Journal of Molecular Biology
Regular articleContact order, transition state placement and the refolding rates of single domain proteins1
Introduction
Numerous theoretical studies have suggested that the size Wolynes 1997, Finkelstein and Badretdinov 1997, Klimov and Thirumalai 1997, Gutin et al 1996, Thirumalai 1995, stability Finkelstein 1991, Sali et al 1994, Bryngelson et al 1995, Onuchic et al 1995, Pande et al 1997 and topology Doyle et al 1997, Gross 1996, Unger and Moult 1996, Wolynes 1996, Abkevich et al 1995, Fersht 1995a, Fersht 1995b, Govindarajan and Goldstein 1995, Karplus and Weaver 1994, Orengo et al 1994, Dill et al 1993 of a protein influence the rate and mechanisms by which it folds. Unfortunately, attempts to demonstrate such relationships (e.g. see Munoz and Serrano 1996, Scalley et al 1998) have been hindered by the difficulties associated with analyzing complex, multiphasic folding kinetics and by the limited amount of experimental evidence available. The recent characterization of the refolding of a number of single domain proteins lacking cis proline residues or disulfide bonds, however, motivated us to re-investigate these relationships. Here we report potentially significant correlations between the folding kinetics and the native, equilibrium properties of a set of kinetically simple, single domain proteins.
Comparisons of the refolding of proteins under differing experimental conditions, of mutant proteins (e.g. Fersht 1995b, Burton et al 1996) and of homologous proteins Kragelund et al 1996, Mines et al 1996, Plaxco et al 1997, Plaxco et al 1998 indicate that minor changes in solvent or sequence can dramatically alter the kinetics of folding. The large range of kinetic behaviors exhibited by a single protein under differing solvent conditions, or by multiple proteins adopting nearly identical folds, suggests that the resolution of sequence and experiment specific effects from the potentially more subtle effects of size, stability and topology might prove very difficult. Our solution to this problem is to search for relationships in a large, diverse data set so that the kinetic consequences of equilibrium properties may be assessed despite this noise. Causal relationships should thus appear as statistically significant, albeit imperfect, correlations between kinetic parameters and equilibrium properties.
Section snippets
Results
We have investigated the influence of three general equilibrium properties, the size, stability and topological complexity of the native state, on the folding kinetics of a non-homologous set of simple single domain proteins. The size (length) and stability (ΔGu) of the native state are easily quantified and were taken directly from the literature. Topological complexity is somewhat more difficult to specify numerically. We have used relative contact order, (CO), which reflects the relative
Discussion
Recent years have seen a large increase in studies of the refolding of simple, single domain proteins. We have used this rapidly increasing data base to investigate the roles played by general, equilibrium properties such as length, topology or stability in defining the rates and mechanisms by which proteins fold. Due to the relatively small size of the data set presently available the results of these investigations should be considered preliminary. However, several statistically significant
Conclusions
The recent characterization of the refolding properties of a number of simple, single domain proteins has provided an opportunity to demonstrate that the relative contact order of the native state is a determinant of both the height and placement of the folding transition state barrier. The influences of other factors, such as equilibrium stability and chain length, are either not apparent or only weakly supported by the test set presently available. No doubt the rapidly increasing protein
Materials and methods
We are aware of 22 monomeric, single domain proteins which lack disulfide bonds and cis proline residues, which have been suggested to fold via two-state kinetics under at least some conditions and for which most of the appropriate structural and kinetic data are available. Multiple members of homologous families were not included in the test set in order to avoid over representation of a single topology or length. Thus, eight of the 22 proteins were excluded because they exhibit significant
Acknowledgements
The authors gratefully acknowledge a long-standing collaboration with Chris Dobson as the source of much of the data used in this analysis. The authors also thank R. Baldwin, H. S. Chan, F. Chiti, K. Dill, V. Daggett, C. Dobson, K. Fiebig, H. Gray, M. Gross, B. Kragelund, T. Oas, M. Scalley, D. Shortle, D. Teller and D. Thirumalai for helpful reviews of this paper and L. Plaxco and I. Ruczinski for invaluable aid and advice on the statistical analysis. We are also deeply indebted to F. Chiti,
References (62)
- et al.
Impact of local and non-local interactions on the thermodynamics and kinetics of protein folding
J. Mol. Biol.
(1995) - et al.
The Protein Data Banka computer-based archival file for macromolecular structures
J. Mol. Biol.
(1977) - et al.
Microsecond protein folding through a compact transition state
J. Mol. Biol.
(1996) - et al.
Folding and stability of a fibronectin type III domain of human tenascin
J. Mol. Biol.
(1997) - et al.
Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
Folding Design
(1997) - et al.
Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family
J. Mol. Biol.
(1996) - et al.
Cytochrome c folding triggered by electron transfer
Chem. Biol.
(1996) - et al.
Local versus non-local interactions in protein folding and stability-an experimentalist’s point of view
Folding Design
(1996) - et al.
On the theory of folding kinetics for short proteins
Folding Design
(1997) - et al.
Comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules
J. Mol. Biol.
(1997)
Kinetic role of early intermediates in protein folding
Curr. Opin. Struc. Biol.
Titration properties and thermodynamics of the transition state for foldingcomparison of two-state and multistate folding pathways
J. Mol. Biol.
Protein denaturation. Part C. Theoretical models for the mechanism of denaturation
Advan. Protein Chem.
Local interactions dominate folding in a simple protein model
J. Mol. Biol.
The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics
J. Mol. Biol.
Favourable native-like helical local interactions can accelerate protein folding
Folding Design
Characterization of the free energy spectrum of peptostreptococcal protein L
Folding Design
Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G
Biochemistry
Principles that govern the folding of protein chains
Science
Funnels, pathways, and the energy landscape of protein foldinga synthesis
Proteins: Struct. Funct. Genet.
Low temperature unfolding of a mutant of phage T4 lysozyme. 2. Kinetic investigations
Biochemistry
From Levinthal to pathways to funnels
Nature Struc. Biol.
Cooperativity in protein-folding kinetics
Proc. Natl Acad. Sci. USA
Local interactions and the optimization of protein folding
Proteins: Struct. Funct. Genet.
Mapping the structures of transition states and intermediates in foldingdelineation of pathways at high resolution
Phil. Trans. Roy. Soc. London
Optimization of rates of protein foldingthe nucleation-condensation mechanism and its implications
Proc. Natl Acad. Sci. U.S.A
Rate of β-structure formation in polypeptides
Proteins: Struct. Funct. Genet.
Theoretical studies of protein folding
Annu. Rev. Biophys. Bioeng.
Optimal local propensities for model proteins
Proteins: Struct. Funct. Genet.
Folding dynamics of the src SH3 domain
Biochemistry
Linguistic analysis of protein folding
FEBS Letters
Cited by (1425)
Folding and functions of knotted proteins
2023, Current Opinion in Structural BiologyK-Pro: Kinetics Data on Proteins and Mutants
2023, Journal of Molecular BiologyStructure–function crosstalk in liver cancer research: Protein structuromics
2023, International Journal of Biological MacromoleculesPathfinder: Protein folding pathway prediction based on conformational sampling
2023, PLoS Computational Biology
- 1
Edited by P. E. Wright