Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 10, 2014, Pages 2574-2584

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

^a YALE UNIVERSITY   (United States)

^b Yale University   (United States)

Author keywords

Dipeptide; Helical segment; Protein crystal structure; Protein structure prediction; Side chain dihedral angle distribution

Indexed keywords

AMINO ACID; CYSTEINE; DIPEPTIDE; ISOLEUCINE; LEUCINE; PHENYLALANINE; SERINE; THREONINE; TRYPTOPHAN; TYROSINE; VALINE; AROMATIC AMINO ACID; OLIGOPEPTIDE; PROTEIN;

ARTICLE; CONFORMATION; CRYSTAL STRUCTURE; PHYSICAL MODEL; PREDICTION; PRIORITY JOURNAL; ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN ENGINEERING; STEREOISOMERISM;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; AMINO ACIDS, AROMATIC; ANIMALS; DATABASES, PROTEIN; DIPEPTIDES; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; OLIGOPEPTIDES; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEINS; STEREOISOMERISM;

EID: 84924657375     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24621     Document Type: Article

References (37)

1. Ramakrishnan GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol 1963;7:95-99.
2. Ramakrishnan C, Ramachandran GN. Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys J 1965;55:909-933.
3. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
4. Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: Structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004;32:W615-619.
5. Dunbrack RL, Jr., Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol 1994;1:334-340.
6. Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
7. Dunbrack RL, Jr., Cohen FE. Bayesian statistical anal- ysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
8. Shapovalov MV, Dunbrack RL, Jr. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure 2011;19:844-858.
9. Zhu X, Lopes PEM, Shim J, MacKerell AD. Intrinsic energy landscapes of amino acid side-chains. J Chem Info Modeling 2012;52:1559-1572.
10. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Jr., Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A Second Generation Force Field for the Simulation of Proteins. J Am Chem Soc 1995;117:5179-5197.
11. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4:187-217.
12. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem 2005;26:1701-1718.
13. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and Reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001;105:6474-6487.
14. MacKerell AD, Jr., Feig M, Brooks CL, III. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:14001415.
15. 2 dihedral angles. J Chem Theory Comput 2012;8:3257-3273.
16. Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 2010;78:1950-1958.
17. Fleishman SJ, Whitehead TA, Ekiert DC, reyfus C, Corn JE, Strauch EM, Wilson IA, Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 2011 332:816-821.
18. Wang G, Dunbrack RL, Jr. PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res 2005;33:W94-W98.
19. Zhou AQ, OHern CS, Regan L. The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val. Biophys J. 2012;102:2345-2352.
20. Zhou AQ, Caballero D, O'Hern CS, Regan L. New insights into the interdependence between amino acid stereochemistry and protein structure. Biophys J 2013;105:2403-2411.
21. Zhou AQ, O'Hern CS, Regan L. Revisiting the Ramachandran plot from a new angle. Protein Sci 2011;20:1166-1171.
22. Bondi A. van der Waals volumes and radii. J Phys Chem 1964;68:441-452.
23. Element data and radii, Cambridge Crystallographic Data Centre. Available at: http://www.ccdc.cam.ac.uk/products/csd/radii. Accessed on December 4, 2013.
24. Seeliger D, de Groot BL. Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps. Proteins 2007;68:595-601.
25. Pauling L. The Nature of the Chemical Bond, 2nd ed. Ithaca, NY: Cornell University Press; 1948. pp 187-193.
26. Chothia C. Structural invariants in protein folding. Nature 1975;254:304-308.
27. Richards FM. The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 1974;82:1-14.
28. Li AJ, Nussinov R. A set of van der Waals and Coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking. Proteins Struct Funct Genet 1998;32:111-127.
29. Momany FA, Carruthers LM, Scheraga HA. 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 1974;78:1595-1630.
30. Allinger NL, Yuh YH. Quantum Chemistry Program Exchange, Indiana University, 1980; Program 395.
31. Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation. J Mol Biol 1999;285:1735-1747.
32. Caballero D, Määttä J, Zhou AQ, Sammalkorpi M, O'Hern CS, Regan L. The intrinsic α-helical and β-sheet preferences: a computational case study of Alanine. Prot Sci 2014;23:970.
33. Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:167-339.
34. Mcgregor MJ, Islam SA, Sternberg MJE. Analysis of the relationship between side-chain conformation and secondary structure in globular-proteins. J Mol Biol 1987;198:295-310.
35. Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci 2010;19:1420-1431.
36. McGregor MJ, Islam SA, Sternberg MJE. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol 1987;198:295-310.
37. Gray TM, Matthews BW. Intrahelical hydrogen bonding of serine, threonine, and cysteine residues within α-helices and its relevance to membrane-bound proteins. J Mol Biol 1984;175:75-81.