Side-chain effects on peptidyl-prolyl cis/trans isomerisation

Journal of Molecular Biology

Volumn 279, Issue 2, 1998, Pages 449-460

  Reimer, Ulf ^a   Scherer, Gerd ^a   Drewello, Mario ^a   Kruber, Susanne ^a   Schutkowski, Mike ^a   Fischer, Gunter ^a  

^a MAX PLANCK RESEARCH UNIT FOR ENZYMOLOGY OF PROTEIN FOLDING   (Germany)

Author keywords

Kinetics; Peptidyl prolyl cis trans isomerisation; Proline; Protein folding; Structure function relationship

Indexed keywords

HISTIDINE; PENTAPEPTIDE; PROLINE; PROTEIN; TYROSINE;

AMINO ACID SUBSTITUTION; AQUEOUS SOLUTION; ARTICLE; CIRCULAR DICHROISM; CIS TRANS ISOMERISM; COVALENT BOND; KINETICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTON NUCLEAR MAGNETIC RESONANCE; THERMODYNAMICS;

EID: 0032486107     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1770     Document Type: Article

References (64)

1. Adzhubei A.A., Sternberg M.J. Left-handed polyproline II helices commonly occur in globular proteins. J. Mol. Biol. 229:1993;472-493
2. Aubry A., Cung M.T., Marraud M. Beta I and beta II-turn conformations in model dipeptides with the Pro-Xaa sequences. J. Am. Chem. Soc. 107:1985;7640-7647
3. Bächinger H.P. The influence of peptidyl-prolyl cis-trans isomerase on the in vitro folding of type III collagen. J. Biol. Chem. 262:1987;17144-17148
4. Bächinger H.P., Bruckner P., Timpl R., Prockop D.J., Engel J. Folding mechanism of the triple helix in type-III collagen and type-III pN collagen. Role of disulfide bridges and peptide bond isomerisation. Eur. J. Biochem. 106:1980;619-632
5. 2-). Chem. Ber. 111:1978;1045-1057
6. Berger A., Loewenstein A., Meiboom S. NMR study of the protolysis and ionization of N-methylacetamide. J. Am. Chem. Soc. 81:1959;62-67
7. Brandsch M., Thunecke F., Schutkowski M., Fischer G., Neubert K. Evidence for the absolute conformational specificity of the intestinal H+/peptide symporter. J. Biol. Chem. 273:1998;3861-3864
8. Case D.A., Dyson H.J., Wright P.E. Use of chemical shift and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins. Methods Enzymol. 239:1994;392-416
9. Chou P.Y., Fasman G.D. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 13:1974;211-222
10. Chou P.Y., Fasman G.D. Beta turns in proteins. J. Mol. Biol. 115:1977;135-175
11. Cox C., Young V.G., Lectka T. Intramolecular catalysis of amide isomerization. J. Am. Chem. Soc. 119:1997;2307-2308
12. Demchuk E., Bashford D., Case D.A. Dynamics of a type VI reverse turn in a linear peptide in aqueous solution. Folding Des. 2:1997;35-46
13. Demchuk E., Bashford D., Gippert G.P., Case D.A. Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing. J. Mol. Biol. 270:1997;305-317
14. Dyson H.J., Rance M., Houghten R.A., Lerner R.A., Wright P.E. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 201:1988;161-200
15. Fischer G., Wöllner S., Schonbrunner R., Scherer G. Inhibitors for peptidyl prolyl cis/trans isomerases. Wünsch E. 5th Akabori Conference. 1994;142 Max-Planck-Gesellschaft, Dresden
16. Fischer S., Dunbrack R.L., Karplus M. Cis-trans imide isomerization of the proline dipeptide. J. Am. Chem. Soc. 116:1994;11931-11937
17. Frömmel C., Preissner R. Prediction of prolyl residues in cis-conformation in protein structures on the basis of the amino acid sequence. 277:1990;159-163
18. Goldschmidt B., Mathiszik B. Trend. 1994;Martin Luther University 06120 Halle/Germany, Kurt Mothes Str. 3
19. Grathwohl C., Wüthrich K. The X-Pro peptide bond as an NMR probe for conformational studies of flexible linear peptides. Biopolymers. 15:1976;2025-2041
20. Grathwohl C., Wüthrich K. NMR studies of the rates of proline cis/trans isomerisation in oligopeptides. Biopolymers. 20:1981;2623-2633
21. Harrison R.K., Stein R.L. Mechanistic studies of peptidyl prolyl cis-trans isomerase evidence for catalysis by distortion. Biochemistry. 29:1990;1684-1689
22. Harrison R.K., Stein R.L. Substrate specificities of the peptidyl prolyl cis-trans isomerase activities of cyclophilin and FK-506 binding protein evidence for the existence of a family of distinct enzymes. Biochemistry. 29:1990;3813-3816
23. Harrison R.K., Stein R.L. Mechanistic studies of enzymatic and nonenzymatic prolyl cis-trans isomerization. J. Am. Chem. Soc. 114:1992;3464-3471
24. Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524
25. Houry W.A., Scheraga H.A. Nature of the unfolded state of ribonuclease A effect of cis-trans X-Pro peptide bond isomerization. Biochemistry. 35:1996;11719-11733
26. Jackson S.E., Fersht A.R. Folding of chymotrypsin inhibitor 2. 2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding. Biochemistry. 30:1991;10436-10443
27. Johnson W.C. Jr. Circular dicroism and its empirical application to biopolymers. Methods Biochem. Anal. 31:1985;61-163
28. Kautz R.A., Fox R.O. NMR analysis of staphylococcal nuclease thermal quench refolding kinetics. Protein Sci. 2:1993;851-858
29. Kemmink J., Creighton T.E. The physical properties of local interactions of tyrosine residues in peptides and unfolded proteins. J. Mol. Biol. 245:1995;251-260
30. Kiefhaber T., Quaas R., Hahn U., Schmid F.X. Folding of ribonuclease T1. 2. Kinetic models for the folding and unfolding reactions. Biochemistry. 29:1990;3061-3070
31. Kofron J.L., Kuzmic P., Kishore V., Colon-Bonilla E., Rich D.H. Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay. Biochemistry. 30:1991;6127-6134
32. Kramer M.L., Fischer G. FKBP-like catalysis of peptidyl-prolyl bond isomerization by micelles and membranes. Biopolymers. 42:1997;49-60
33. Lin L.-N., Brandts J.F. Kinetic mechanism for conformational transitions between poly- L-prolines I and II: a study utilizing the cis-trans specificity ofa proline-specific protease. Biochemistry. 19:1980;3055-3059
34. Llinás M., Klein M.P. Charge relay at the peptide bond. A proton magnetic resonance study of solvation effects on the amide electron density distribution. J. Am. Chem. Soc. 97:1975;4731-4737
35. MacArthur M.W., Thornton J.M. Influence of proline residues on protein conformation. J. Mol. Biol. 218:1991;397-412
36. Mayr L.M., Odefey C., Schutkowski M., Schmid F.X. Kinetic analysis of the unfolding and refolding of ribonuclease T1 by a stopped-flow double-mixing technique. Biochemistry. 35:1996;5550-5561
37. Merker M.P., Armitage I.M., Audi S.H., Kakalis L.T., Linehan J.H., Maehl J.R., Roerig D.L., Dawson C.A. Impact of angiotensin-converting enzyme substrate conformation on fractional hydrolysis in lung. Am. J. Physiol.-Lung Cell Mol. Physiol. 14:1996;L251-L259
38. Minor D.L. Jr, Kim P.S. Measurement of the β-sheet-forming propensities of amino acids. Nature. 367:1994;660-663
39. Mohanty D., Elber R., Thirumalai D., Beglov D., Roux B. Kinetics of peptide folding computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272:1997;423-442
40. Montelione G.T., Arnold E., Meinwald Y.C., Stimson E.R., Denton J.B., Huang S.-G., Clardy J., Scheraga H.A. Chain folding initiation structures in RNase A conformational analysis of trans Ac-Asn-Pro-Tyr-NHMe and trans Ac-Tyr-Pro-Asn-NHMe in water and in the solid state. J. Am. Chem. Soc. 106:1984;7946-7958
41. Nardi F., Worth G.A., Wade R.C. Local interactions of aromatic residues in short peptides in aqueous solution a combined database and energetic analysis. Folding Des. 2:1997;S62-S68
42. Odefey C., Mayr L.M., Schmid F.X. Non-prolyl cis-trans peptide bond isomerization as a rate-determining step in protein unfolding and refolding. J. Mol. Biol. 245:1995;69-78
43. Oka M., Montelione G.T., Scheraga H.A. Chain-folding initiation structures in RNase A conformational free energy caculations on Ac-Asn-Pro-Tyr-NHMe, Ac-Tyr-Pro-NHMe and related peptides. J. Am. Chem. Soc. 106:1984;7959-7969
44. Perczel A., Hóllosi M. Turns. Fasman G.D. Circular Dichroism and the Conformational Analysis of Biomolecules. 285:1996;Plenum Press, New York
45. Plaxco K.W., Spitzfaden C., Campbell I.D., Dobson C.M. Rapid refolding of a proline-rich all-beta-sheet fibronectin type III module. Proc. Natl Acad. Sci. USA. 93:1996;10703-10706
46. Ramirez-Alvarado M., Blanco F.J., Niemann H., Serrano L. Role of β-turn residues in β-hairpin formation and stability in designed peptides. J. Mol. Biol. 273:1997;898-912
47. Reimer U., Drewello M., Jakob M., Fischer G., Schutkowski M. Conformational state of a 25-mer peptide from the cyclophilin-binding loop of the HIV type 2 capsid protein. Biochem. J. 326:1997;181-185
48. Reimer U., El Mokdad N., Schutkowski M., Fischer G. Intramolecular assistance of cis/trans isomerisation of the His-Pro moiety. Biochemistry. 36:1997;13802-13808
49. Schmid F.X. Prolyl isomerase enzymatic catalysis of slow protein-folding reactions. Annu. Rev. Biophys. Biomed. 22:1993;123-142
50. Schutkowski M., Wöllner S., Fischer G. Inhibition of peptidyl-prolyl cis/trans isomerase activity by substrate analog structures thioxo tetrapeptide-4-nitroanilides. Biochemistry. 34:1995;13016-13026
51. Schutkowski M., Bernhardt A., Zhou X.Z., Shen M., Reimer U., Rahfeld J.-U., Lu K.P., Fischer G. Role of phosphorylation in determining the backbone dynamics of the serine/threonine-proline motif and Pin1 substrate recognition. Biochemistry,. 1998;. in the press
52. Siligardi G., Drake A.F. The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides. Biopolymers. 37:1995;281-292
53. Stein R.L. Mechanistic studies of enzymatic and nonenzymatic prolyl cis-trans isomerization. Advan. Protein Chem. 44:1993;1-24
54. Steinberg I.Z., Harrington W.F., Berger A., Sela M., Katchalski E. The configurational changes of poly-L-proline in solution. J. Am. Chem. Soc. 82:1960;5263-5279
55. Steinmann B., Bruckner P., Superti-Furga A. Cyclosporine A slows collagen triple-helix formation in vivo indirect evidence for a physiological role of peptidyl-prolyl-cis-trans-isomerase. J. Biol. Chem. 266:1991;1299-1303
56. 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
57. Tan Y.-J., Oliveberg M., Otzen D.E., Fersht A.R. The rate of isomerisation of peptidyl-proline bonds as a probe for interactions in the physiological denatured state of chymotrypsin inhibitor 2. J. Mol. Biol. 269:1997;611-622
58. Texter F.L., Spencer D.B., Rosenstein R., Matthews C.R. Intramolecular catalysis of a proline isomerization reaction in the folding of dihydrofolate reductase. Biochemistry. 31:1992;5687-5691
59. 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
60. Vanhoof G., Goosens F., De Meester I., Hendriks D., Scharpé S. Proline motifs in peptides and their biological processing. FASEB J. 9:1995;736-744
61. Vanhove M., Raquet X., Palzkill T., Pain R.H., Frere J.M. The rate-limiting step in the folding of the cis-Pro167Thr mutant of TEM-1 beta-lactamase is the trans to cis isomerization of a non-proline peptide bond. Proteins: Struct. Funct. Genet. 25:1996;104-111
62. Williamson M.P. The structure and function of proline-rich regions in proteins. Biochem. J. 197:1994;249-260
63. Yao J., Feher V.A., Espejo B.F., Reymond M.T., Wright P.E., Dyson H.J. Stabilisation of a type VI turn in a family of linear peptides in water solution. J. Mol. Biol. 243:1994;736-753
64. Yao J., Dyson H.J., Wright P.E. Three-dimensional structure of a type VI turn in a linear peptide in water solution evidence for stacking of aromatic rings as a major stabilizing factor. J. Mol. Biol. 243:1994;754-766