studied: Cold shock protein B (CspB), Histidine-containing phosphocarrier protein, Ubiquitin, Ribonucleases Sa2, Sa3, T1, and HI, Tryptophan synthetase alpha-subunit, and Maltose binding protein. Of the 15 single proline mutations, 11 increased stability (Average = 0.8 +/- 0.3; Range = 0.3-1.5 kcal/mol), and the stabilizing effect of double proline mutants was additive. On the basis of this and our previous work, we conclude that proteins can generally be stabilized by replacing nonproline residues with proline residues at the i + 1 position of Type I and II beta-turns and at the i position in Type II beta-turns. Other turn positions can sometimes be used if the phi angle is near -60 degrees for the residue replaced. It is important that the side chain of the residue replaced is less than 50% buried. Identical substitutions in beta-turns in related proteins give similar results. Proline substitutions increase stability mainly by decreasing the entropy of the denatured state. In contrast, the large, diverse group of proteins considered here had almost no residues in beta-turns that could be replaced by Gly to increase protein stability. Improving beta-turns by substituting Pro residues is a generally useful way of increasing protein stability.
Research Interests: Biochemistry, Chemistry, Protein Folding, Medicine, Protein Stability, and 13 moreBiological Sciences, Mutation, Mathematical Sciences, Protein structure, Proline, Proteins, Plasmids, Protein Secondary Structure Prediction, Molecular Conformation, Protein Conformation, Glycine, Protein Denaturation, and Histidine
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Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent... more
Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (delta Cp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and delta Cp.
Research Interests: Mathematics, Thermodynamics, Protein Folding, Kinetics, Protein Science, and 14 moreEnzymes, Humans, Animals, Regression Analysis, Research article, Protein folding/unfolding, Proteins, Heat Capacity, Calorimetry, Guanidines, Protein Denaturation, Surface Protein, Biochemistry and cell biology, and Ribonucleases
High concentration protein delivery is difficult to achieve for several protein pharmaceuticals due to low solubility. In this review, we discuss different types of low protein solubility, including low in vitro solubility, which is... more
High concentration protein delivery is difficult to achieve for several protein pharmaceuticals due to low solubility. In this review, we discuss different types of low protein solubility, including low in vitro solubility, which is relevant to the formulation of protein pharmaceuticals. We also discuss different methods of measuring protein solubility with an emphasis on the method of inducing amorphous precipitation using ammonium sulfate. Finally, we discuss strategies for increasing protein solubility, including site-directed mutagenesis. Evidence from solubility-changing mutations in the literature indicate that some hydrophilic residues (aspartic acid, glutamic acid, and serine) contribute significantly more favorably to protein solubility than other hydrophilic residues (asparagine, glutamine, threonine, lysine, and arginine). These findings should prove useful especially in cases where protein structure is not known. In these cases, instead of targeting hydrophobic residues that are often buried, one could target hydrophilic residues that do not contribute favorably to protein solubility and replace them with hydrophilic residues that contribute more favorably.
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Research Interests: Biochemistry, Chemistry, Molecular Biology, Medicine, Threonine, and 15 moreD-Aspartic Acid, Proteins, Solubility, Amino Acids, High Resolution, Glutamine, Salts, Structure activity Relationship, Hydrogen-Ion Concentration, Asparagine, Electric Conductivity, Glutamic Acid, Ammonium Sulfate, Biochemistry and cell biology, and Ribonucleases
The ionizable groups in proteins with the lowest pKs are the carboxyl groups of aspartic acid side-chains. One of the lowest, pK=0.6, is observed for Asp76 in ribonuclease T1. This low pK appeared to result from hydrogen bonds to a water... more
The ionizable groups in proteins with the lowest pKs are the carboxyl groups of aspartic acid side-chains. One of the lowest, pK=0.6, is observed for Asp76 in ribonuclease T1. This low pK appeared to result from hydrogen bonds to a water molecule and to the side-chains of Asn9, Tyr11, and Thr91. The results here confirm this by showing that the pK of Asp76 increases to 1.7 in N9A, to 4.0 in Y11F, to 4.2 in T91V, to 4.4 in N9A+Y11F, to 4.9 in N9A+T91V, to 5.9 in Y11F+T91V, and to 6.4 in the triple mutant: N9A+Y11F+T91V. In ribonuclease Sa, the lowest pK=2.4 for Asp33. This pK increases to 3.9 in T56A, which removes the hydrogen bond to Asp33, and to 4.4 in T56V, which removes the hydrogen bond and replaces the -OH group with a -CH(3) group. It is clear that hydrogen bonds are able to markedly lower the pK values of carboxyl groups in proteins. These same hydrogen bonds make large contributions to the conformational stability of the proteins. At pH 7, the stability of D76A ribonuclease T1 is 3.8 kcal mol(-1) less than wild-type, and the stability of D33A ribonuclease Sa is 4.1 kcal mol(-1) less than wild-type. There is a good correlation between the changes in the pK values and the changes in stability. The results suggest that the pK values for these buried carboxyl groups would be greater than 8 in the absence of hydrogen bonds, and that the hydrogen bonds and other interactions of the carboxyl groups contribute over 8 kcal mol(-1) to the stability.
Research Interests: Thermodynamics, Chemistry, Molecular Biology, Medicine, Protein Stability, and 15 moreUrea, D-Aspartic Acid, Proteins, Hydrogen Bond, Hydrogen Bonding, Side-chain, Amino Acid Substitution Rates, Molecule, Hydrogen-Ion Concentration, Protein Denaturation, Static Electricity, Biochemistry and cell biology, Molecular Structure, Ribonucleases, and ribonuclease
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Organophosphorus hydrolase (OPH, EC 8.1.3.1) is a homodimeric enzyme that catalyzes the hydrolysis of organophosphorus pesticides and nerve agents. We have analyzed the urea- and guanidinium chloride-induced equilibrium unfolding of OPH... more
Organophosphorus hydrolase (OPH, EC 8.1.3.1) is a homodimeric enzyme that catalyzes the hydrolysis of organophosphorus pesticides and nerve agents. We have analyzed the urea- and guanidinium chloride-induced equilibrium unfolding of OPH as monitored by far-ultraviolet circular dichroism and intrinsic tryptophan fluorescence. These spectral methods, which monitor primarily the disruption of protein secondary structure and tertiary structure, respectively, reveal biphasic unfolding transitions with evidence for an intermediate form of OPH. By investigating the protein concentration dependence of the unfolding curves, it is clear that the second transition involves dissociation of the monomeric polypeptide chains and that the intermediate is clearly dimeric. The dimeric intermediate form of OPH is devoid of enzymatic activity, yet clearly behaves as a partially folded, dimeric protein by gel filtration. Therefore, we propose an unfolding mechanism in which the native dimer converts to an inactive, well-populated dimeric intermediate which finally dissociates and completely unfolds to individual monomeric polypeptides. The denaturant-induced unfolding data are described well by a three-state mechanism with delta G for the interconversion between the native homodimer (N2) and the inactive dimeric intermediate (I2) of 4.3 kcal/mol while the overall standard state stability of the native homodimer relative to the unfolded monomers (2U) is more than 40 kcal/mol. Thus, OPH is a remarkably stable protein that folds through an inactive, dimeric intermediate and will serve as a good model system for investigating the energetics of protein association and folding in a system where we can clearly resolve these two steps.