The flexibility in the proline ring couples to the protein backbone

Protein Science

Volumn 14, Issue 4, 2005, Pages 1011-1018

  Ho, Bosco K ^a   Coutsias, Evangelos A ^b   Seok, Chaok ^c   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

^c Seoul National University   (South Korea)

Author keywords

Backbone; Cyclic ring; Proline; Pucker

Indexed keywords

PROLINE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COMPUTER SYSTEM; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; GEOMETRY; MOLECULAR MODEL; PHYSICAL STRESS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN STRUCTURE; STEREOCHEMISTRY; STRUCTURE ANALYSIS;

ALGORITHMS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROLINE; PROTEINS;

EID: 15244362919     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041156905     Document Type: Article

References (18)

1. Altona, C. and Sundaralingam, M. 1972. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94: 8205-8212.
2. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
3. Bhattacharyya, R. and Chakrabarti, P. 2003. Stereospecific interactions of proline residues in protein structures and complexes. J. Mol. Biol. 311: 925-940.
4. Bricard, R.J. 1897. Mémoire sur la théorie de l'octaèdre articulé. J. Math. Pures. Appl. 3: 113-150.
5. Chakrabarti, P. and Pal, D. 2001. The interrelationships of side-chain and main-chain conformations in proteins. Prog. Biophys. Mol. Biol. 76: 1-102.
6. Coutsias, E.A., Seok, C., Jacobson, M.P., and Dill, K.A. 2004. A kinematic view of loop closure. J. Comput. Chem. 25: 510-528.
7. DeTar, D.F. and Luthra, N.P. 1977. Conformations of proline. J. Am. Chem. Soc. 99: 1232-1244.
8. EU 3-D Validation Network. 1998. Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276: 417-436.
9. Ho, B.K., Thomas, A., and Brasseur, R. 2003. Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the α-helix. Protein Sci. 12: 2508-2522.
10. Lovell, S.C., Davis, I.W., Arendall III, W.B., de Bakker, P.I., Word, J.M., Prisant, M.G., Richardson, J.S., and Richardson, D.C. 2003. Structure validation by Cα geometry: φ,ψ and Cβ deviation. Proteins 50: 437-450.
11. MacArthur, M.W. and Thornton, J.M. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 218: 397-412.
12. Mackerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B102: 3586-3616.
13. Milner-White, E.J. 1990. Situations of γ-turns in proteins: Their relation to α-helices, β-sheets and ligand binding sites. J. Mol. Biol. 216: 386-397.
14. Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H.A. 1992. 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: 6472-6484.
15. Pal, D. and Chakrabarti, P. 1999. Cis peptide bonds in proteins: Residues involved, their conformations, interactions and locations. J. Mol. Biol. 294: 271-288.
16. Ramachandran, G.N., Lakshminarayanan, A.V., Balasubramanian, R., and Tegoni, G. 1970. Studies on the conformation of amino acids, XII: Energy calculations on propyl residue. Biochim. Biophys. Acta 221: 165-181.
17. Schimmel, P.R. and Flory, P.J. 1968. Conformational energies and configurational statistics of copolypeptides containing L-proline. J. Mol. Biol. 34: 105-120.
18. Summers, L.N. and Karplus, M. 1990. Modeling of globular proteins: A distance-based data search procedure for the construction of insertion/deletion regions and Pro-non-Pro mutations. J. Mol. Biol. 216: 991-1016.