Folding of the human protein FKBP. Lattice Monte-Carlo simulations

Comptes Rendus de l'Academie des Sciences - Serie III

Volumn 321, Issue 10, 1998, Pages 835-843

  Papandreou, Nikolaos ^a   Kanehisa, Makoto ^a   Chomilier, Jacques ^b  

^a CNRS   (France)

^b UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

Author keywords

Cubic lattice simulations; FKBP; Monte Carlo; Protein folding

Indexed keywords

FK 506 BINDING PROTEIN; GLOBULAR PROTEIN;

ARTICLE; HYDROPHOBICITY; MOLECULAR INTERACTION; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE HOMOLOGY; SIMULATION; SYSTEM ANALYSIS; TEMPERATURE;

EID: 0345363153     PISSN: 07644469     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0764-4469(99)80023-7     Document Type: Article

References (35)

1. [1] Richards F.M., Folded and unfolded proteins: an introduction, in: Creighton T. (Ed.), Protein Folding, Freeman, New York, 1992, pp. 1-58.
2. [2] Anfinsen C.B., Principles that govern the folding of protein chains, Science 181 (1973) 223-230.
3. [3] Levinthal C., Are there pathways for protein folding?, J. Chem. Phys. 65 (1968) 44-45.
4. [4] Ballew R.M., Sabelko J., Gruebele M., Direct observation of fast protein folding: the inital collapse of apomyoglobin, Proc. Natl. Acad. Sci. USA 93 (1996) 5759-5764.
5. [5] Go N., Theoretical studies of globular folding, Annu. Rev. Biophys. Bioeng. 12 (1983) 183-210.
6. [6] Lau K.F., Dill K.A., A lattice statistical mechanics model of the conformational and sequence spaces of proteins, Macromolecules 22 (1989) 3986.
7. [7] Skolnick J., Kolinski A., Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics, J. Mol. Biol. 221 (1991) 499-531.
8. [8] Covell D.G., Lattice model simulations of polypeptide chain folding, J. Mol. Biol. 235 (1994) 1032-1043.
9. [9] Shakhnovich E.I., Proteins with seleceted sequences fold into unique native conformation, Phys. Rev. Lett. 72 (1994) 3907-3910.
10. [10] Chan H.S., Dill K.A., Origins of structure in globular proteins, Proc. Natl. Acad. Sci. USA 87 (1990) 6388-6392.
11. [11] Covell D.G., Jernigan R.L., Conformations of folded proteins in restricted spaces, Biochemistry 29 (1990) 3287.
12. [12] Sali A., Shakhnovich E.I., Karplus M., Kinetics of protein folding. A lattice model study of the requirements for folding to the native state, J. Mol. Biol. 235 (1994) 1614-1636.
13. [13] Li H., Helling R., Tang C., Wingreen N., Emergence of prefered structures in a simple model of protein folding, Science 273 (1996) 666-669.
14. [14] Miyazawa S., Jernigan R.L., Estimation of effective inter residue contact energies from protein crystal structures: quasi chemical approximation, Macromolecules 18 (1985) 534, 552.
15. [15] Miyazawa S., Jernigan R.L., Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading, J. Mol. Biol. 256 (1996) 623-644.
16. [16] Casari G., Sippl M.J., Structure derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds, J. Mol. Biol. 224 (1992) 725-732.
17. [17] Bryant S.H., Lawrence C.E., An empirical energy function for threading protein sequence through folding motif, Proteins 16 (1993) 92-112.
18. [18] van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L., Clardy J., Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex, Science 252 (1991) 839-842.
19. [19] Chan H.S., Dill K.A., Protein folding in the landscape perspective: chevron plots and non Arrehenius kinetics, Proteins 30 (1998) 2-33.
20. [20] Abkevich V.I., Gutin A.M., Shaknovich E.I., Specific nucleus as the transition state for protein folding: evidence from the lattice model, Biochemistry 33 (1994) 10026-10036.
21. [21] Hilhorst H.J., Deutch J.M., Analysis of Monte Carlo results on the kinetics of lattice polymer chains with excluded volume, J. Chem. Phys. 63 (1975) 5153-5161.
22. [22] Chan H.S., Dill K.A., Energy landscapes and the collapse dynamics of homopolymers, J. Chem. Phys. 99 (1993) 2116-2127.
23. [23] Cieplak M., Vishveshwara S., Banavar J.R., Cell dynamics of model proteins, Phys. Rev. Lett. 77 (1996) 3681-3684.
24. [24] Kolinski A., Skolnick K., Yaris R., Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of b barrel proteins, Biopolymers 26 (1987) 937-962.
25. [25] Unger R., Moult J., Local interactions dominate folding in a simple protein model, J. Mol. Biol. 259 (1996) 988-994.
26. [26] Veitschans T., Klimov D., Thirumalai D., Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence dependent properties, Folding & Design 2 (1996) 1-22.
27. [27] Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer Jr. E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M., The Protein Data Bank a computer based archive file for macromolecular structures, J. Mol. Biol. 112 (1977) 535-542.
28. [28] Michnick S.W., Rosen M.K., Wandless T.J., Karplus M., Schreiber S.L., Solut on structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin, Science 252 (1991) 836-839.
29. [29] Callebaut I., Renoir J.-M., Lebeau M.-C., Massol N., Burny A., Baulieu E.-E., Mornon J.-P., An immunophilin that binds Mr90,000 heat shock protein: main structurual features of a mammalian p59 protein, Proc. Natl. Acad. Sci. USA 89 (1992) 6270-6274.
30. [30] Callebaut I., Mornon J.-P., Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family, FEBS Lett. 374 (1995) 211-215.
31. [31] Abkevich V.I., Gutin A.M., Shakhnovich E.I., Domains in folding of model proteins, Prot. Sci. 4 (1995) 1167-1177.
32. [32] Guo Z., Thirumalai D., The nucleation collapse mechanism in protein folding: evidence for the nonuniqueness of the folding nucleus, Folding & Desing 2 (1997) 377-391.
33. [33] Kraulis P., MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, J. Appl. Crystal. 24 (1991) 946-950.
34. a, Comp. Appl. Biosci. 13 (1997) 291-295.
35. [35] Shakhnovich E., Abkevich V., Ptitsyn O., Conserved residues and the mechanism of protein folding, Nature 379 (1996) 96-98.