Hydrogen exchange and protein folding
Current Opinion in Structural BiologyPublished 1 February 1998
Jane Clarke, Laura S. Itzhaki
Citations120
SJR quartileQ1
SJR score2.91
SNIP1.48
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TL;DR
Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins and recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.
Abstract
Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins. The significant increase in the number of small, model proteins that have been studied has allowed a better understanding of the structural fluctuations that lead to hydrogen exchange. Recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.
Keywords
Materials ScienceBiochemistry, Genetics and Molecular Biology
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The results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo‐ and polypeptides.
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Quantitative measurements of the rate of hydrogen exchange in a given protein, under specified experimental conditions, provide a multiparameter characterization of the protein conformation (or distribution of conformations) present under these conditions.
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999 Citations1995Yawen Bai, Tobin R. Sosnick +2 more
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Journal of Molecular BiologyThe Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding
744 Citations1995Laura S. Itzhaki, Daniel E. Otzen +1 more
It is suggested that the mechanism of folding ofCI2 may be a common theme in protein folding whereby fundamental folding units of larger proteins, which are modelled by the folding of CI2, form by nucleation-condensation events and coalesce, perhaps in a hierarchical manner.
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622 Citations1992George I. Makhatadze, Peter L. Privalov
It is found that the binding of urea and guanidinium chloride by protein is accompanied by a significant decrease of enthalpy and entropy, which raises a doubt as to whether a polypeptide chain in concentrated solutions of denaturants can be considered as a standard of a random coil conformation.
ScienceDetection of Transient Protein Folding Populations by Mass Spectrometry
547 Citations1993Andrew D. Miranker, Carol V. Robinson +3 more
Electrospray ionization mass spectrometry has been used to obtain the distribution of masses within a population of protein molecules that had undergone hydrogen exchange in solution, helping to detail the pathways available to a protein during refolding.
BiochemistryPrimary structure effects on peptide group hydrogen exchange
471 Citations1972Robert S. Molday, S. W. Englander +1 more
The results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured oligo- and polypeptides.
Annual Review of BiochemistryHydrogen Exchange
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A new method that uses acid proteases and mass spectrometry to determine amide hydrogen exchange rates in proteins makes this approach particularly attractive for a wide range of studies, particularly in the areas of sensitivity, protein solubility, detection of correlated exchange and high molecular mass proteins.
Journal of Biological ChemistryThe Solubility of Amino Acids, Diglycine, and Triglycine in Aqueous Guanidine Hydrochloride Solutions
354 Citations1970Yasuhiko Nozaki, Charles Tanford
The results show similarity between the patterns of solubilizing effects of guanidine hydrochloride and urea, although Guanidine Hydrochloride is 2 to 3 times more effective than urea at the same concentrations.
Nature Structural & Molecular BiologyDetection of rare partially folded molecules in equilibrium with the native conformation of RNaseH
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Proteins Structure Function and BioinformaticsProtein stability parameters measured by hydrogen exchange
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The hydrogen exchange (HX) rates of the slowest peptide group NH hydrogens in oxidized cytochrome c (equine) are controlled by the transient global unfolding equilibrium and can be measured by one‐dimensional nuclear magnetic resonance and used to determine the thermodynamic parameters of global unfolding at mild solution conditions well below the melting transition.
Molecular and Cellular BiochemistryHydrogen exchange and the dynamic structure of proteins
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Recent reports of hydrogen exchange in proteins are reviewed, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen Exchange in folded proteins.
BiochemistryThermodynamics of the denaturation of lysozyme by guanidine hydrochloride. II. Dependence on denaturant concentration at 25°
271 Citations1969Kirk C. Aune, Charles Tanford
Journal of Molecular BiologyStructure-based Calculation of the Equilibrium Folding Pathway of Proteins. Correlation with Hydrogen Exchange Protection Factors
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Journal of Molecular BiologyThe folding of an enzyme
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ScienceAn Antibody Binding Site on Cytochrome C Defined by Hydrogen Exchange and Two-Dimensional NMR
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The interaction of a protein antigen, horse cytochrome c (cyt c), with a monoclonal antibody has been studied by hydrogen-deuterium (H-D) exchange labeling and two-dimensional nuclear magnetic resonance (2D NMR) methods.
ScienceGuanidinium Chloride Induction of Partial Unfolding in Amide Proton Exchange in RNase A
181 Citations1993Stephen L. Mayo, Robert L. Baldwin
The results indicate that these concentrations of GdmCl do induce exchange by means of a partial unfolding mechanism for all 23 protons; this implies that exchange reactions can be used to study the unfolding and stability of local regions.
BiochemistryHydrogen exchange identifies native-state motional domains important in protein folding
180 Citations1993Key Sun Kim, J A Fuchs +1 more
In the mutant proteins, the rates for exchange by the unfolding mechanism are accelerated by a factor corresponding to the increase in the unfolding/folding equilibrium constant.
Journal of Molecular BiologyThe folding of an enzyme
172 Citations1992Luis Serrano, Andreas Matouschek +1 more
The sequence of events in the refolding pathway of barnase has been analysed to search for general principles in protein folding and it is plausible that there are stop signals encoded in the linear sequence that prevent the elongation of isolated secondary structure elements in solution to a larger extent than is found in the folded protein.
Proteins Structure Function and BioinformaticsHydrogen exchange in native and denatured states of hen egg‐white lysozyme
167 Citations1992Sheena E. Radford, Matthias Buck +3 more
The pattern of exchange rates from the native protein at high temperature, pH 3.8 69°C, resembles that of the acid‐denatured state, suggesting that under these conditions the exchange kinetics are dominated by transient global unfolding.
Proteins Structure Function and BioinformaticsFuture directions in folding: The multi-state nature of protein structure
164 Citations1996Yawen Bai, S. W. Englander
Hydrogen exchange methods can be used to detect and characterize these partially unfolded forms at native conditions and as a function of mild denaturant and temperature, which illuminates the requirements that govern the ability of kinetic and equilibrium methods to study folding intermediates.
ScienceCatalysis of Amide Proton Exchange by the Molecular Chaperones GroEL and SecB
135 Citations1996Ralph Zahn, Sarah Perrett +2 more
Both chaperones have the potential to correct misfolding in proteins by annealing and catalyzed exchange of deeply buried amide protons with solvent.
Current Opinion in Structural BiologyTime-resolved biophysical methods in the study of protein folding
130 Citations1996Kevin W. Plaxco, Christopher M. Dobson
Many of the biophysical techniques developed to characterize native proteins at equilibrium have now been adapted to the structural and thermodynamic characterization of transient intermediate populations during protein folding.
BiochemistryAmide proton exchange in proteins by EX1 kinetics: studies of the basic pancreatic trypsin inhibitor at variable p2H and temperature
130 Citations1985Heinrich Röder, Gerhard Wagner +1 more
It can be concluded that the amide proton exchange in globular proteins is quite generally via EX2 processes, with rare exceptions for measurements with extremely stable protons at high temperature and basic p2H.
Biophysical JournalHydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor
126 Citations1980Clare Woodward, Bruce D. Hilton
Rates for exchange from the folded state of proteins are not correlated to thermal lability, as proposed by Wuthrich et al, and the rates for exchange of single protons from folded BPTI are consistent with previous hydrogen-tritium exchange results and with a penetration model of the dynamic processes limiting hydrogen exchange.
BiochemistryProtein Stability as a Function of Denaturant Concentration: The Thermal Stability of Barnase in the Presence of Urea
125 Citations1995Christopher M. Johnson, Alan R. Fersht
Values for delta GU-F at 298 K (delta G298U-F) for each concentration of urea were extrapolated from the calorimetrically measured enthalpies and the denaturational heat capacity change measured for that concentration of Urea, consistent with an overall exothermic interaction between urea and protein with a net increase on unfolding.
BiochemistryProtein internal flexibility and global stability: Effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor
118 Citations1993Key Sun Kim, Clare Woodward
Several unassigned side-chain NH's of arginine or lysine are highly protected from exchange by urea, suggesting that they are the location of urea binding sites on the surface of the molecule.
Methods in enzymology on CD-ROM/Methods in enzymology[22] Structural characterization of protein folding intermediates by proton magnetic resonance and hydrogen exchange
105 Citations1989Heinrich Röder
The most pertinent test is to perform hydrogen exchange measurements under the conditions chosen for unfolding, and to compare the results with free peptide rates, under most circumstances rapid mixing is required for these measurements.
Folding and DesignAn evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway
104 Citations1996Jane Clarke, Alan R. Fersht
Measurement of H/2H-exchange of amide protons at equilibrium, when applied correctly, is an excellent method for analyzing the equilibrium distribution of unfolded and partly folded states but cannot, in theory and in practice, be used for determining protein folding pathways by itself.
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103 Citations1996Ralph Zahn, Sarah Perrett +1 more
Molecular chaperones GroEL and SecB have the potential to act in vivo and in vitro as a folding/transport-scaffold to prevent aggregation of partially folded states by binding; as an annealing-machine to generate continuous unfolding of misfolded states until a low-affinity state is formed; and as an unfoldase to catalyse unfolding of the mis Folded states.
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99 Citations1993Clare Woodward
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98 Citations1991Torben Graves Pedersen, Bent W. Sigurskjold +5 more
The results indicate that the spectrum of fluctuations giving rise to hydrogen exchange may be significantly altered by the intermolecular interactions present within the crystalline state.
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97 Citations1995Aijun Wang, Andrew Robertson +1 more
To investigate the interrelationships between protein stability, function, and internal dynamics, a hydrogen exchange (HX) quench method was established and used to study the effects of sucrose on the structural fluctuations of ribonuclease A.
ScienceHydrogen Exchange Measurement of the Free Energy of Structural and Allosteric Change in Hemoglobin
92 Citations1992S. Walter Englander, Joan J. Englander +5 more
In tests with a number of modified hemoglobin forms, the loss in structural free energy obtained locally from hydrogen exchange results matches the loss of allosteric free energy measured globally by oxygen-binding and subunit dissociation experiments.
Protein ScienceA statistical mechanical model for hydrogen exchange in globular proteins
89 Citations1995D. W. Miller, Ken A. Dill
The present model indicates that the stable‐state mechanism of exchange occurs through an ensemble of conformations, some of which may bear very little resemblance to the native structure.
Journal of Molecular BiologyHydrogen exchange in chymotrypsin inhibitor 2 probed by denaturants and temperature
89 Citations1997Laura S. Itzhaki, José L. Neira +1 more
Hydrogen exchange of chymotrypsin inhibitor 2 has been measured in the presence of low concentrations of GdmCl and at different temperatures and an m-value, which is a measure of the new surface area exposed to solvent in the equilibrium between open and closed forms, can be determined for individual protons, provides information about the structural nature of the opening reactions.
Proteins Structure Function and BioinformaticsPredicting the equilibrium protein folding pathway: Structure-based analysis of staphylococcal nuclease
86 Citations1997Vincent J. Hilser, Ernesto Freire
The equilibrium folding pathway of staphylococcal nucleas (SNase) has been approximated using a statistical thermodynamic formalism that utilizes the high‐resolution structure of the native state as a template to generate a large ensemble of partially folded states.
Proceedings of the National Academy of SciencesNative-like structure of a protein-folding intermediate bound to the chaperonin GroEL
86 Citations1997Matthew S. Goldberg, Jing Zhang +4 more
It is concluded that significant native-like structure is present in protein-folding intermediates bound to GroEL, and the pattern and magnitude of amide proton protection indicate that the central parallel beta-sheet found in native DHFR is presentIn a moderately stable state in GroEL-bound DHFR.
BiochemistryTemperature and pH Dependences of Hydrogen Exchange and Global Stability for Ovomucoid Third Domain
82 Citations1996Liskin Swint‐Kruse, Andrew D. Robertson
Results suggest that EX2 kinetics should not be assumed when interpreting exchange studies, and a subset of 6-11 residues exhibits a one-to-one correlation with global stability in turkey ovomucoid third domain.
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79 Citations1997Martin J. Parker, Anthony R. Clarke
The denaturant-dependent relaxation kinetics of folding and unfolding of an isolated all-beta domain of rat CD2 have been measured and suggest that the solvent isotope effect arises from enhanced hydrophobic interactions which, in turn, results from an increased strength of the solvent-solvent hydrogen bond in D2O.
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The parameters derived by Molday et al. from measurements with small model peptides can be used to calculate intrinsic exchange rates in unfolded proteins and thus provide a reliable reference for the interpretation of exchange rates measured under native conditions.
Proceedings of the National Academy of SciencesKinetics of hydrogen bond breakage in the process of unfolding of ribonuclease A measured by pulsed hydrogen exchange.
77 Citations1995Thomas Kiefhaber, Robert L. Baldwin
The results indicate that a single rate-limiting step in unfolding breaks the entire network of peptide hydrogen bonds and causes the overall unfolding of ribonuclease A.
Protein ScienceDirect evidence for a two‐state protein unfolding transition from hydrogen‐deuterium exchange, mass spectrometry, and NMR
75 Citations1996Yi Qian, David Baker
A simple model in which exchange results from rapid (>105/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at ∼0.06/s is supported by qualitative agreement between the observed mass spectra and themass spectra simulated according to the model using NMR‐derived estimates of the proton exchange rates.
BiochemistryEffect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR
71 Citations1992Leland Mayne, Yvonne Paterson +2 more
Hydrogen-exchange labeling detected by 2D NMR is used to study antibody-protein interactions for two monoclonal antibodies raised against horse cytochrome c and provides some suggestive evidence concerning units of local structural flexibility in cy tochrome c.
Journal of Molecular BiologyHydrogen exchange in chymotrypsin inhibitor 2 probed by mutagenesis
70 Citations1997José L. Neira, Laura S. Itzhaki +3 more
Comparison of the exchange rates of a number of mutants of CI2 with those of wild-type identifies the pathway of exchange, whether by local breathing, global unfolding or a mixture of the two pathways.
BiochemistryRelationship between Equilibrium Amide Proton Exchange Behavior and the Folding Pathway of Barnase
70 Citations1995Sarah Perrett, Jane Clarke +2 more
A three-part strategy for analyzing the relationship between equilibrium amide proton exchange behavior of barnase and its folding/unfolding pathway is described, determining from which state exchange takes place for residues that nominally exchange by a global process: the fully unfolded state or the folding intermediate.
Journal of Molecular BiologyNuclear magnetic resonance studies of the internal dynamics in apo, (Cd2+)1 and (Ca2+)2 Calbindin D9k
65 Citations1992Nicholas J. Skelton, Johan Kördel +2 more
The backbone dynamics of the EF-hand Ca(2+)-binding protein, calbindin D9k, has been investigated in the apo, (Cd2+)1 and (Ca2+)2 states by measuring the rate constants for amide proton exchange with solvent, consistent with a reorganization of the hydrogen-bonding networks in the metal ion-binding loops.
Journal of Molecular BiologyGlobal Changes in Amide Hydrogen Exchange Rates for a Protein Antigen in Complex with Three Different Antibodies
65 Citations1996David C. Williams Jr, David C. Benjamin +2 more
Trends in Biochemical SciencesHydrogen exchange at equilibrium: a short cut for analysing protein-folding pathways?
64 Citations1997Jane Clarke, Laura S. Itzhaki +1 more
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63 Citations1997Yi Qian, Michelle L. Scalley +3 more
For protein L under native conditions, there do not appear to be partially folded states with free energies intermediate between that of the folded and unfolded states.
Protein ScienceSignificant hydrogen exchange protection in GroEL‐bound DHFR is maintained during iterative rounds of substrate cycling
63 Citations1996Michael L. Gross, Carol V. Robinson +3 more
It is suggested that GroEL‐assisted folding of DHFR occurs by minor structural adjustments to the partially folded substrate protein during iterative cycling, rather than by complete unfolding of this protein substrate on the chaperonin surface.
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54 Citations1993Torben Graves Pedersen, Niels Kirk Thomsen +3 more
The pH dependence of the amide/solvent hydrogen exchange of individual amide groups in hen egg-white lysozyme has been studied by nuclear magnetic resonance spectroscopy and the pH dependent exchange of the examined amides was shown to be in agreement with the Linderstrøm-Lang model.
BiochemistryAssessment of Stability Differences in the Protein G B1 and B2 Domains From Hydrogen-Deuterium Exchange: Comparison with Calorimetric Data
53 Citations1995John Orban, Patrick Alexander +2 more
Hydrogen-deuterium exchange experiments have been used to measure exchange rates for almost all of the main-chain amide protons (NHs) in the B1 and B2 IgG-binding domains of protein G and NH exchange rates provide a very sensitive measure of local stability differences between B2 and B1.
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52 Citations1997Aaron K. Chamberlain, Susan Marqusee
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Journal of Molecular BiologyThree-Dimensional Structure of Acidic Fibroblast Growth Factor in Solution: Effects of Binding to a Heparin Functional Analog
51 Citations1996Antonio Pineda‐Lucena, M. Ángeles Jiménez +5 more
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Archives of Biochemistry and BiophysicsEffects of denaturants at low concentrations on the reversible denaturation of staphylococcal nuclease
49 Citations1989David Shortle, Alan K. Meeker +1 more
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Journal of Molecular BiologyLocal Perturbations by Ligand Binding of Hydrogen Deuterium Exchange Kinetics in a Four-helix Bundle Protein, Acyl Coenzyme A Binding Protein (ACBP)
49 Citations1995Birthe B. Kragelund, Jens Knudsen +1 more
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BiochemistryMicrosecond Protein Folding Kinetics from Native-State Hydrogen Exchange
49 Citations1997Cammon B. Arrington, Andrew D. Robertson
Proceedings of the National Academy of SciencesLocal breathing and global unfolding in hydrogen exchange of barnase and its relationship to protein folding pathways.
49 Citations1993Jane Clarke, Andrea M. Hounslow +2 more
There is thus no direct relationship between hydrogen-exchange behavior and the protein folding pathway, however, experiments on mutants of varying stability may provide further evidence on the sequence of events in folding.
BiochemistryComparison of the Hydrogen-Exchange Behavior of Reduced and Oxidized Escherichia Coli Thioredoxin
47 Citations1995Mei‐Fen Jeng, H. Jane Dyson
Amide proton exchange rates provide a qualitative estimate of the backbone mobility, and the differences in hydrogen exchange behavior between the two forms of thioredoxin are consistent with those observed in calculations of polypeptide chain dynamics obtained from 15N relaxation measurements.
BiochemistryProtein Hydrogen Exchange in Denaturant: Quantitative Analysis by a Two-Process Model.
45 Citations1994Hong Qian, Stephen L. Mayo +1 more
BiochemistryRole of arginine 67 in the stabilization of chymotrypsin inhibitor 2: examination of amide proton exchange rates and denaturation thermodynamics of an engineered protein
45 Citations1990Sati K. Jandu, Sanjoy Ray +2 more
This work has examined the contribution to protein stability of an interaction involving a charged hydrogen bond from an arginyl side chain in the serine proteinase inhibitor chymotrypsin inhibitor 2 (CI-2), by replacing this side chain with an alanyl residue by protein engineering.
BiochemistryThermodynamics of Transient Conformations in the Folding Pathway of Barnase: Reorganization of the Folding Intermediate at low pH
43 Citations1996Mikael Oliveberg, Alan R. Fersht
It is argued that protonation of folding intermediates disrupts their structural integrity and allows isoenergetic reorganizations that increase the solvation of charged residues, which are compact denatured states that are sometimes observed at equilibrium at low pH and high ionic strength.
BiochemistryEnergetics and dynamics of molecular recognition by calmodulin
39 Citations1995Mark R. Ehrhardt, Jeffrey L. Urbauer +1 more
Observations suggest that the collapsed complex reorganizes with an associated free energy change of 5.5 kcal/mol to a more open state where the helical peptide is highly solvated and undergoes helix-coil transitions leading to exchange.
Protein ScienceSolvent isotope effects on the refolding kinetics of hen egg‐white lysozyme
39 Citations1996Laura S. Itzhaki, Philip A. Evans
The isotope effect on the rate‐determining step was found to be qualitatively reversed on going to low pH, suggesting that one component is probably associated with changes in the environments of carboxylate groups in forming the folding transition state.
Proceedings of the National Academy of Sciencesbeta-Lactamase binds to GroEL in a conformation highly protected against hydrogen/deuterium exchange.
39 Citations1996Pietro Gervasoni, Werner Staudenmann +3 more
It is concluded that, for beta-lactamase, a state with significant native structure is bound to GroEL, and different proteins are recognized by GroEL in very different states, ranging from totally unfolded to native-like, and this recognition may depend on which state can provide sufficient accessible hydrophobic amino acids in a suitably clustered arrangement.
FEBS LettersIdentification of the barstar binding site of barnase by NMR spectroscopy and hydrogen‐deuterium exchange
38 Citations1993David N. M. Jones, Mark Bycroft +2 more
The barstar binding site on barnase was characterised by comparing the differences in the chemical shift and hydrogen‐deuterium exchange rates between free and bound barnase, indicating that barstar inhibits barnase activity by sterically blocking the active site.
BiochemistryHydrogen-Deuterium Exchange in the Free and Immunoglobulin G-Bound Protein G B-Domain
36 Citations1994John Orban, Patrick Alexander +1 more
Hydrogen-deuterium exchange experiements have been used to measure backbone amide proton (NH) exchange rates in the free and IgG-bound protein G B2-domain (GB2), indicating that the majority of detectable NHs exchange through a global unfolding mechanism, reflecting the cooperative two-state unfolding behavior observed thermodynamically.
Protein ScienceAmide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c
33 Citations1993Jennifer L. Marmorino, Douglas S. Auld +4 more
It is found that slowly exchanging backbone amide protons tend to lack solvent‐accessible surface area, possess backbone hydrogen bonds, and are present in regions of regular secondary structure as well as in Ω‐loops, consistent with the local unfolding model.
Proceedings of the National Academy of SciencesA general two-process model describes the hydrogen exchange behavior of RNase A in unfolding conditions.
33 Citations1996Stewart N. Loh, Carol A. Rohl +2 more
The model predicts properties that are very different from the observed properties of the EX2 exchange reactions of RNase A in conditions where guanidine-induced unfolding takes place, and results and simulations indicate that moderate or high denaturant concentrations readily give rise to EX1 exchange in native proteins.
Journal of Molecular BiologyFolding intermediates of wild-type and mutants of barnase. II. correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate
30 Citations1998Paul A. Dalby, Jane Clarke +2 more
This work has measured the stability of the folding intermediate of barnase (I) in 2H2O under a variety of conditions and calculated its population at different temperatures and found that changes in kinetics correlates with the change in the population of the folded intermediate.
Journal of Molecular BiologyDisulfide Mutants of Barnase II: Changes in Structure and Local Stability Identified by Hydrogen Exchange
29 Citations1995Jane Clarke, Andrea M. Hounslow +1 more
The hydrogen exchange behaviour of two stabilised disulfide mutants of barnase has been examined using NMR H/2H exchange measurements and it is found that disulfides can stabilise or destabilise local structures as well as having an effect upon global stability.
BiochemistryUnusual Effects of an Engineered Disulfide on Global and Local Protein Stability
29 Citations1996Stephen F. Betz, Jennifer L. Marmorino +4 more
Observations about local stability changes for hydrophobic core residues seem to be greater than the global stability change, which is interpreted as cross-link-induced changes in exchange competent states and relate them to changes in the denatured state.
Journal of Molecular BiologyReduction in the amide hydrogen exchange rates of an anti-lysozyme Fv fragment due to formation of the Fv-Lysozyme complex
26 Citations1997D. Clive Williams, Gordon S. Rule +2 more
The Fv fragment of the monoclonal antibody D1.3.3 Fv was expressed in bacteria and reduced dynamics are a general feature of antibody binding to antigen.
Journal of Molecular BiologyMultiple cycles of global unfolding of GroEL-bound cyclophilin A evidenced by NMR
26 Citations1997Sabine E. Nieba-Axmann, Marcel Ottiger +2 more
GroE, the chaperonin system of Escherichia coli, prevents the aggregation of partially folded or misfolded proteins by complexing them in a form competent for subsequent folding to the native state, and protection factors were found to be quite uniform along the sequence suggesting that CypA with native-like structure undergoes multiple cycles of unfolding while bound to GroEL, which are faster than unfolding in free solution.
Biochemical and Biophysical Research CommunicationsA novel application of nuclear Overhauser enhancement (NOE) in proteins: Analysis of correlated events in the exchange of internal labile protons
26 Citations1980Gerhard Wagner
A quantitative evaluation of nuclear Overhauser enhancements between slowly exchanging labile protons in a globular protein can be used to decide between correlated and uncorrelated exchange processes.
BiochemistryInfluence of N-Cap Mutations on the Structure and Stability of <i>Escherichia coli</i> HPr
26 Citations1996Roopa Thapar, Eric M. Nicholson +4 more
Three mutants of E. coli HPr are characterized: Ser46 has been mutated to an Asp, Asn, and Ala in S46D, S46N, and S46A HPrs, respectively, and results indicate that these N-cap replacements have a marked influence on helix B stability.
Journal of Biomolecular NMRComparison of amide proton exchange in reduced and oxidizedRhodobacter capsulatus cytochrome c2: A1H−15N NMR study
25 Citations1991Paul R. Gooley, Dezheng Zhao +1 more
Journal of Molecular BiologyLow Energy of Activation for Amide Hydrogen Exchange Reactions in Proteins Supports a Local Unfolding Model
18 Citations1993Niels Kirk Thomsen, Flemming M. Poulsen
Hydrogen exchange reactions of amides in hen egg white lysozyme that are pH dependent and have a low energy of activation have been shown to be in accordance with a reaction mechanism in two steps, an equilibrium step and an exchange step, which is not in agreement with the model proposed.
European Journal of BiochemistryHydrogen Exchange in the Carbon Monoxide Complex of Soybean Leghemoglobin
18 Citations1996Dimitrios Morikis, Peter E. Wright
The F-helix, which is located on the proximal side of the heme pocket and is well formed in solution as demonstrated by characteristic medium range NOE connectivities, exhibits fast exchange for all amide protons, which may be functionally important in facilitating movement of the helix upon ligand binding.
Protein ScienceNMR studies of structure, hydrogen exchange, and main‐chain dynamics in a disrupted‐core mutant of thioredoxin
17 Citations1996Robert de Lorimier, Homme W. Hellinga +1 more
Study of a core‐packing mutant of thioredoxin, L78K, in which a leucine residue is substituted by lysine, using 15N heteronuclear two‐ and three‐dimensional NMR reveals that mispacking of the protein core in one location affects local dynamics and stability throughout.
BiochemistryThree-Dimensional Solution Structure and Stability of Phage 434 Cro Protein<sup>,</sup>
17 Citations1997S. Padmanabhan, M. Ángeles Jiménez +4 more
Values for 434 Cro stability show good correspondence to the free energy for global unfolding determined by NMR hydrogen exchange measurements for the slowest exchanging amide protons, as indicated by coincident urea denaturation curves from circular dichroism and intrinsic fluorescence measurements.
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13 Citations1996Michael D. Finucane, Oleg Jardetzky
The pH dependence of amide proton exchange rates have been measured for trp‐repressor, and one class of protons exchanges too fast to be measured in these experiments, which characterized by much higher protection against exchange at higher pH.
Journal of Molecular BiologyThermodynamic hierarchy and local energetics of folded proteins
13 Citations1997Hong Qian
A hierarchical thermodynamic analysis is presented for the protein energetics, which includes both global two-state folding-unfolding transition and local cooperative fluctuations within the folded state.
Biophysical ChemistryHydrogen exchange and the unfolding pathway of ribonuclease A
9 Citations1996Thomas Kiefhaber, Robert L. Baldwin
It is shown here that any such unfolding intermediates must have large protection factors because the EX2 reactions of ribonuclease A under these unfolding conditions have protection factors > or = 2500.
BiopolymersA two-dimensional NMR study of exchange behavior of amide hydrogens in a lysozyme derivative with an extra cross-link between Glu35 and Trp 108—quenching of cooperative fluctuations and effects on the protein stability
8 Citations1997Yasuo Noda, Yasuo Fukuda +1 more
The contribution of cross-linking to the stabilization of the folded structure of protein by cross-link results in the great suppression of large-scale and concerted motions in the cross-linked lysozyme.
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