Rate of Loop Formation in Peptides: A Simulation Study

Journal of Molecular Biology

Volumn 382, Issue 2, 2008, Pages 556-565

  Feige, Matthias J ^a   Paci, Emanuele ^b  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

loop formation; molecular dynamics simulation; peptide dynamics; protein folding

Indexed keywords

PEPTIDE; POLYPEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER SIMULATION; ENERGY TRANSFER; MOLECULAR DYNAMICS; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 50049104164     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.07.011     Document Type: Article

References (48)

1. Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9 (2002) 646-652
2. Bieri O., Wirz J., Hellrung B., Schutkowski M., Drewello M., and Kiefhaber T. The speed limit for protein folding measured by triplet-triplet energy transfer. Proc. Natl Acad. Sci. USA 96 (1999) 9597-9601
3. Eaton W.A., Muñoz V., Hagen S.J., Jas G.S., Lapidus L.J., Henry E.R., and Hofrichter J. Fast kinetics and mechanisms in protein folding. Annu. Rev. Biophys. Biomol. Struct. 29 (2000) 327-359
4. Karplus M., and Weaver D.L. Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci. 3 (1994) 650-668
5. Bryngelson J.D., Onuchic J.N., Socci N.D., and Wolynes P.G. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins: Struct. Funct. Genet. 21 (1995) 167-195
6. McLeish T.C. Protein folding in high-dimensional spaces: hypergutters and the role of non-native interactions. Biophys. J. 88 (2005) 172-183
7. Krieger F., Fierz B., Bieri O., Drewello M., and Kiefhaber T. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J. Mol. Biol. 332 (2003) 265-274
8. Krieger F., Möglich A., and Kiefhaber T. Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains. J. Am. Chem. Soc. 127 (2005) 3346-3352
9. Möglich A., Krieger F., and Kiefhaber T. Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains. J. Mol. Biol. 345 (2005) 153-162
10. Fierz B., Satzger H., Root C., Gilch P., Zinth W., and Kiefhaber T. Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale. Proc. Natl Acad. Sci. USA 104 (2007) 2163-2168
11. Hudgins R.R., Huang F., Gramlich G., and Nau W.M. A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides. J. Am. Chem. Soc. 124 (2002) 556-564
12. Huang F., and Nau W.M. A conformational flexibility scale for amino acids in peptides. Angew. Chem., Int. Ed. 42 (2003) 2269-2272
13. Lapidus L.J., Eaton W.A., and Hofrichter J. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl Acad. Sci. USA 97 (2000) 7220-7225
14. Yeh I.C., and Hummer G. Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J. Am. Chem. Soc. 124 (2002) 6563-6568
15. Gnanakaran S., Nymeyer H., Portman J.J., Sanbonmatsu K.Y., and Garcia A.E. Peptide folding simulations. Curr. Opin. Struct. Biol. 13 (2003) 168-174
16. Ferrara P., Apostolakis J., and Caflisch A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins: Struct. Funct. Genet. 46 (2002) 24-33
17. Lazaridis T., and Karplus M. Effective energy function for protein dynamics and thermodynamics. Proteins: Struct. Funct. Genet. 35 (1999) 133-152
18. Schaefer M., and Karplus M. A comprehensive treatment of continuum electrostatic. J. Phys. Chem. 100 (1996) 1578-1599
19. Im W., Feig M., and Brooks C.L.I. An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins. Biophys. J. 85 (2003) 2900-2918
20. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
21. Brunger A., Brooks C.L., and Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105 (1984) 495-500
22. Skeel R.D., and Izaguirre J. An impulse integrator for Langevin dynamics. Mol. Phys. 100 (2002) 3885-3891
23. Kramers H.A. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica (Amsterdam) 7 (1940) 284
24. Hänggi P., Talkner P., and Borkovec M. Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62 (1990) 251-341
25. van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J.C. GROMACS: fast, flexible and free. J. Comp. Chem. 26 (2005) 1701-1718
26. Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 45 (1996) 11225-11236
27. Jorgensen W.J., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
28. Darden T.A., York D.M., and Pedersen L. Particle mesh Ewald: an N log(N) method for computing Ewald sums. J. Chem. Phys. 98 (1993) 10089-10092
29. Hess B., Bekker H., and Berendsen H.J.C. LINCS: a linear constraint solver for molecular simulations. J. Comp. Chem. 18 (1997) 1463-1472
30. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
31. Eisenberg D., and Kauzmann W. The structure and properties of water (1969), Oxford University Press, New York
32. Likhtman A.E., and Marques C.M. First-passage problem for the Rouse polymer chain: an exact solution. Europhys. Lett. 75 (2006) 971-977
33. Doi M., and Edwards S.F. The theory of polymer dynamics (1986), Oxford Science Publications, Oxford, UK
34. Jun S., Bechhoefer J., and Ha B.Y. Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing. Europhys. Lett. 64 (2003) 420-426
35. Friedman B.A., and Yeung C. Renormalization group analysis of polymer cyclization with non-equilibrium initial conditions. Eur. Phys. J., E Soft Matter 21 (2006) 25-31
36. Haas E., Wilchek M., Katchalski-Katzir E., and Steinberg I.Z. Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transfer. Proc. Natl. Acad. Sci. USA 72 (1975) 1807-1811
37. Haas E., Katchalski-Katzir E., and Steinberg I.Z. Brownian motion of the ends of oligopeptide chains in solution as estimated by energy transfer between chain ends. Biopolymers 17 (1978) 11-31
38. Möglich A., Joder K., and Kiefhaber T. End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation. Proc. Natl Acad. Sci. USA 103 (2006) 12394-12399
39. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometric features. Biopolymers 22 (1983) 2577-2637
40. Kohn J.E., Millett I.S., Jacob J., Zagrovic B., Dillon T.M., Cingel N., et al. Random-coil behavior and the dimensions of chemically unfolded proteins. Proc. Natl. Acad. Sci. USA 101 (2004) 12491-12496
41. Guillou J.C.L., and Zinn-Justin J. Critical exponents for the n-vector model in three dimensions from field theory. Phys. Rev. Lett. 39 (1977) 95-98
42. Tanford C., Kawahara K., and Lapanje S. Proteins in 6-M guanidine hydrochloride. Demonstration of random coil behavior. J. Biol. Chem. 241 (1966) 1921-1923
43. Uversky V.N. Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11 (2002) 739-756
44. Dyson H.J., and Wright P.E. Unfolded proteins and protein folding studied by NMR. Chem. Rev. 104 (2004) 3607-3622
45. Dyson H.J., and Wright P.E. Intrinsically unstructured proteins and their functions. Nat. Rev., Mol. Cell Biol. 6 (2005) 197-208
46. Caflisch A., and Paci E. Molecular dynamics simulations to study protein folding and unfolding (chapter 32) (2004), Wiley-VCH, Weinheim 1143-1169
47. Chen J., Brooks C.L., and Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr. Opin. Struct. Biol. 18 (2008) 140-148
48. Fitzkee N.C., and Rose G.D. Reassessing random-coil statistics in unfolded proteins. Proc. Natl Acad. Sci. USA 101 (2004) 12497-12502