151
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Abstract
The strong correlation between protein folding rates and the contact order suggests that folding rates are largely determined by the topology of the native structure. However, for a given topology, there may be several possible low free energy paths to the native state and the path that is chosen (the lowest free energy path) may depend on differences in interaction energies and local free energies of ordering in different parts of the structure. For larger proteins whose folding is assisted by chaperones, such as the Escherichia coli chaperonin GroEL, advances have been made in understanding both the aspects of an unfolded protein that GroEL recognizes and the mode of binding to the chaperonin. The possibility that GroEL can remove non-native proteins from kinetic traps by unfolding them either during polypeptide binding to the chaperonin or during the subsequent ATP-dependent formation of folding-active complexes with the co-chaperonin GroES has also been explored.
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Affiliation(s)
- V Grantcharova
- Center for Genomics Research, Harvard University, Cambridge, MA 02138, USA
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152
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Abstract
The basic rules governing the folding of small, single-domain proteins are being discovered. New algorithms that can predict the major features of the folding process give the opportunity to design and optimise protein folding in a rational way. Recent experimental works suggest that sequence-specific features should be integrated in folding models to improve their performance.
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Affiliation(s)
- R Guerois
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany.
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153
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Gunasekaran K, Eyles SJ, Hagler AT, Gierasch LM. Keeping it in the family: folding studies of related proteins. Curr Opin Struct Biol 2001; 11:83-93. [PMID: 11179896 DOI: 10.1016/s0959-440x(00)00173-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigators have recently turned to studies of protein families to shed light on the mechanism of protein folding. In small proteins for which detailed analysis has been performed, recent studies show that transition-state structure is generally conserved. The number and structures of populated folding intermediates have been found to vary in homologous families of larger (greater than 100-residue) proteins, reflecting a balance of local and global interactions.
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Affiliation(s)
- K Gunasekaran
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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154
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Cecconi F, Micheletti C, Carloni P, Maritan A. Molecular dynamics studies on HIV-1 protease: Drug resistance and folding pathways. Proteins 2001. [DOI: 10.1002/prot.1049] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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155
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Guerois R, Serrano L. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J Mol Biol 2000; 304:967-82. [PMID: 11124040 DOI: 10.1006/jmbi.2000.4234] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the relationships between protein topology, amino acid sequence and folding mechanisms, the folding transition state of the Sso7d protein has been characterised both experimentally and theoretically. Although Sso7d protein has a similar topology to that of the SH3 domains, the structure of its transition state is different from that of alpha-spectrin and src SH3 domains previously studied. The folding algorithm, Fold-X, including an energy function with specific sequence features, accounts for these differences and reproduces with a good agreement the set of experimental phi(double dagger-U) values obtained for the three proteins. Our analysis shows that taking into account sequence features underlying protein topology is critical for an accurate prediction of the folding process.
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Affiliation(s)
- R Guerois
- EMBL, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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156
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Rath A, Davidson AR. The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis. Protein Sci 2000; 9:2457-69. [PMID: 11206067 PMCID: PMC2144507 DOI: 10.1110/ps.9.12.2457] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We have characterized the thermodynamic stability of the SH3 domain from the Saccharomyces cerevisiae Abp1p protein and found it to be relatively low compared to most other SH3 domains, with a Tm of 60 degrees C and a deltaGu of 3.08 kcal/mol. Analysis of a large alignment of SH3 domains led to the identification of atypical residues at eight positions in the wild-type Abp1p SH3 domain sequence that were subsequently replaced by the residue seen most frequently at that position in the alignment. Three of the eight mutants constructed in this way displayed increases in Tm ranging from 8 to 15 degrees C with concomitant increases in deltaGu of up to 1.4 kcal/mol. The effects of these substitutions on folding thermodynamics and kinetics were entirely additive, and a mutant containing all three was dramatically stabilized with a Tm greater than 90 degrees C and a deltaGu more than double that of the wild-type domain. The folding rate of this hyperstable mutant was 10-fold faster than wild-type, while its unfolding rate was fivefold slower. All of the stabilized mutants were still able to bind a target peptide with wild-type affinity. We have analyzed the stabilizing amino acid substitutions isolated in this study and several other similar sequence alignment based studies. In approximately 25% of cases, increased stability can be explained by enhanced propensity of the substituted residue for the local backbone conformation at the mutagenized site.
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Affiliation(s)
- A Rath
- Department of Biochemistry, University of Toronto, Ontario, Canada
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157
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Vega MC, Martínez JC, Serrano L. Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot. Protein Sci 2000; 9:2322-8. [PMID: 11206053 PMCID: PMC2144520 DOI: 10.1110/ps.9.12.2322] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Residue Asn47 at position L1 of a type II' beta-turn of the alpha-spectrin SH3 domain is located in a disallowed region of the Ramachandran plot (phi = 56 +/- 12, psi = -118 +/- 17). Therefore, it is expected that replacement of Asn47 by Gly should result in a considerable stabilization of the protein. Thermodynamic analysis of the N47G and N47A mutants shows that the change in free energy is small (approximately 0.7 kcal/mol; approximately 3 kJ/mol) and comparable to that found when mutating a Gly to Ala in a alpha-helix or beta-sheet. X-ray structural analysis of these mutants shows that the conformation of the beta-turn does not change upon mutation and, therefore, that there is no relaxation of the structure, nor is there any gain or loss of interactions that could explain the small energy change. Our results indicate that the energetic definition of II' region of the Ramachandran plot (phi = 60 +/- 30, psi = -115 +/- 15) should be revised for at least Ala and Asn in structure validation and protein design.
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158
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Abstract
The high structural resolution of the main transition states for the formation of native structure for the six small proteins of which Phi-values for a large set of mutants have become available, barstar, barnase, chymotrypsin inhibitor 2, Arc repressor, the src SH3 domain, and a tetrameric p53 domain reveals that for the first 5 of these proteins: (1) Residues that belong to regular secondary structure have a significantly larger average fraction of native structural consolidation than residues in loops; (2) on the other hand, secondary and tertiary structures have built up to the same degree, or at least a high degree, but nonuniformly distributed over the molecule; (3) the most consolidated parts of each protein molecule in the transition state cluster together, and these clusters contain a significantly higher percentage of residues that belong to regular secondary structure than the rest of the molecule. These observations further reconcile the framework model with the nucleation-condensation mechanism for folding: The amazing speed of protein folding can be understood as caused by the catalytic effect of the formation of clusters of residues which have particularly high preferences for the early formation of regular secondary structure in the presence of significant amounts of tertiary structure interactions.
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Affiliation(s)
- B Nölting
- Prussian Private Institute of Technology at Berlin, Berlin, Germany.
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159
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160
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Larson SM, Davidson AR. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci 2000; 9:2170-80. [PMID: 11152127 PMCID: PMC2144485 DOI: 10.1110/ps.9.11.2170] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The SH3 domain, comprised of approximately 60 residues, is found within a wide variety of proteins, and is a mediator of protein-protein interactions. Due to the large number of SH3 domain sequences and structures in the databases, this domain provides one of the best available systems for the examination of sequence and structural conservation within a protein family. In this study, a large and diverse alignment of SH3 domain sequences was constructed, and the pattern of conservation within this alignment was compared to conserved structural features, as deduced from analysis of eighteen different SH3 domain structures. Seventeen SH3 domain structures solved in the presence of bound peptide were also examined to identify positions that are consistently most important in mediating the peptide-binding function of this domain. Although residues at the two most conserved positions in the alignment are directly involved in peptide binding, residues at most other conserved positions play structural roles, such as stabilizing turns or comprising the hydrophobic core. Surprisingly, several highly conserved side-chain to main-chain hydrogen bonds were observed in the functionally crucial RT-Src loop between residues with little direct involvement in peptide binding. These hydrogen bonds may be important for maintaining this region in the precise conformation necessary for specific peptide recognition. In addition, a previously unrecognized yet highly conserved beta-bulge was identified in the second beta-strand of the domain, which appears to provide a necessary kink in this strand, allowing it to hydrogen bond to both sheets comprising the fold.
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Affiliation(s)
- S M Larson
- Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada
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161
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Rodriguez HM, Vu DM, Gregoret LM. Role of a solvent-exposed aromatic cluster in the folding of Escherichia coli CspA. Protein Sci 2000; 9:1993-2000. [PMID: 11106173 PMCID: PMC2144470 DOI: 10.1110/ps.9.10.1993] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Escherichia coli CspA is a member of the cold shock protein family. All cold shock proteins studied to date fold rapidly by an apparent two-state mechanism. CspA contains an unusual cluster of aromatic amino acids on its surface that is necessary for nucleic acid binding and also provides stability to CspA (Hillier et al., 1998). To elucidate the role this aromatic cluster plays in the determining the folding rate and pathway of CspA, we have studied the folding kinetics of mutants containing either leucine or serine substituted for Phe 18, Phe20, and/or Phe31. The leucine substitutions are found to accelerate folding and the serine substitutions to decelerate folding. Because these residues exert effects on the free energy of the folding transition state, they may be necessary for nucleating folding. They are not responsible, however, for the very compact, native-like transition state ensemble seen in the cold shock proteins, as the refolding rates of the mutants all show a similar, weak dependence of unfolding rate on denaturant concentration. Using mutant cycle analysis, we show that there is energetic coupling among the three residues between the unfolded and transition states, suggesting that the cooperative nature of these interactions helps to determine the unfolding rate. Overall, our results suggest that separate evolutionary pressures can act simultaneously on the same group of residues to maintain function, stability, and folding rate.
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Affiliation(s)
- H M Rodriguez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
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162
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Grantcharova VP, Riddle DS, Baker D. Long-range order in the src SH3 folding transition state. Proc Natl Acad Sci U S A 2000; 97:7084-9. [PMID: 10860975 PMCID: PMC16503 DOI: 10.1073/pnas.97.13.7084] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One of the outstanding questions in protein folding concerns the degree of heterogeneity in the folding transition state ensemble: does a protein fold via a large multitude of diverse "pathways," or are the elements of native structure assembled in a well defined order? Herein, we build on previous point mutagenesis studies of the src SH3 by directly investigating the association of structural elements and the loss of backbone conformational entropy during folding. Double-mutant analysis of polar residues in the distal beta-hairpin and the diverging turn indicates that the hydrogen bond network between these elements is largely formed in the folding transition state. A 10-glycine insertion in the n-src loop (which connects the distal hairpin and the diverging turn) and a disulfide crosslink at the base of the distal beta-hairpin exclusively affect the folding rate, showing that these structural elements are nearly as ordered in the folding transition state as in the native state. In contrast, crosslinking the base of the RT loop or the N and C termini dramatically slows down the unfolding rate, suggesting that dissociation of the termini and opening of the RT loop precede the rate-limiting step in unfolding. Taken together, these results suggest that essentially all conformations in the folding transition state ensemble have the central three-stranded beta-sheet formed, indicating that, for the src homology 3 domain, there is a discrete order to structure assembly during folding.
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Affiliation(s)
- V P Grantcharova
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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163
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Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:87-152. [PMID: 10751944 DOI: 10.1016/s0065-3233(00)53003-4] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- J N Onuchic
- Department of Physics, University of California at San Diego, La Jolla 92093-0319, USA
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164
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Affiliation(s)
- O Bilsel
- Department of Chemistry, Pennsylvania State University, University Park 16802, USA
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165
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Serrano L. The relationship between sequence and structure in elementary folding units. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:49-85. [PMID: 10751943 DOI: 10.1016/s0065-3233(00)53002-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- L Serrano
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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166
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Plotkin SS, Onuchic JN. Investigation of routes and funnels in protein folding by free energy functional methods. Proc Natl Acad Sci U S A 2000; 97:6509-14. [PMID: 10841554 PMCID: PMC18640 DOI: 10.1073/pnas.97.12.6509] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can lower the free energy barrier to folding. Correlating stronger contact energies with entropically likely contacts of a given native structure lowers the barrier, and anticorrelating the energies has the reverse effect. Designing in relatively mild energetic heterogeneity can eliminate the barrier completely at the transition temperature. Sequences with native energies tuned to fold uniformly, as well as sequences tuned to fold reliably by a single or a few routes, are rare. Sequences with weak native energetic heterogeneity are more common; their folding kinetics is more strongly determined by properties of the native structure. Sequences with different distributions of stability throughout the protein may still be good folders to the same structure. A measure of folding route narrowness is introduced that correlates with rate and that can give information about the intrinsic biases in ordering arising from native topology. This theoretical framework allows us to investigate systematically the coupled effects of energy and topology in protein folding and to interpret recent experiments that investigate these effects.
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Affiliation(s)
- S S Plotkin
- Department of Physics, University of California at San Diego, La Jolla, CA 92093-5003, USA.
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167
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Narita M, Mochizuki A, Ohuchi S. Assingments of Tri- and Tetrapeptide Sequences in Globular Proteins to the 18 Kinds of Local Structures along Helices and Their Propensities for Specific Local Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2000. [DOI: 10.1246/bcsj.73.1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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168
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Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 2000; 298:937-53. [PMID: 10801360 DOI: 10.1006/jmbi.2000.3693] [Citation(s) in RCA: 954] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small, fast-folding proteins. To investigate the extent of the topological control of the folding process, we studied the folding of simplified models of five small globular proteins constructed using a Go-like potential to retain the information about the native structures but drastically reduce the energetic frustration and energetic heterogeneity among residue-residue native interactions. By comparing the structure of the transition state ensemble (experimentally determined by Phi-values) and of the intermediates with those obtained using our models, we show that these energetically unfrustrated models can reproduce the global experimentally known features of the transition state ensembles and "en-route" intermediates, at least for the analyzed proteins. This result clearly indicates that, as long as the protein sequence is sufficiently minimally frustrated, topology plays a central role in determining the folding mechanism.
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Affiliation(s)
- C Clementi
- Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA.
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169
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Abstract
We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotrypsin inhibitor 2 (CI2) with an implicit solvation model for a total simulation time of 0.4 microseconds. Folding requires that the three-dimensional structure of the native state is known. It was simulated at 300 K by supplementing the force field with a harmonic restraint which acts on the root-mean-square deviation and allows to decrease the distance to the target conformation. High temperature and/or the harmonic restraint were used to induce unfolding. Of the 62 folding simulations started from random conformations, 31 reached the native structure, while the success rate was 83% for the 66 trajectories which began from conformations unfolded by high-temperature dynamics. A funnel-like energy landscape is observed for unfolding at 475 K, while the unfolding runs at 300 K and 375 K as well as most of the folding trajectories have an almost flat energy landscape for conformations with less than about 50% of native contacts formed. The sequence of events, i.e., secondary and tertiary structure formation, is similar in all folding and unfolding simulations, despite the diversity of the pathways. Previous unfolding simulations of CI2 performed with different force fields showed a similar sequence of events. These results suggest that the topology of the native state plays an important role in the folding process.
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Affiliation(s)
- P Ferrara
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
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170
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Crane JC, Koepf EK, Kelly JW, Gruebele M. Mapping the transition state of the WW domain beta-sheet. J Mol Biol 2000; 298:283-92. [PMID: 10764597 DOI: 10.1006/jmbi.2000.3665] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The folding kinetics of a three-stranded antiparallel beta-sheet (WW domain) have been measured by temperature jump relaxation. Folding and activation free energies were determined as a function of temperature for both the wild-type and the mutant domain, W39F, which modifies the beta(2)-beta(3) hydrophobic interface. The folding rate decreases at higher temperatures as a result of the increase in the activation free energy for folding. Phi-Values were obtained for thermal perturbations allowing the primary features of the folding free energy surface to be determined. The results of this analysis indicate a significant shift from an "early" (Phi(T)=0. 4) to a "late" (Phi(T)=0.8) transition state with increasing temperature. The temperature-dependent Phi-value analysis of the wild-type WW domain and of its more stable W39F hydrophobic cluster mutant reveals little participation of residue 39 in the transition state at lower temperature. As the temperature is raised, hydrophobic interactions at the beta(2)-beta(3) interface gain importance in the transition state and the barrier height of the wild-type, which contains the larger tryptophan residue, increases more slowly than the barrier height of the mutant.
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Affiliation(s)
- J C Crane
- School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, Urbana, IL 61801, USA
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171
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Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D. Evolutionary conservation in protein folding kinetics. J Mol Biol 2000; 298:303-12. [PMID: 10764599 DOI: 10.1006/jmbi.1999.3663] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sequence and structural conservation of folding transition states have been predicted on theoretical grounds. Using homologous sequence alignments of proteins previously characterized via coupled mutagenesis/kinetics studies, we tested these predictions experimentally. Only one of the six appropriately characterized proteins exhibits a statistically significant correlation between residues' roles in transition state structure and their evolutionary conservation. However, a significant correlation is observed between the contributions of individual sequence positions to the transition state structure across a set of homologous proteins. Thus the structure of the folding transition state ensemble appears to be more highly conserved than the specific interactions that stabilize it.
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Affiliation(s)
- K W Plaxco
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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172
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Kortemme T, Kelly MJ, Kay LE, Forman-Kay J, Serrano L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J Mol Biol 2000; 297:1217-29. [PMID: 10764585 DOI: 10.1006/jmbi.2000.3618] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have expanded our description of the energy landscape for folding of the SH3 domain of chicken alpha-spectrin by a detailed structural characterization of its denatured state ensemble (DSE). This DSE is significantly populated under mildly acidic conditions in equilibrium with the folded state. Evidence from heteronuclear nuclear magnetic resonance (NMR) experiments on (2)H, (15)N-labeled protein suggests the presence of conformers whose residual structure bears some resemblence to the structure of the folding transition state of this protein. NMR analysis in a mutant with an engineered, non-native alpha-helical tendency shows a significant amount of local non-native structure in the mutant, while the overall characteristics of the DSE are unchanged. Comparison with recent theoretical predictions of SH3 domain folding reactions reveals an interesting correlation with the predicted early events. Based on these results and recent data from other systems, we propose that the DSE of a protein will resemble the intermediate or transition state of its nearest rate-limiting step, as a consequence of simple energetic and kinetic principles.
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Affiliation(s)
- T Kortemme
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, D-6917, Germany.
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173
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Hamill SJ, Steward A, Clarke J. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J Mol Biol 2000; 297:165-78. [PMID: 10704314 DOI: 10.1006/jmbi.2000.3517] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
TNfn3, the third fibronectin type III domain of human tenascin, is an immunoglobulin-like protein that is a good model for experimental and theoretical analyses of Greek key folding. The third fibronectin type III domain of human tenascin folds and unfolds in a two-state fashion over a range of temperature and pH values, and in the presence of stabilising salts. Here, we present a high resolution protein engineering analysis of the single rate determining transition state. The 48 mutations report on the contribution of side-chains at 32 sites in the core and loop regions. Three areas in the protein exhibit high Phi-values, indicating that they are partially structured in the transition state. First, a common-core ring of four positions in the central strands B, C, E and F, that are in close contact, form a nucleus of tertiary interactions. The two other regions that appear well-formed are the C' region and the E-F loop. The Phi-values gradually decrease away from these regions such that the very ends of the two terminal strands A and G, have Phi-values of zero. We propose a model for the folding of immunoglobulin-like proteins in which the common-core "ring" forms the nucleus for folding, whilst the C' and E-F regions are constrained by topology to pack early. Folding characteristics of a group of structurally related proteins appear to support this model.
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Affiliation(s)
- S J Hamill
- MRC Centre Protein Engineering, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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174
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Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Identifying the protein folding nucleus using molecular dynamics. J Mol Biol 2000; 296:1183-8. [PMID: 10698625 DOI: 10.1006/jmbi.1999.3534] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as "accelerator pedals" used by molecular evolution to control protein folding rate.
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Affiliation(s)
- N V Dokholyan
- Physics Department, Center for Polymer Studies, Boston, MA 02215, USA
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175
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Ma B, Nussinov R. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. J Mol Biol 2000; 296:1091-104. [PMID: 10686106 DOI: 10.1006/jmbi.2000.3518] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
How is the native structure encoded in the amino acid sequence? For the traditional backbone centric view, the dominant forces are hydrogen bonds (backbone) and phi-psi propensity. The role of hydrophobicity is non-specific. For the side-chain centric view, the dominant force of protein folding is hydrophobicity. In order to understand the balance between backbone and side-chain forces, we have studied the contributions of three components of a beta-hairpin peptide: turn, backbone hydrogen bonding and side-chain interactions, of a 16-residue fragment of protein G. The peptide folds rapidly and cooperatively to a conformation with a defined secondary structure and a packed hydrophobic cluster of aromatic side-chains. Our strategy is to observe the structural stability of the beta-hairpin under systematic perturbations of the turn region, backbone hydrogen bonds and the hydrophobic core formed by the side-chains, respectively. In our molecular dynamics simulations, the peptides are solvated. with explicit water molecules, and an all-atom force field (CFF91) is used. Starting from the original peptide (G41EWTYDDATKTFTVTE56), we carried out the following MD simulations. (1) unfolding at 350 K; (2) forcing the distance between the C(alpha) atoms of ASP47 and LYS50 to be 8 A; (3) deleting two turn residues (Ala48 and Thr49) to form a beta-sheet complex of two short peptides, GEWTYDD and KTFTVTE; (4) four hydrophobic residues (W43, Y45, F52 and T53) are replaced by a glycine residue step-by-step; and (5) most importantly, four amide hydrogen atoms (T44, D46, T53, and T55, which are crucial for backbone hydrogen bonding), are substituted by fluorine atoms. The fluorination not only makes it impossible to form attractive hydrogen bonding between the two beta-hairpin strands, but also introduces a repulsive force between the two strands due to the negative charges on the fluorine and oxygen atoms. Throughout all simulations, we observe that backbone hydrogen bonds are very sensitive to the perturbations and are easily broken. In contrast, the hydrophobic core survives most perturbations. In the decisive test of fluorination, the fluorinated peptide remains folded under our simulation conditions (5 ns, 278 K). Hydrophobic interactions keep the peptide folded, even with a repulsive force between the beta-strands. Thus, our results strongly support a side-chain centric view for protein folding.
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Affiliation(s)
- B Ma
- Laboratory of Experimental and Computational Biology, NCI-FCRDC, Bldg 469 Rm 151, Frederick, MD 21702, USA
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176
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Brockwell DJ, Smith DA, Radford SE. Protein folding mechanisms: new methods and emerging ideas. Curr Opin Struct Biol 2000; 10:16-25. [PMID: 10679463 DOI: 10.1016/s0959-440x(99)00043-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
During the past year, advances in our understanding of folding mechanisms have been made through detailed experimental and theoretical studies of a number of proteins. The development of new methods has allowed the earliest events in folding to be probed and the measurement of folding at the level of individual molecules is now possible, opening the door to exciting new experiments.
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Affiliation(s)
- D J Brockwell
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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177
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Nymeyer H, Socci ND, Onuchic JN. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proc Natl Acad Sci U S A 2000; 97:634-9. [PMID: 10639131 PMCID: PMC15382 DOI: 10.1073/pnas.97.2.634] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a method for determining structural properties of the ensemble of folding transition states from protein simulations. This method relies on thermodynamic quantities (free energies as a function of global reaction coordinates, such as the percentage of native contacts) and not on "kinetic" measurements (rates, transmission coefficients, complete trajectories); consequently, it requires fewer computational resources compared with other approaches, making it more suited to large and complex models. We explain the theoretical framework that underlies this method and use it to clarify the connection between the experimentally determined Phi value, a quantity determined by the ratio of rate and stability changes due to point mutations, and the average structure of the transition state ensemble. To determine the accuracy of this thermodynamic approach, we apply it to minimalist protein models and compare these results with the ones obtained by using the standard experimental procedure for determining Phi values. We show that the accuracy of both methods depends sensitively on the amount of frustration. In particular, the results are similar when applied to models with minimal amounts of frustration, characteristic of rapid-folding, single-domain globular proteins.
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Affiliation(s)
- H Nymeyer
- Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA.
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178
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Cota E, Clarke J. Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module. Protein Sci 2000; 9:112-20. [PMID: 10739253 PMCID: PMC2144439 DOI: 10.1110/ps.9.1.112] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
An analysis of the folding of the 94 residue tenth fibronectin type III (fnIII) domain of human fibronectin (FNfn10) is presented. Use of guanidine isothiocyanate as a denaturant allows us to obtain equilibrium and kinetic data across a broad range of denaturant concentrations that are unavailable in guanidine hydrochloride. Equilibrium unfolding experiments show that FNfn10 is significantly more stable than has been reported previously. Comparison of equilibrium and kinetic parameters reveals the presence of an intermediate that accumulates at low denaturant concentrations. This is the first demonstration of three-state folding kinetics for a fnIII domain. We have previously shown that a homologous domain from human tenascin (TNfn3) folds by a two-state mechanism, but this does not necessarily indicate that the two proteins fold by different folding pathways.
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Affiliation(s)
- E Cota
- MRC Centre for Protein Engineering and Cambridge University Chemical Laboratory, United Kingdom
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179
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Ternström T, Mayor U, Akke M, Oliveberg M. From snapshot to movie: phi analysis of protein folding transition states taken one step further. Proc Natl Acad Sci U S A 1999; 96:14854-9. [PMID: 10611302 PMCID: PMC24737 DOI: 10.1073/pnas.96.26.14854] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinetic anomalies in protein folding can result from changes of the kinetic ground states (D, I, and N), changes of the protein folding transition state, or both. The 102-residue protein U1A has a symmetrically curved chevron plot which seems to result mainly from changes of the transition state. At low concentrations of denaturant the transition state occurs early in the folding reaction, whereas at high denaturant concentration it moves close to the native structure. In this study we use this movement to follow continuously the formation and growth of U1A's folding nucleus by phi analysis. Although U1A's transition state structure is generally delocalized and displays a typical nucleation-condensation pattern, we can still resolve a sequence of folding events. However, these events are sufficiently coupled to start almost simultaneously throughout the transition state structure.
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Affiliation(s)
- T Ternström
- Department of Biochemistry, Lund University, S-221 00 Lund, Sweden
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180
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Abstract
During protein folding, many of the events leading to secondary and tertiary structure occur in milliseconds or faster. Modern nuclear magnetic resonance and laser detection techniques, coupled with fast initiation of the folding reaction, are probing these events in great detail. Theory, ranging from analytical models to molecular dynamics calculations, is beginning to match up with experiment. As a result, timescales, from such elementary steps as the addition of a residue to a helix to strange kinetics of collapsing protein backbones, can now be measured and interpreted.
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Affiliation(s)
- M Gruebele
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL 61801, USA.
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181
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Galzitskaya OV, Finkelstein AV. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci U S A 1999; 96:11299-304. [PMID: 10500171 PMCID: PMC18028 DOI: 10.1073/pnas.96.20.11299] [Citation(s) in RCA: 278] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
When a protein folds or unfolds, it has to pass through many half-folded microstates. Only a few of them can be seen experimentally. In a two-state transition proceeding with no accumulation of metastable intermediates [Fersht, A. R. (1995) Curr. Opin. Struct. Biol. 5, 79-84], only the semifolded microstates corresponding to the transition state can be outlined; they influence the folding/unfolding kinetics. Our aim is to calculate them, provided the three-dimensional protein structure is given. The presented approach follows from the capillarity theory of protein folding and unfolding [Wolynes, P. G. (1997) Proc. Natl. Acad. Sci. USA 94, 6170-6175]. The approach is based on a search for free-energy saddle point(s) on a network of protein unfolding pathways. Under some approximations, this search is rapidly performed by dynamic programming and, despite its relative simplicity, gives a good correlation with experiment. The computed folding nuclei look like ensembles of those compact and closely packed parts of the three-dimensional native folds that contain a small number of disordered protruding loops. Their estimated free energy is consistent with the rapid (within seconds) folding and unfolding of small proteins at the point of thermodynamic equilibrium between the native fold and the coil.
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Affiliation(s)
- O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
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182
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Alm E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci U S A 1999; 96:11305-10. [PMID: 10500172 PMCID: PMC18029 DOI: 10.1073/pnas.96.20.11305] [Citation(s) in RCA: 318] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Guided by recent experimental results suggesting that protein-folding rates and mechanisms are determined largely by native-state topology, we develop a simple model for protein folding free-energy landscapes based on native-state structures. The configurations considered by the model contain one or two contiguous stretches of residues ordered as in the native structure with all other residues completely disordered; the free energy of each configuration is the difference between the entropic cost of ordering the residues, which depends on the total number of residues ordered and the length of the loop between the two ordered segments, and the favorable attractive interactions, which are taken to be proportional to the total surface area buried by the ordered residues in the native structure. Folding kinetics are modeled by allowing only one residue to become ordered/disordered at a time, and a rigorous and exact method is used to identify free-energy maxima on the lowest free-energy paths connecting the fully disordered and fully ordered configurations. The distribution of structure in these free-energy maxima, which comprise the transition-state ensemble in the model, are reasonably consistent with experimental data on the folding transition state for five of seven proteins studied. Thus, the model appears to capture, at least in part, the basic physics underlying protein folding and the aspects of native-state topology that determine protein-folding mechanisms.
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Affiliation(s)
- E Alm
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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183
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Clarke J, Cota E, Fowler SB, Hamill SJ. Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway. Structure 1999; 7:1145-53. [PMID: 10508783 DOI: 10.1016/s0969-2126(99)80181-6] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Are folding pathways conserved in protein families? To test this explicitly and ask to what extent structure specifies folding pathways requires comparison of proteins with a common fold. Our strategy is to choose members of a highly diverse protein family with no conservation of function and little or no sequence identity, but with structures that are essentially the same. The immunoglobulin-like fold is one of the most common structural families, and is subdivided into superfamilies with no detectable evolutionary or functional relationship. RESULTS We compared the folding of a number of immunoglobulin-like proteins that have a common structural core and found a strong correlation between folding rate and stability. The results suggest that the folding pathways of these immunoglobulin-like proteins share common features. CONCLUSIONS This study is the first to compare the folding of structurally related proteins that are members of different superfamilies. The most likely explanation for the results is that interactions that are important in defining the structure of immunoglobulin-like proteins are also used to guide folding.
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Affiliation(s)
- J Clarke
- Department of Chemistry, Centre for Protein Engineering, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK.
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184
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Moran LB, Schneider JP, Kentsis A, Reddy GA, Sosnick TR. Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. Proc Natl Acad Sci U S A 1999; 96:10699-704. [PMID: 10485889 PMCID: PMC17946 DOI: 10.1073/pnas.96.19.10699] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have investigated the folding behavior of dimeric and covalently crosslinked versions of the 33-residue alpha-helical GCN4-p1 coiled coil derived from the leucine zipper region of the transcriptional activator GCN4. The effects of multisite substitutions indicate that folding occurs along multiple routes with nucleation sites located throughout the protein. The similarity in activation energies of the different routes together with an analysis of intrinsic helical propensities indicate that minimal helix is present before a productive collision of the two chains. However, approximately one-third to one-half of the total helical structure is formed in the postcollision transition state ensemble. For the crosslinked, monomeric version, folding occurs along a single robust pathway. Here, the region nearest the crosslink, with the least helical propensity, is structured in the transition state whereas the region farthest from the tether, with the most propensity, is completely unstructured. Hence, the existence of transition state heterogeneity and the selection of folding routes critically depend on chain topology.
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Affiliation(s)
- L B Moran
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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185
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Abstract
The long-held views on lock-and-key versus induced fit in binding arose from the notion that a protein exists in a single, most stable conformation, dictated by its sequence. However, in solution proteins exist in a range of conformations, which may be described by statistical mechanical laws and their populations follow statistical distributions. Upon binding, the equilibrium will shift in favor of the bound conformation from the ensemble of conformations around the bottom of the folding funnel. Hence here we extend the implications and the usefulness of the folding funnel concept to explain fundamental binding mechanisms.
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Affiliation(s)
- B Ma
- Laboratory of Experimental and Computational Biology and Intramural Research Support Program-SAIC, Laboratory of Experimental and Computational Biology, NCI-FCRDC, Frederick, MD 21702, USA
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186
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Tsai J, Levitt M, Baker D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol 1999; 291:215-25. [PMID: 10438616 DOI: 10.1006/jmbi.1999.2949] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To complement experimental studies of the src SH3 domain folding, we studied 30 independent, high-temperature, molecular dynamics simulations of src SH3 domain unfolding. These trajectories were observed to differ widely from each other. Thus, rather than analyzing individual trajectories, we sought to identify the recurrent features of the high-temperature unfolding process. The conformations from all simulations were combined and then divided into groups based on the number of native contacts. Average occupancies of each side-chain hydrophobic contact and hydrogen bond in the protein were then determined. In the symmetric funnel limit, the occupancies of all contacts should decrease in concert with the loss in total number of native contacts. If there is a lack of symmetry or hierarchy to the unfolding process, the occupancies of some contacts should decrease more slowly, and others more rapidly. Despite the heterogeneity of the individual trajectories, the ensemble averaging revealed an order to the unfolding process: contacts between the N and C-terminal strands are the first to disappear, whereas contacts within the distal beta-hairpin and a hydrogen-bonding network involving the distal loop beta-turn and the diverging turn persist well after the majority of the native contacts are lost. This hierarchy of events resembles but is somewhat less pronounced than that observed in our experimental studies of the folding of src SH3 domain.
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Affiliation(s)
- J Tsai
- Department of Biochemistry, University of Washington, Seattle, WA, 19195, USA
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187
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Mirny LA, Shakhnovich EI. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 1999; 291:177-96. [PMID: 10438614 DOI: 10.1006/jmbi.1999.2911] [Citation(s) in RCA: 303] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we provide an analysis of molecular evolution of five of the most populated protein folds: immunoglobulin fold, oligonucleotide-binding fold, Rossman fold, alpha/beta plait, and TIM barrels. In order to distinguish between "historic", functional and structural reasons for amino acid conservations, we consider proteins that acquire the same fold and have no evident sequence homology. For each fold we identify positions that are conserved within each individual family and coincide when non-homologous proteins are structurally superimposed. As a baseline for statistical assessment we use the conservatism expected based on the solvent accessibility. The analysis is based on a new concept of "conservatism-of-conservatism". This approach allows us to identify the structural features that are stabilized in all proteins having a given fold, despite the fact that actual interactions that provide such stabilization may vary from protein to protein. Comparison with experimental data on thermodynamics, folding kinetics and function of the proteins reveals that such universally conserved clusters correspond to either: (i) super-sites (common location of active site in proteins having common tertiary structures but not function) or (ii) folding nuclei whose stability is an important determinant of folding rate, or both (in the case of Rossman fold). The analysis also helps to clarify the relation between folding and function that is apparent for some folds.
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Affiliation(s)
- L A Mirny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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188
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Abstract
Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly, with a range of complexed conformations. Hence, knowledge of the shape of the folding funnels is biologically very useful. The converse also holds: If kinetic and thermodynamic data are available, hints regarding the role of the protein and its binding selectivity may be obtained. Thus, the utility of the concept of the funnel carries over to the origin of the protein and to its function.
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Affiliation(s)
- C J Tsai
- Laboratory of Experimental and Computational Biology, NCI-FCRDC, Frederick, Maryland 21702, USA
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189
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Affiliation(s)
- S E Radford
- School of Biochemistry and Molecular Biology, University of Leeds, United Kingdom
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190
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Thirumalai D, Klimov DK. Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol 1999; 9:197-207. [PMID: 10322218 DOI: 10.1016/s0959-440x(99)80028-1] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Considerable insights into the mechanisms and timescales of protein folding have been obtained from detailed studies of minimal off-lattice models. These models are coarse-grained representations of polypeptide chains. Many novel predictions of the mechanisms and timescales of the folding of proteins have been made using simulations of off-lattice models. The concepts derived from these simulations have been used to analyze the recent experiments and simulations of proteins and peptides.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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191
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Abstract
There has been considerable progress made over the past year in linking experimental and theoretical approaches to protein folding. Recent results from several independent lines of investigation suggest that protein folding mechanisms and landscapes are largely determined by the topology of the native state and are relatively insensitive to details of the interatomic interactions. This dependence on low-resolution structural features, rather than high-resolution detail, suggests that it should be possible to describe the fundamental physics of the folding process using relatively low-resolution models. Recent experiments have set benchmarks for testing new models and progress has been made in developing theoretical models for interpreting and predicting experimental results.
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Affiliation(s)
- E Alm
- Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195, USA
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192
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Goldberg JM, Baldwin RL. A specific transition state for S-peptide combining with folded S-protein and then refolding. Proc Natl Acad Sci U S A 1999; 96:2019-24. [PMID: 10051587 PMCID: PMC26729 DOI: 10.1073/pnas.96.5.2019] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the alpha-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the alpha-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of -0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state.
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Affiliation(s)
- J M Goldberg
- Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307, USA.
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193
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194
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Dobson CM, Karplus M. The fundamentals of protein folding: bringing together theory and experiment. Curr Opin Struct Biol 1999; 9:92-101. [PMID: 10047588 DOI: 10.1016/s0959-440x(99)80012-8] [Citation(s) in RCA: 313] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimental and theoretical studies together are providing insights into the mechanism by which proteins fold. Our present knowledge of the essential aspects of the folding reaction is outlined and some approaches, both theoretical and experimental, that are being developed to obtain a more detailed understanding of this complex process are described.
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Affiliation(s)
- C M Dobson
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QT, UK.
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195
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Abstract
The folding reactions of some small proteins show clear evidence of a hierarchic process, whereas others, lacking detectable intermediates, do not. Evidence from folding intermediates and transition states suggests that folding begins locally, and that the formation of native secondary structure precedes the formation of tertiary interactions, not the reverse. Some notable examples in the literature have been interpreted to the contrary. For these examples, we have simulated the local structures that form when folding begins by using the LINUS program with nonlocal interactions turned off. Our results support a hierarchic model of protein folding.
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Affiliation(s)
- R L Baldwin
- Dept of Biochemistry, Beckman Center, Stanford University Medical Center, School of Medicine, CA 94305-5307, USA
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196
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Shakhnovich EI. Folding nucleus: specific or multiple? Insights from lattice models and experiments. FOLDING & DESIGN 1999; 3:R108-11; discussion R107. [PMID: 9889170 DOI: 10.1016/s1359-0278(98)00056-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- E I Shakhnovich
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA 02138, USA.
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197
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Thirumalai D, Klimov DK. Fishing for folding nuclei in lattice models and proteins. FOLDING & DESIGN 1999; 3:R112-8; discussion R107. [PMID: 9889171 DOI: 10.1016/s1359-0278(98)00057-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- D Thirumalai
- Institute for Advanced Studies, Hebrew University of Jerusalem, Givat Ram, Israel.
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198
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Villegas V, Martínez JC, Avilés FX, Serrano L. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J Mol Biol 1998; 283:1027-36. [PMID: 9799641 DOI: 10.1006/jmbi.1998.2158] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The transition state for the folding pathway of the activation domain of human procarboxypeptidase A2 (ADA2h) has been analyzed by the protein engineering approach. Recombinant ADA2h is an 81-residue globular domain with no disulfide bridges or cis-prolyl bonds, which follows a two-state folding transition. Its native fold is arranged in two alpha-helices packing against a four-stranded beta-sheet. Application of the protein engineering analysis for 20 single-point mutants spread throughout the whole sequence indicates that the transition state for this molecule is quite compact, possessing some secondary structure and a hydrophobic core in the process of being consolidated. The core (folding nucleus) is made by the packing of alpha-helix 2 and the two central beta-strands. The other two strands, at the edges of the beta-sheet, and alpha-helix 1 seem to be completely unfolded. These results, together with previous analysis of ADA2h with either of its two alpha-helices stabilized through improved local interactions, suggest that alpha-helix 1 does not contribute to the folding nucleus, even though it is partially folded in the denatured state under native conditions. On the other hand, alpha-helix 2 folds partly in the transition state and is part of the folding nucleus. It is suggested that a good strategy to improve folding speed in proteins would be to stabilize the helices that are not folded in the denatured state but are partly present in the transition state. Comparison with other proteins shows that there is no clear relationship between fold and/or size with folding speed and level of structure in the transition state of proteins.
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Affiliation(s)
- V Villegas
- Departament de Bioquímica i Institut de Biologia Fonamental, Universitat Autònoma de Barcelona (UAB), Barcelona, Bellaterra, 08193, Spain
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Gruebele M, Wolynes PG. Satisfying turns in folding transitions. NATURE STRUCTURAL BIOLOGY 1998; 5:662-5. [PMID: 9699621 DOI: 10.1038/1354] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein engineering studies show that conformations in the folding transition state ensemble can be structurally polarized. In two SH3 beta-sheet domains, the formation of hydrophobic contacts goes hand in hand with the formation of the solvated distal loop beta-turn, while large parts of the molecule remain unstructured in the ensemble.
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200
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Grantcharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. NATURE STRUCTURAL BIOLOGY 1998; 5:714-20. [PMID: 9699636 DOI: 10.1038/1412] [Citation(s) in RCA: 253] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Experimental and theoretical studies on the folding of small proteins such as the chymotrypsin inhibitor 2 (CI-2) and the P22 Arc repressor suggest that the folding transition state is an expanded version of the native state with most interactions partially formed. Here we report that this picture does not hold generally: a hydrogen bond network involving two beta-turns and an adjacent hydrophobic cluster appear to be formed in the folding transition state of the src SH3 domain, while the remainder of the polypeptide chain is largely unstructured. Comparison with data on other small proteins suggests that this structural polarization is a consequence of the topology of the SH3 domain fold. The non-uniform distribution of structure in the folding transition state provides a challenging test for computational models of the folding process.
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Affiliation(s)
- V P Grantcharova
- Department of Biochemistry, University of Washington, Seattle 98195, USA
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