Nonrandom distribution of intramolecular contacts in native single-domain proteins

Proteins: Structure, Function and Bioinformatics

Volumn 75, Issue 2, 2009, Pages 404-412

  Mounce, Bryan C ^a   Kurt, Neşe ^a   Ellison, Paul A ^a   Cavagnero, Silvia ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

C terminus; Contact maps; Intramolecular interactions; N terminus; Protein structure

Indexed keywords

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CROSS LINKING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE;

PROTEIN;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 66149124852     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22258     Document Type: Article

References (16)

1. Kubelka J, Hofrichter J, Eaton WA. The protein folding 'speed limit'. Curr Opin Struct Biol 2004;14:76-88.
2. Scalley-Kim M, Baker D. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J Mol Biol 2004;338:573-583.
3. Taylor WR, Lin K. Protein knots: a tangled problem. Nature 2003;421:25.
4. Chothia C, Hubbard T, Brenner S, Barns H, Murzin A. Protein folds in the all-beta and all-alpha classes. Annu Rev Biophys Biomol Struct 1997;26:597-627.
5. Przytycka T, Aurora R, Rose GD. A protein taxonomy based on secondary structure. Nat Struct Biol 1999;6:672-682.
6. Richardson JS. Beta-sheet topology and relatedness of proteins. Nature 1977;268:495-500.
7. Krishna M, Englander S. The N-terminal to C-terminal motif in protein folding and function. Proc Natl Acad Sci USA 2005;102: 1053-1058.
8. Jacob E, Unger R. A tale of two tails: why are terminal residues of proteins exposed? Bioinformatics 2007;23:E225-E230.
9. Cavagnero S, Kurt N. Folding and misfolding as a function of poly-peptide chain elongation: conformational trends and implications for intracellular events. In: Murphy R, Tsai A, editors. Misbehaving proteins: protein (mis)folding, aggregation and stability. New York: Springer; 2006. pp 217-246.
10. Kurt N, Mounce BC, Ellison P, Cavagnero S. Residue-specific contact order and contact breadth in single-domain proteins: implications for folding as a function of chain elongation. Biotechnol Prog 2008;24:570-575.
11. 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.
12. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
13. Noguchi T, Akiyama Y. PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res 2003;31:492-493.
14. Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
15. Laio A, Micheletti C. Are structural biases at protein termini a signature of vectorial folding? Proteins 2006;62:17-23.
16. Kurt N, Cavagnero S. The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation. J Am Chem Soc 2005;127:15690-15691.