The power of hard-sphere models: Explaining side-chain dihedral angle distributions of thr and val

Biophysical Journal

Volumn 102, Issue 10, 2012, Pages 2345-2352

  Zhou, Alice Qinhua ^a   O'Hern, Corey S ^a   Regan, Lynne ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIPEPTIDE; THREONINE; VALINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE;

DATABASES, PROTEIN; DIPEPTIDES; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; THREONINE; VALINE;

EID: 84861144327     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.01.061     Document Type: Article

References (43)

1. C. Ramakrishnan, and G.N. Ramachandran Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units Biophys. J. 5 1965 909 933
2. J.C. Kendrew, and G. Bodo D.C. Phillips A three-dimensional model of the myoglobin molecule obtained by x-ray analysis Nature 181 1958 662 666
3. R.A. Laskowski, and M.W. MacArthur J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
4. I.W. Davis, and A. Leaver-Fay D.C. Richardson MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 Web Server issue 2007 W375 W383
5. R.H. Yun, and J. Hermans Conformational equilibria of valine studied by dynamics simulation Protein Eng. 4 1991 761 766
6. M. Makowski, and E. Sobolewski H.A. Scheraga Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains J. Phys. Chem. B 112 2008 11385 11395
7. M.P. Jacobson, and G.A. Kaminski C.S. Rapp Force field validation using protein side chain prediction J. Phys. Chem. B 106 2002 11673 11680 (Pubitemid 35361141)
8. G.A. Kaminski, and R.A. Friesner W.L. Jorgensen Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 105 2001 6474 6487 (Pubitemid 35339015)
9. B.R. Brooks, and R.E. Bruccoleri M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
10. W.D. Cornell, and P. Cieplak P.A. Kollman A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 1995 5179 5197
11. D. Van Der Spoel, and E. Lindahl H.J. Berendsen GROMACS: fast, flexible, and free J. Comput. Chem. 26 2005 1701 1718 (Pubitemid 43076182)
12. S.C. Lovell, and J.M. Word D.C. Richardson The penultimate rotamer library Proteins 40 2000 389 408 (Pubitemid 30624447)
13. M.V. Shapovalov, and R.L. Dunbrack Jr. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions Structure 19 2011 844 858
14. F. Ding, S. Yin, and N.V. Dokholyan Rapid flexible docking using a stochastic rotamer library of ligands J. Chem. Inf. Model. 50 2010 1623 1632
15. D.B. Gordon, and G.K. Hom N.A. Pierce Exact rotamer optimization for protein design J. Comput. Chem. 24 2003 232 243
16. P.S. Shah, G.K. Hom, and S.L. Mayo Preprocessing of rotamers for protein design calculations J. Comput. Chem. 25 2004 1797 1800
17. J.J. Havranek, and D. Baker Motif-directed flexible backbone design of functional interactions Protein Sci. 18 2009 1293 1305
18. L. Jiang, and B. Kuhlman D. Baker A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces Proteins 58 2005 893 904 (Pubitemid 40271254)
19. S.J. Shandler, and M.V. Shapovalov W.F. DeGrado Development of a rotamer library for use in β-peptide foldamer computational design J. Am. Chem. Soc. 132 2010 7312 7320
20. R.L. Dunbrack Jr., and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681 (Pubitemid 27333069)
21. M.J. McGregor, S.A. Islam, and M.J.E. Sternberg Analysis of the relationship between side-chain conformation and secondary structure in globular proteins J. Mol. Biol. 198 1987 295 310 (Pubitemid 18007539)
22. T.M. Gray, and B.W. Matthews Intrahelical hydrogen bonding of serine, threonine and cysteine residues within α-helices and its relevance to membrane-bound proteins J. Mol. Biol. 175 1984 75 81
23. A.K. Chamberlain, and J.U. Bowie Analysis of side-chain rotamers in transmembrane proteins Biophys. J. 87 2004 3460 3469 (Pubitemid 40468599)
24. J.S. Richardson The anatomy and taxonomy of protein structure Adv. Protein Chem. 34 1981 167 339
25. J.M. Word, and S.C. Lovell D.C. Richardson Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285 1999 1735 1747 (Pubitemid 29060467)
26. O. Carugo Detailed estimation of bioinformatics prediction reliability through the fragmented prediction performance plots BMC Bioinformatics 8 2007 380 386
27. A.Q. Zhou, C.S. O'Hern, and L. Regan Revisiting the Ramachandran plot from a new angle Protein Sci. 20 2011 1166 1171
28. R.W. Hoffmann, and M. Stahl G. Frenking Conformation design of hydrocarbon backbones: a modular approach Chemistry 4 1998 559 566 (Pubitemid 28286160)
29. K.B. Wiberg, and M.A. Murcko Rotational barriers: 2. Energies of alkane rotamers. An examination of gauche interactions J. Am. Chem. Soc. 110 1988 8029 8038
30. H. Förster, and F. Vögtle Steric interactions in organic chemistry: spatial requirements of substituents Angew. Chem. Int. Ed. Engl. 16 1977 429 441
31. F.M. Beckelhaupt, and E.J. Baerends The case for steric repulsion causing the staggered conformation of ethane Angew. Chem. Int. Ed. 42 2003 4183 4188
32. W.S. Horne, and S.H. Gellman Foldamers with heterogeneous backbones Acc. Chem. Res. 41 2008 1399 1408
33. Bondi, A. 1964. Van der waals volumes and radii. J. Phys. Chem. 68:441-452 and http://periodictable.com/Properties/A/VanDerWaalsRadius.v.html Accessed December 4, 2011.
34. Element data and radii, Cambridge Crystallographic Data Centre, http://www.ccdc.cam.ac.uk/products/csd/radii Accessed December 4, 2011.
35. D. Seeliger, and B.L. de Groot Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps Proteins 68 2007 595 601 (Pubitemid 47068299)
36. L. Pauling The Nature of the Chemical Bond 2nd ed. 1948 Cornell University Press Ithaca, NY 187-193
37. L.L. Porter, and G.D. Rose Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints Proc. Natl. Acad. Sci. USA 108 2011 109 113
38. J. Tsai, and R. Taylor M. Gerstein The packing density in proteins: standard radii and volumes J. Mol. Biol. 290 1999 253 266 (Pubitemid 29308589)
39. C. Chothia Structural invariants in protein folding Nature 254 1975 304 308
40. F.M. Richards The interpretation of protein structures: total volume, group volume distributions and packing density J. Mol. Biol. 82 1974 1 14
41. A.J. Li, and R. Nussinov A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking Proteins 32 1998 111 127 (Pubitemid 28313257)
42. F.A. Momany, L.M. Carruthers, and H.A. Scheraga Intermolecular potentials from crystal data. III Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines and amides J. Phys. Chem. 78 1974 1595 1630
43. Allinger N. L. and Y. H. Yuh. 1980. Quantum Chemistry Program Exchange, Indiana University, Program 395.