Large-scale context in protein folding: Villin headpiece

Biochemistry

Volumn 42, Issue 3, 2003, Pages 664-671

  Fernández, Ariel ^a,d   Shen, Min yi ^b   Colubri, Andrés ^d   Sosnick, Tobin R ^a,c   Berry, R Stephen ^b   Freed, Karl F ^b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSIDAD NACIONAL DEL SUR   (Argentina)

^c UNIVERSITY OF CHICAGO   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS; MOLECULES; PROTEINS; WATER;

AB INITIO SIMULATIONS;

BIOCHEMISTRY;

AMIDE; CARBONYL DERIVATIVE; SOLVENT; VILLIN; WATER;

AB INITIO CALCULATION; ALPHA HELIX; ARTICLE; COMPUTER SIMULATION; DIELECTRIC CONSTANT; HYDROGEN BOND; HYDROPHOBICITY; IN VITRO STUDY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

ALANINE; ALGORITHMS; AMINO ACID SEQUENCE; CARRIER PROTEINS; COMPUTER SIMULATION; FORECASTING; HYDROGEN BONDING; HYDROPHOBICITY; MICROFILAMENT PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NEUROFILAMENT PROTEINS; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SERINE; THERMODYNAMICS;

EID: 0346665548     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi026510i     Document Type: Article

References (44)

1. Muñoz, V., and Eaton, W. A. (1999) A simple model for calculating the kinetics of protein folding from three-dimensional structures, Proc. Natl. Acad. Sci. U.S.A. 96, 11311-6.
2. Fersht, A. (2000) Transition state structure as a unifying basis in protein folding mechanisms: contact order, chain topology, stability and the extended nucleus mechanism, Proc. Natl. Acad. Sci. U.S.A. 97, 1525-1529.
3. Nymeyer, H., Socci, N. D., and Onuchic, J. N. (1998) Landscape approaches for determining the ensemble of folding transition states: success and failure hinges on the degree of frustration, Proc. Natl. Acad. Sci. U.S.A. 95, 5921-5928.
4. Lacroix, E., Viguera, A. R., and Serrano, L. (1998) Elucidating the folding problem of alpha helices: local motifs, long-range electrostatics, ionic strength dependence and prediction of NMR parameters, J. Mol. Biol. 284, 173-181.
5. Baldwin, R., and Rose, G. D. (1999) Is protein folding hierarchic? II. Folding intermediates and transition states, Trends Biochem. Sci. 24, 77-83.
6. Bashford, D., Karplus, M., and Weaver, D. (1990) in Protein folding (Gierasch, L. M., and King, J., Eds.) pp 283-290, Am. Assoc. Adv. Sci., Washington.
7. Park, K., Vendruscolo, M., and Domany, E. (2000) Towards an energy function for the contact map representation of proteins, Proteins 40, 237-248.
8. Minor, D. L., and Kim, P. S. (1996) Context-dependent secondary structure formation of a designed protein sequence, Nature 380, 730-734.
9. Vendruscolo, M., and Domany, E. (1998) Efficient dynamics in the space of contact maps, Folding Des. 3, 329-336.
10. Forge, V., Hoshino, M., Kuwata, K., Arai, M., Kuwajima, K., Batt, C. A., and Goto, Y. (2000) Is folding of β-lactoglobulin nonhierarchic? Intermediate with nativelike β-sheet and nonnative α-helix, J. Mol. Biol. 296, 1039-1051.
11. Fernández, A., Colubri, A., and Berry, R. S. (2001) Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios, J. Chem. Phys. 114, 5871-5887.
12. Fernández, A., Colubri, A., and Berry, R. S. (2000) Topology to geometry in protein folding: β-lactoglobulin, Proc. Natl. Acad. Sci. U.S.A. 97, 14062-14066.
13. Kuwata, K., Shastry, R., Cheng, H., Hoshino, M., Batt, C. A., Goto, Y., and Roder, H. (2001) Structural and kinetic characterization of early folding events in β-lactoglobulin, Nat. Struct. Biol. 8, 151-155.
14. McKnight, C. J., Matsudaira, P. T., and Kim, P. S. (1997) NMR structure of the 35-residue villin headpiece subdomain, Nat. Struct. Biol. 4, 180-184.
15. Duan, Y., and Kollman, P. A. (1998) Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution, Science 282, 740-744.
16. Plaxco, K. W., Simons, K. T., and Baker, D. (1998) Contact order, transition state placement and the refolding rates of single-domain proteins, J. Mol. Biol. 277, 985-994.
17. Fernández, A. (2001) Conformation-dependent environments in folding proteins, J. Chem. Phys. 114, 2489-2502.
18. Daggett, V., Li A., Itzhaki, L. S., Otzen, D. E., and Fersht, A. R. (1996) Structure of the transition state for folding of a protein derived from experiment and simulation, J. Mol. Biol. 257, 430-440.
19. Martínez, J. C., Pisabarro, M. T., and Serrano, L. (1998) Obligatory steps in protein folding and the conformational diversity of the transition state, Nat. Struct. Biol. 5, 721-729.
20. Alm, E., and Baker, D. (1999) Prediction of protein folding mechanisms from free energy landscapes derived from native structures, Proc. Natl. Acad. Sci. U.S.A. 96, 11305-11310.
21. Baldwin, R. L., and Rose, G. D. (1999) Is protein folding hierarchic? I. Trends Biochem. Sci. 24, 26-37.
22. Vendruscolo M., Paci, E., Dobson, C. M., and Karplus, M. (2001) Three key residues form a critical contact network in a protein folding transition state, Nature 409, 641-645.
23. Fernández, A., Kostov, K., and Berry, R. S. (1999) From residue matching patterns to protein folding topographies: General model and bovine pancreatic trypsin inhibitor, Proc. Natl. Acad. Sci. U.S.A. 96, 12991-12996.
24. Fernández, A., Kostov, K., and Berry, R. S. (2000) Coarsely resolved topography along protein folding pathways, J. Chem. Phys. 112, 5223-5229.
25. Fernández, A., and Berry, R. S. (2000) Self-organization and mismatch tolerance in protein folding. General theory and an application, J. Chem. Phys. 112, 5212-5222.
26. Fernández, A. (2001) Cooperative walks in a cubic lattice: Protein folding as a many-body problem, J. Chem. Phys. 115, 7293-7297.
27. Thornton, J. (1992) in Protein Folding (Creighton, T. E., Ed.) pp 59-63, Freeman, New York.
28. Fernández, A. (2000) Protein design from in silico dynamic information: the emergence of the "turn-dock-lock" motif, Protein Eng. 15, 1-6.
29. Fernández, A., Colubri, A., and Berry, R. S. (2002) Three-body correlations in folding proteins: The origin of cooperativity, Physica A 307, 235-259.
30. Ponder, J. W., Rubenstein, S., Kundrot, C., Huston, S., Dudek, M., Kong, Y., Hart, R., Hodsdon, M., Pappu, R., Mooij, W., and Loeffler, G. (1999) TINKER: Software tools for molecular design, version 3.7, Washington University, St. Louis.
31. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc. 117, 5179-15197.
32. Ooi, T., Oobatake, M., Nemethy, G., and Scheraga, H. A. (1987) Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides, Proc. Natl. Acad. Sci. U.S.A. 84, 3086-3090.
33. Ramstein, J., and Lavery, R. (1988) Energetic coupling between DNA bending and base pair opening, Proc. Natl. Acad. Sci. U.S.A. 85, 7231-7235.
34. Allen, M. P., and Tildesley, D. J. (1987) Computer simulation of liquids, Oxford University Press, Oxford.
35. Pastor, R. W., and Karplus, M. (1988) Parametrization of the friction constant for stochastic simulations of polymers, J. Phys. Chem. 92, 2636-2641.
36. Shen, M.-y., and Freed, K. F. (2000), All-atom fast protein folding: The villin headpiece, Proteins 44, 439-445.
37. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81, 3684-3690.
38. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992) Numerical Recipes, Cambridge University Press, Cambridge.
39. Kabsch, W., and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577-2637.
40. Shen, M.-y., and Freed, K. F. (2002) Long Time Dynamics of Met-Enkephalin: Comparison of Explicit and Implicit Solvent Models, Biophys. J. 82, 1791-1808.
41. Krantz, B., Moran, L. B., Kentsis, A., and Sosnick, T. R. (2000) D/H amide isotope effects reveal when hydrogen bonds form during protein folding, Nat. Struct. Biol. 7, 62-71.
42. Makhatadze, G., and Privalov, P. (1995) Energetics of protein structure, Adv. Protein Chem. 47, 307-425.
43. Garcia, A. E., and Sanbonmatsu, K. Y. (2001) Exploring the energy landscape of a beta-hairpin in explicit solvent, Proteins 42, 345-354.
44. Frank, B. S., Vardar, D., Buckley, D. A., and McKnight, C. J. (2002) The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain, Protein Sci. 11, 680-687.