Non-proline cis peptide bonds in proteins

Journal of Molecular Biology

Volumn 286, Issue 1, 1999, Pages 291-304

  Jabs, Andreas ^a   Weiss, Manfred S ^a   Hilgenfeld, Rolf ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

C H ... interaction; cis peptide bond; Detection algorithm; Protein structure

Indexed keywords

AMIDE; AMINO ACID; CARBOHYDRATE BINDING PROTEIN; GLYCINE; NITROGEN; PEPTIDE; PROTEIN;

ALGORITHM; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL BOND; CIS ISOMER; DATA BASE; GEOMETRY; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN STRUCTURE;

EID: 0033548058     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2459     Document Type: Article

References (41)

1. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
2. Bouckaert J., Poortmans F., Wyns L., Loris R. Sequential structural changes upon zinc and calcium binding to metal-free concanavalin A. J. Biol. Chem. 271:1996;16144-16150.
3. Brandts J. F., Halvorson H. R., Brennan M. Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry. 14:1975;4953-4963.
4. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
5. Christensen D. H., Kortzeborn R. N., Bak B., Led J. J. Results of ab initio calculations on formamide. J. Chem. Phys. 53:1970;3912-3922.
6. Clark M., Cramer R. D. III, Van Opdenbusch N. Validation of the general purpose Tripos 5.2 force field. J. Comp. Chem. 10:1989;982-1012.
7. Colovos C., Cascio D., Yeates T. O. The 1.8 Å crystal structure of the ycaC gene product from E. coli reveals an octameric hydrolase of unknown specificity. Structure. 6:1998;1329-1337.
8. Deacon A., Gleichmann T., Kalb (Gilboa) A. J., Price H., Raftery J., Bradbrook G., Yariv J., Helliwell J. R. The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 Å resolution. J. Chem. Soc. Faraday Trans. 93:1997;4305-4312.
9. Drakenberg T., Forsén S. The barrier to internal rotation in monosubstituted amides. J. Chem. Soc. Chem. Commun. 1971;1404-1405.
10. Engh R. A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog., sect. A. 47:1991;392-400.
11. J. Mol. Biol. 276:1998;417-436.
12. Fischer G., Bang H., Mech C. Detection of enzyme catalysis for cis-trans isomerization of peptide binding using proline-containing peptides as substrates. Biomed. Biochim. Acta. 43:1984;1101-1111.
13. n-L-Pro-OH. Biopolymers. 15:1976;2043-2057.
14. Herzberg O., Moult J. Analysis of steric strain in the polypeptide backbone of protein molecules. Proteins. 11:1991;223-229.
15. Hobohm U., Scharf M., Schneider R., Sander C. Selection of representative protein data sets. Protein Sci. 3:1992;409-417.
16. Huber R., Steigemann W. Two cis prolines in the Bence-Jones protein Rei and the cis -Pro bend. FEBS Letters. 48:1974;235-237.
17. J. Mol. Biol. 52:1970;1-17.
18. Jorgensen W. L., Gao J. Cis-trans energy difference for the peptide bond in the gas phase and in aqueous solution. J. Am. Chem. Soc. 110:1988;4212-4216.
19. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
20. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
21. MacArthur M. W., Thornton J. M. Influence of proline residues on protein conformation. J. Mol. Biol. 218:1991;397-412.
22. Maigret B., Perahia D., Pullman B. Molecular orbital calculations on the conformation of polypeptides and proteins. J. Theoret. Biol. 29:1970;275-291.
23. 1are strongly altered by the replacement ofcis -proline 39 with alanine. J. Mol. Biol. 231:1993;897-912.
24. McCaldon P., Argos P. Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences. Proteins. 4:1988;99-122.
25. Pearson M. A., Karplus P. A., Dodge R. W., Laity J. H., Scheraga H. A. Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A. Protein Sci. 7:1998;1255-1258.
26. Perricaudet M., Pullman A. An ab initio quantun-mechanical investigation on the rotational isomerism in amides and esters. Int. J. Peptide Protein Res. 5:1973;99-107.
27. Radzicka A., Pedersen L., Wolfenden R. Influences of solvent water on protein folding: free energies of solvation of cis and trans peptides are nearly identical. Biochemistry. 27:1988;4538-4541.
28. Ramachandran G. N., Mitra A. K. An explanation for the rare occurrence of cis peptide units in proteins and polypeptides. J. Mol. Biol. 107:1976;85-92.
29. Ramachandran G. N., Sasisekharan V. Conformation of polypeptides and proteins. Advan. Prot. Chem. 23:1968;283-437.
30. Scherer G., Kramer M. L., Schutkowski M., Reimer U., Fischer G. Barriers to rotation in secondary amide peptide bonds. J. Am. Chem. Soc. 120:1998;5568-5574.
31. Scholz C., Mücke M., Rape M., Pecht A., Pahl A., Bang H., Schmid F. X. Recognition of protein substrates by the prolyl-isomerase trigger factor is independent of proline residues. J. Mol. Biol. 277:1998a;723-732.
32. Scholz C., Scherer G., Mayr L. M., Schindler T., Fischer G., Schmid F. X. Prolyl isomerases do not catalyze isomerization of non-prolyl peptide bonds. Biol. Chem. 379:1998b;361-365.
33. Schultz D. A., Baldwin R. L. Cis proline mutants of ribonuclease A. I. Thermal stability. Protein Sci. 1:1992;910-916.
34. Stewart D. E., Sarkar A., Wampler J. E. Occurrence and role of cis peptide bonds in protein structures. J. Mol. Biol. 214:1990;253-260.
35. Stoddard B. L., Pietrokovski S. Breaking up is hard to do. Nature Struct. Biol. 5:1998;3-5.
36. Stoller G., Rücknagel K. P., Nierhaus K., Schmid F. X., Fischer G., Rahfeld J.-U. Identification of the peptidyl-prolyl cis/trans isomerase bound to the Escherichia coli ribosome as the trigger factor. EMBO J. 14:1995;4939-4948.
37. Tweedy N. B., Nair S. K., Paterno S. A., Fierke C. A., Christianson D. W. Structure and energetics of a non-proline cis -peptidyl linkage in a proline-202→alanine carbonic anhydrase II variant. Biochemistry. 32:1993;10944-10949.
38. Weiss M. S., Jabs A., Hilgenfeld R. Peptide bonds revisited. Nature Struct. Biol. 5:1998a;676.
39. Weiss M. S., Metzner H. J., Hilgenfeld R. Two non-proline cis peptide bonds may be important for factor XIII function. FEBS Letters. 423:1998b;291-296.
40. Yee V. C., Pedersen L. C., Le Trong I., Bishop P. D., Stenkamp R. E., Teller D. C. Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII. Proc. Natl Acad. Sci. USA. 91:1994;7296-7300.
41. Yee V. C., Pedersen L. C., Bishop P. D., Stenkamp R. E., Teller D. C. Structural evidence that the activation peptide is not released upon thrombin cleavage of factor XIII. Thromb. Res. 78:1995;389-397.