Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH

Journal of Molecular Biology

Volumn 339, Issue 4, 2004, Pages 915-925

  Ripoll, Daniel R ^a   Vila, Jorge A ^a,b   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

Author keywords

all atom simulations; EDMC, electrostatically driven Monte Carlo; electrostatic interactions; ionization equilibria; protein folding; RMSD, root mean square deviations; SRFOPT, solvent radii fixed with atomic solvation parameters optimized

Indexed keywords

AMINO ACID; PEPTIDE; PHENYLALANINE; VILLIN;

AB INITIO CALCULATION; ALPHA HELIX; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPARATIVE STUDY; ELECTRICITY; ENERGY; EVALUATION; EXPERIMENT; FORCE; GEOMETRY; HYDROPHOBICITY; MODEL; MOLECULE; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE; PH; POLARIZATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; RANDOMIZATION; SEQUENCE ANALYSIS; SOLVATION; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

EID: 2542462060     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.002     Document Type: Article

References (47)

1. Anfinsen C.B. Principles that govern the folding of protein chains. Science. 181:1973;223-230
2. Vila J.A., Ripoll D.R., Scheraga H.A. Atomically-detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc. Natl Acad. Sci. USA. 100:2003;14812-14816
3. Duan Y., Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:1998;740-744
4. Shen M., Freed K.F. All-atom fast protein folding simulations: the villin headpiece. Proteins: Struct. Funct. Genet. 49:2002;439-445
5. Hansmann U.H.E., Wille T.L. Global optimization by energy landscape paving. Phys. Rev. Letters. 88:2002;068105
6. Zagrovic B., Snow C.D., Shirts M.R., Pande V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323:2002;927-937
7. Pande V.S., Baker I., Chapman J., Elmer S.P., Khaliq S., Larson S.M., et al. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers. 68:2003;91-109
8. McKnight C.J., Matsudaira P.T., Kim P.S. NMR structure of the 35-residue villin headpiece subdomain. Nature Struct. Biol. 4:1997;180-184
9. Friederich E., Vancompernolle K., Huet C., Goethals M., Finidori J., Vanderkerckhove J., Louvard D. An actin-binding site containing a conserved motif of charged amino acid residues is essential for the morphogenic effect of villin. Cell. 70:1992;81-92
10. Laskowski M. Jr, Scheraga H.A. Thermodynamic considerations of protein reactions. I. Modified reactivity of polar groups. J. Am. Chem. Soc. 76:1954;6305-6319
11. Neurath H., Greenstein J.P., Putnam F.W., Erickson J.O. The chemistry of protein denaturation. Chem. Rev. 34:1944;157-265
12. Perutz M.F. Electrostatic effects in proteins. Science. 201:1978;1187-1191
13. Spassov V.Z., Karshikoff A.D., Ladenstein R. Optimization of the electrostatic interactions in proteins of different functional and folding type. Protein Sci. 3:1994;1556-1569
14. Pace C.N., Alston R.W., Shaw K.L. Charge-charge interactions influence the denaturated state ensemble and contribute to protein stability. Protein Sci. 9:2000;1395-1398
15. Börjesson U., Hünenberger P.H. Effect of mutations involving charged residues on the stability of staphylococcal nuclease: a continuum electrostatics study. Protein Eng. 16:2003;831-840
16. Yang A.-S., Honig B. On the pH dependence of protein stability. J. Mol. Biol. 231:1993;459-474
17. Gilson M.K. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins: Struct. Funct. Genet. 15:1993;266-282
18. Vorobjev Y.N., Scheraga H.A., Hitz B., Honig B. Theoretical modeling of electrostatic effects of titratable side-chain groups on protein conformation in a polar ionic solution. 1. Potential of mean force between charged lysine residues and titration of poly-(L-lysine) in 95% methanol solution. J. Phys. Chem. 98:1994;10940-10948
19. You T.J., Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys. J. 69:1995;1721-1733
20. B, in the reaction center. Biophys. J. 68:1995;2233-2250
21. Ripoll D.R., Vorobjev Y.N., Liwo A., Vila J.A., Scheraga H.A. Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptide. J. Mol. Biol. 264:1996;770-783
22. Vorobjev Y.N., Scheraga H.A. A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. J. Comput. Chem. 18:1997;569-583
23. Momany F.A., McGuire R.F., Burgess A.W., Scheraga H.A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:1975;2361-2381
24. Némethy G., Pottle M.S., Scheraga H.A. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1983;1883-1887
25. Sippl M.J., Némethy G., Scheraga H.A. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H⋯OC hydrogen bonds from packing configurations. J. Phys. Chem. 88:1984;6231-6233
26. Némethy G., Gibson K.D., Palmer K.A., Yoon C.N., Paterlini G., Zagari A., et al. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96:1992;6472-6484
27. Ooi T., Oobatake M., Némethy G., Scheraga H.A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl Acad. Sci, USA. 84:1978;3086-3090
28. Vila J., Williams R.L., Vasquez M., Scheraga H.A. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins: Struct. Funct. Genet. 10:1991;199-218
29. Ripoll D.R., Scheraga H.A. On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine). Biopolymers. 27:1988;1283-1303
30. Vila J., Williams R.L., Grant J.A., Wojcik J., Scheraga H.A. The intrinsic helix-forming tendency of L-alanine. Proc. Natl Acad. Sci. USA. 89:1992;7821-7825
31. Vila J.A., Ripoll D.R., Scheraga H.A. Influence of lysine content and pH on the stability of alanine based copolypeptides. Biopolymers. 58:2001;235-246
32. Perrin D.D. Dissociation Constants of Organic Bases in Aqueous Solution: Supplement. 1972;Butterworths, London
33. Edsall J.T., Wyman J. Biophysical Chemistry. Polybasic acids, bases and ampholytes, including proteins. vol. 1:1958;Academic Press, New York. p. 536
34. Frank B.S., Vardar D., Buckley D.A., McKnight C.J. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain. Protein Sci. 11:2002;680-687
35. Vardar D., Buckley D.A., Frank B.S., McKnight C.J. NMR structure of an F-actin-binding "headpiece" motif from villin. J. Mol. Biol. 294:1999;1299-1310
36. Pope B., Way M., Matsudaira P.T., Weeds A. Characterisation of the F-actin binding domains of villin: classification of F-actin binding proteins into two groups according to their binding sites on actin. FEBS Letters. 338:1994;58-62
37. Arnautova Y.A., Jagielska A., Pillardy J., Scheraga H.A. Derivation of a new force field for crystal-structure prediction using global optimization: nonbonded potential parameters for hydrocarbons and alcohols. J. Phys. Chem. ser. B. 107:2003;7143-7154
38. Sitkoff D., Sharp K.A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1994;1978-1988
39. Simonson T., Brünger A.T. Solvation free energies estimated from macroscopic continuum theory: an accuracy assessment. J. Phys. Chem. 98:1994;4683-4694
40. as of ionizable groups in proteins. Atomic detail from a continuum electrostatic model. Biochemistry. 29:1990;10219-10225
41. as in proteins. Proteins: Struct. Funct. Genet. 15:1993;252-265
42. Gay D.M. Algorithm 611: subroutines for unconstrained minimization using a model/trust-region approach. ACM Trans. Math. Software. 9:1983;503-524
43. Ripoll D.R., Ni F. Refinement of the thrombin-bound structure of a hirudin peptide by a restrained electrostatic driven Monte Carlo method. Biopolymers. 32:1992;359-365
44. Braun W., Gō N. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. Mol. Biol. 186:1985;611-626
45. Vásquez M., Scheraga H.A. Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. J. Biomol. Struct. Dynam. 5:1988;757-784
46. Kruskal J.B. Jr. On the shortest spanning subtree of a graph and the traveling salesman problem. Proc. Am. Math. Soc. 7:1956;48-50
47. Ripoll D.R., Liwo A., Czaplewski C. The ECEPP package for conformational analysis of polypeptides. TASK Quart. 3:1999;313-323