A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics

Journal of Biomolecular NMR

Volumn 24, Issue 2, 2002, Pages 149-154

  Schubert, Mario ^a,b,c   Labudde, Dirk ^a   Oschkinat, Hartmut ^a,b   Schmieder, Peter ^a  

^a LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

13C chemical shifts; Cis peptide bond conformation; Proline; Protein structure

Indexed keywords

CARBON 13; PEPTIDE; POLYPEPTIDE; PROLINE DERIVATIVE; AMINO ACID; CARBON; PROLINE; PROTEIN;

CALCULATION; CIS ISOMER; COMPUTER PROGRAM; CONTROLLED STUDY; METHODOLOGY; NUCLEAR OVERHAUSER EFFECT; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; TRANS ISOMER; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; STATISTICS; STEREOISOMERISM; THERMODYNAMICS;

AMINO ACIDS; CARBON ISOTOPES; COMPUTATIONAL BIOLOGY; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES; PROLINE; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; STEREOISOMERISM; THERMODYNAMICS;

EID: 0036814981     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1020997118364     Document Type: Review

References (24)

1. Badger, J., Kumar, R.A., Yip, P. and Szalma, S. (1999) Proteins, 35, 25-33.
2. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucl. Acids Res., 28, 235-242.
3. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, JR., Kennard, O. Shimanouchi, I and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
4. Bronstein, I.N. and Semendjajew, K.A. (1985) Taschenbuch der Mathematik, Teubner Verlag, Leipzig.
5. Brünger, AT (1992) X-Plor, Version 3.1: A system for X-Ray Crystallography and NMR, Yale University Press, New Haven.
6. Dorman, D.E. and Bovey, F.A. (1973) J. Org. Chem., 38, 2379-2383 and references cited therein.
7. Giessner-Prettre, C., Cung, M.T. and Marraud, M. (1987) Eur. J. Biochem., 163, 79-87.
8. Haasnoot, C.A.G., de Leeuw, F.A.A.M., de Leeuw, H.P.M, and Altona, C. (1981) Biopolymers, 20, 1211-1245.
9. Herrmann, T., Güntert, P. and Wüthrich, K. (2002) J. Mol. Biol., 319, 209-227.
10. Jabs, A., Weiss, M.S. and Hilgenfeld, R. (1999) J. Mol. Biol., 286, 291-304.
11. Kang, Y.K. (1996) J. Phys. Chem., 100, 11589-11595.
12. Linge, J.P., O'Donoghue, S.I. and Nilges, M. (2001) Meth. Enzymol., 339, 71-90.
13. London, R.E. (1978) J. Am. Chem. Soc., 100, 2678-2685.
14. Milner-White, E.J., Bell, L.H. and Maccallum, P.H. (1992) J. Mol. Biol., 228, 725-734.
15. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283-298.
16. Nilges, M., Macias, M.J., O'Donoghue, S.I. and Oschkinat, H. (1997) J. Mol. Biol., 269, 408-422.
17. Ramachandran, G. N. and Sasisekharan, V. (1968) Adv. Prot. Chem., 23, 283-437.
18. Schmidt, J.M., Brüschweiler, R., Ernst, R.R., Dunbrack, R.L., Joseph, D. and Karplus, M. (1993) J. Am. Chem. Soc., 115, 8747-8756.
19. Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J.L. (1991) J. Biomol. NMR, 1, 217-236.
20. Siemion, LZ., Wieland, T. and Pook, K.-H. (1975) Angew. Chem., 87, 712-714.
21. Stanczyk, S.M., Bolton, P.H., Dell'Acqua, M. and Gerlt, J.A. (1989) J. Am. Chem. Soc., 111, 8317-8318.
22. Torchia, D.A., Sparks, S.W., Young, P.E. and Bax, A. (1989) J. Am. Chem. Soc., 111, 8315-8317.
23. Weiss, M.S., Jabs, A. and Hilgenfeld, R. (1998) Nat. Struct. Biol., 5, 676.
24. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY