Comparison of Sequence-based and Structure-based Energy Functions for the Reversible Folding of a Peptide

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2005 Mar 8

PMID 15749768

Citations 6

Authors

Andrea Cavalli

Michele Vendruscolo

Emanuele Paci

Affiliations

Soon will be listed here.

Abstract

We used computer simulations to compare the reversible folding of a 20-residue peptide, as described by sequence-based and structure-based energy functions. Sequence-based energy functions are transferable and can be used to describe the behavior of different proteins, since interactions are defined between atomic species. Conversely, structure-based energy functions are not transferable, since the interactions are defined relative to the native conformation, which is assumed to correspond to the global minimum of the energy. Our results indicate that the sequence-based and the structure-based descriptions are in qualitative agreement in characterizing the two-state behavior of the peptide that we studied. We also found, however, that several equilibrium properties, including the free-energy landscape, can be significantly different in the various models. These results suggest that the fact that a model describes the native state of a polypeptide chain does not necessarily imply that the thermodynamic and kinetic properties will also be reproduced correctly.

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References

Cavalli A, Haberthur U, Paci E, Caflisch A . Fast protein folding on downhill energy landscape. Protein Sci. 2003; 12(8):1801-3. PMC: 2323966. DOI: 10.1110/ps.0366103. View

Ghosh A, Elber R, Scheraga H . An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proc Natl Acad Sci U S A. 2002; 99(16):10394-8. PMC: 124925. DOI: 10.1073/pnas.142288099. View

Zhou Y, Karplus M . Interpreting the folding kinetics of helical proteins. Nature. 1999; 401(6751):400-3. DOI: 10.1038/43937. View

Sali A, Shakhnovich E, Karplus M . How does a protein fold?. Nature. 1994; 369(6477):248-51. DOI: 10.1038/369248a0. View

Paci E, Cavalli A, Vendruscolo M, Caflisch A . Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc Natl Acad Sci U S A. 2003; 100(14):8217-22. PMC: 166209. DOI: 10.1073/pnas.1331838100. View

Wang F, Landau D . Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram. Phys Rev E Stat Nonlin Soft Matter Phys. 2001; 64(5 Pt 2):056101. DOI: 10.1103/PhysRevE.64.056101. View

Taketomi H, Ueda Y, Go N . Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res. 1975; 7(6):445-59. View

Ding F, Dokholyan N, Buldyrev S, Stanley H, Shakhnovich E . Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J. 2002; 83(6):3525-32. PMC: 1302427. DOI: 10.1016/S0006-3495(02)75352-6. View

Shea J, Onuchic J, Brooks 3rd C . Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A. 2002; 99(25):16064-8. PMC: 138565. DOI: 10.1073/pnas.242293099. View

10.

Zhou H, Zhou Y . Folding rate prediction using total contact distance. Biophys J. 2001; 82(1 Pt 1):458-63. PMC: 1302485. DOI: 10.1016/S0006-3495(02)75410-6. View

11.

Ferrenberg , Landau , Swendsen . Statistical errors in histogram reweighting. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995; 51(5):5092-5100. DOI: 10.1103/physreve.51.5092. View

12.

Dinner A, Sali A, Smith L, Dobson C, Karplus M . Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci. 2000; 25(7):331-9. DOI: 10.1016/s0968-0004(00)01610-8. View

13.

Clementi C, Garcia A, Onuchic J . Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. J Mol Biol. 2003; 326(3):933-54. DOI: 10.1016/s0022-2836(02)01379-7. View

14.

Ding F, Dokholyan N, Buldyrev S, Stanley H, Shakhnovich E . Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol. 2002; 324(4):851-7. DOI: 10.1016/s0022-2836(02)01112-9. View

15.

Kaya H, Chan H . Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding?. J Mol Biol. 2002; 315(4):899-909. DOI: 10.1006/jmbi.2001.5266. View

16.

Karanicolas J, Brooks 3rd C . The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 2002; 11(10):2351-61. PMC: 2373711. DOI: 10.1110/ps.0205402. View

17.

Ferrara P, Apostolakis J, Caflisch A . Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins. 2001; 46(1):24-33. DOI: 10.1002/prot.10001. View

18.

Karanicolas J, Brooks 3rd C . Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. J Mol Biol. 2003; 334(2):309-25. DOI: 10.1016/j.jmb.2003.09.047. View

19.

Wang F, Landau D . Efficient, multiple-range random walk algorithm to calculate the density of states. Phys Rev Lett. 2001; 86(10):2050-3. DOI: 10.1103/PhysRevLett.86.2050. View

20.

Ferrara P, Caflisch A . Folding simulations of a three-stranded antiparallel beta -sheet peptide. Proc Natl Acad Sci U S A. 2000; 97(20):10780-5. PMC: 27100. DOI: 10.1073/pnas.190324897. View