Polyproline II Helix Is the Preferred Conformation for Unfolded Polyalanine in Water

Proteins: Structure, Function and Genetics

Volumn 55, Issue 3, 2004, Pages 502-507

  Mezei, Mihaly ^a,e   Fleming, Patrick J ^b   Srinivasan, Rajgopal ^c   Rose, George D ^b,d  

^a NEW YORK UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c TATA CONSULTANCY SERVICES   (India)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Free energy; Monte Carlo; Polyalanine; Polyproline II

Indexed keywords

ALANINE DERIVATIVE; POLYALANYL PEPTIDE; POLYPROLINE; PROLINE DERIVATIVE; UNCLASSIFIED DRUG;

AQUEOUS SOLUTION; ARTICLE; COMPUTER SIMULATION; DNA HELIX; HUMAN; HYDROPHOBICITY; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SOLVATION;

COMPUTER SIMULATION; ENTROPY; MODELS, MOLECULAR; MONTE CARLO METHOD; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SOLVENTS; THERMODYNAMICS; WATER;

EID: 1842500992     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20050     Document Type: Article

References (52)

1. Tanford C. Protein denaturation. Adv Prot Chem 1968;23:121-282.
2. Flory PJ. Statistical mechanics of chain molecules. New York: Wiley; 1969.
3. Avbelj F, Baldwin RL. Role of backbone solvation in determining thermodynamic beta propensities of the amino acids. Proc Natl Acad Sci USA 2002;99:1309-1313.
4. Avbelj F, Baldwin RL. Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: distributions of phi. Proc Natl Acad Sci USA 2003;100:5742-5747.
5. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein M. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
6. Mezei M. Direct calculation of the excess free energy of the dense Lennard-Jones fluid with nonlinear thermodynamic integration. Mol Simul 1989;2:201-207.
7. Mezei M. Calculation of solvation free energy differences for large solute change from computer simulations with quadrature-based nearly linear thermodynamic integration. Mol Simul 1993;10:225-240.
8. Creamer TP. Left-handed polyproline II helix formation is (very) locally driven. Proteins 1998;33:218-226.
9. Mezei M, Beveridge DL. Structural chemistry of biomolecular hydration via computer simulation; the proximity criterion. Methods Enzymol 1986;127:21-47.
10. McCammon AJ. Computer-aided molecular design. Science 1987; 238:486-491.
11. Straatsma TP, McCammon JA. Computational alchemy. Annu Rev Phys Chem 1992;43:407-435.
12. Mezei M. Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water. J Comput Chem 1992;43:651-656.
13. Resat H, Mezei M. Studies in the free energy calculations: I. Thermodynamic integration using a polynomial path. J Chem Phys 1993;99:6052-6061.
14. Mezei M. MMC, Monte Carlo Program: http://inka.mssm.edu/~mezei/mmc.
15. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953;21:1087-1092.
16. Rao M, Pangali CS, Berne BJ. Mol Phys 1979;37:1779.
17. Mezei M. Distance-scaled force biased Monte Carlo simulation for solutions containing a strongly interacting solute. Mol Simul 1991;5:405-408.
18. MacKerell J et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3585-3616.
19. Owicki JC. Computer modeling of matter. In: Lykos PG, Editor. Washington, DC: American Chemical Society; 1978.
20. Mezei M. Simulaid, simulation setup utilities: http://inka.mssm.edu/~mezei/simulaid.
21. Mezei M. Modified proximity criterion for the analysis of the solvation environment of a polyfunctional solute. Mol Simul 1988;1:327-332.
22. Pauling L, Corey RB, Branson HR. The structures of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1951;37:205-210.
23. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
24. Edsall JT, McKenzie HA. Water and proteins: I. The significance and structure of water: its interaction with electrolytes and non-electrolytes. Adv Biophys 1978;10:137-207.
25. Paulaitis ME, Pratt LR. Hydration theory for molecular biophysics. Adv Prot Chem 2002;62:283-310.
26. Tanford C. The hydrophobic effect: formation of micelles and biological membranes. 2nd edition. New York: Wiley Interscience; 1980.
27. Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Prot Chem 1959;14:1-63.
28. Baldwin RL. Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci USA 1986;83:8069-8072.
29. Avbelj F, Luo P, Baldwin RL. Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities. Proc Natl Acad Sci USA 2000;97: 10786-10791.
30. Dunitz JD. The entropic cost of bound water in crystals and biomolecules. Science 1994;264:670.
31. Hillson N, Onuchic JN, Garcia AE. Pressure-induced protein folding/unfolding kinetics. Proc Natl Acad Sci USA 1999;96:14848-14853.
32. 3OH in crystals. Proc Natl Acad Sci USA 1988;85:299-303.
33. Pappu RV, Rose GD. A simple model for polyproline II structure in unfolded states of alanine-based peptides. Protein Sci 2002;11: 2437-2455.
34. Kentsis A, Mezei M, Gindin T, Osman R. Unfolded state of polyalanine is a segmented polyproline II helix. 2003. Submitted for publication.
35. Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR. Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 2002;99:9190-9195.
36. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
37. Stapley BJ, Creamer TP. A survey of left-handed polyproline II helices. Protein Sci 1999;8:587-595.
38. Stickle DF, Presta LG, Dill KA, Rose GD. Hydrogen bonding in globular proteins. J Mol Biol 1992;225:1143-1159.
39. Rose GD, Editor. Unfolded proteins [Special issue]. Adv Prot Chem 2002;62.
40. Brandts JF. The thermodynamics of protein denaturation: II. A model of reversible denaturation and interpretations regarding the stability of chymotrypsinogen. J Am Chem Soc 1964;86:4302-4314.
41. Brandts JF. The termodynamics of protein denaturation: I. The denaturation of chymotrypsinogen. J Am Chem Soc 1964;86:4291-4301.
42. Pappu RV, Srinivasan R, Rose GD. The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc Natl Acad Sci USA 2000;97:12565-12570.
43. Tiffany MI, Krimm S. New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 1968;6:1379-1382.
44. Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG, Miller AF, Creamer TP. Host-guest study of left-handed polyproline Ii helix formation. Biochemistry 2001;40:14376-14383.
45. Creamer TP, Campbell MN. Determinants of the polyproline II helix from modeling studies. Adv Prot Chem 2002;62:263-282.
46. Rucker AL, Creamer TP. Polyproline II helical structures in protein unfolded states: lysine peptides revisited. Protein Sci 2002;11:980-985.
47. Garcia AE. Characterization of non-alpha helical conformations in Ala peptides. 2003. Submitted for publication.
48. Sreerama N, Woody RW. Molecular dynamics simulations of polypeptide conformations. Proteins 1999;36:400-406.
49. Zaman MH, Shen MY, Berry S, Freed KF, Sosnick TR. Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. J Mol Biol 2003;331:693-711.
50. Poon C-D, Samulski ET, Weise CF, Weisshaar JC. Do bridging water molecules dictate the structure of a model dipeptide in aqueous solution? J Am Chem Soc 2000;122:5642-5643.
51. Hinderaker MP, Raines RT. An electronic effect on protein structure. Protein Sci 2003;12:1188-1194.
52. Stikoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.