Conformational study of Ac-Xaa-Pro-NHMe dipeptides: Proline puckering and trans/cis imide bond

Journal of Peptide Research

Volumn 53, Issue 1, 1999, Pages 30-40

  Kang, Young Kee ^a   Jhon, J S ^a   Han, S J ^b  

^a Chungbuk National University   (South Korea)

^b C and C Research Laboratories   (South Korea)

Author keywords

Ac Xaa Pro NHMe dipeptides; Proline puckering; Trans cis imide bond

Indexed keywords

IMIDE; PEPTIDE; PROLINE DERIVATIVE;

AMINO ACID SEQUENCE; AROMATIZATION; ARTICLE; CHEMICAL BINDING; CHEMICAL INTERACTION; CIS ISOMER; COMPLEX FORMATION; COVALENT BOND; GEOMETRY; HYDROGEN BOND; MATHEMATICAL COMPUTING; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; STRUCTURE ANALYSIS; TRANS ISOMER;

EID: 0032988379     PISSN: 1397002X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1399-3011.1999.tb01614.x     Document Type: Article

References (47)

1. 1. Momany, F.A., McGuire, R.F., Burgess, A.W. & Scheraga, H.A. (1975) Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79, 2361-2381.
2. 2. Madison, V. (1977) Flexibility of the pyrrolidine ring in proline peptides. Biopolymers 16, 2671-2692.
3. 3. DeTar, D.F. & Luthra, N.P. (1977) Conformations of proline. J. Am. Chem. Soc. 99, 1232-1244.
4. 4. de Leeuw, F.A.A.M., van Kampen, P.N., Altona, C., Díez, E. & Esteban, A.L. (1984) Relationships between torsion angles and ring-puckering coordinates. Part III. Application to heterocyclic puckered five-membered rings. J. Mol. Struct. 125, 67-88.
5. 5. Kang, Y.K. (1996) Ab initio molecular orbital calculations on low-energy conformers of N-acetyl-N′-methylprolineamide. J. Phys. Chem. 100, 11589-11595.
6. 6. Han, S.J. & Kang, Y.K. (1996) Pseudorotation in heterocyclic five-membered rings: tetrahydrofuran and pyrrolidine. J. Mol. Struct. (Theochem.). 369, 157-165.
7. 7. Ramachandran, G.N. & Mitra, A.K. (1976) An explanation for the rare occurrence of cis peptide units in proteins and polypeptides. J. Mol. Biol. 107, 85-92.
8. 8. Stewart, D.E., Sarkar, A. & Wampler, J.E. (1990) Occurrence and role of cis peptide bonds in protein structures. J. Mol. Biol. 214, 253-260.
9. 9. MacArthur, M.W. & Thornton, J.M. (1991) Influence of proline residues on protein conformation. J. Mol. Biol. 218, 397-412.
10. 10. Zimmerman, S.S. & Scheraga, H.A. (1976) Stability of cis, trans, and nonplanar peptide groups. Macromolecules 9, 408-416.
11. 11. Lewis, P.N., Momany, F.A. & Scheraga, H.A. (1973) Chain reversals in proteins. Biochim. Biophys. Acta 303, 211-229.
12. 12. Brandts, J.F., Halvorson, H.R. & Brennan, M. (1975) Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 14, 4953-4963.
13. 13. Schmid, F.X., Mayr, L.M., Mücke, M. & Schönbrunner, E.R. (1993) Prolyl isomerases: role in protein folding. Adv. Protein Chem. 44, 25-66.
14. 14. Williams, K.A. & Deber, C.M. (1991) Proline residues in transmembrane helices: structural or dynamic role? Biochemistry 30, 8919-8923.
15. 13C spin-lattice relaxation resulting from ring puckering in proline. J. Am. Chem. Soc. 100, 2678-2685.
16. 16. de Leeuw, F.A.A.M., Altona, C., Kessler, H., Bermel, W., Friedrich, A., Krack, G. & Hull, W.E. (1983) Conformational analysis of proline rings from proton spin-spin coupling constants and force-field calculations: application to three cyclic tripeptides. J. Am. Chem. Soc. 105, 2237-2246.
17. 2H nuclear magnetic resonance study. J. Am. Chem. Soc. 108, 6459-6464.
18. 18. Oka, M., Montelione, G.T. & Scheraga, H.A. (1984) Chain-folding initiation structures in ribonuclease A: conformational free energy calculations on Ac-Asn-Pro-Tyr-NHMe, Ac-Tyr-Pro-Asn-NHMe, and related peptides. J. Am. Chem. Soc. 106, 7959-7969.
19. 19. Stein, R.L. (1993) Mechanism of enzymatic and nonenzymatic prolyl cis-trans isomerization. Adv. Protein Chem. 44, 1-24.
20. 1. J. Phys. Chem. 97, 9248-9258.
21. 21. Han, S.J. & Kang, Y.K. (1993) Conformational study of trans-and cis-N-acetyl-N′-methylamides of Pro-Xaa dipeptides. Int. J. Peptide Protein Res. 42, 518-526.
22. 22. Choi, S.H., Yu, J.Y., Shin, J.K. & Jhon, M.S. (1994) Molecular dynamics simulations of trans-and cis-N-acetyl-N′-methylamides of Xaa-Pro dipeptides. J. Mol. Struct. 323, 233-242.
23. 23. Fischer, S., Dunbrack Jr, R.L. & Karplus, M. (1994) Cis-trans imide isomerization of the proline dipeptide. J. Am. Chem. Soc. 116, 11931-11937.
24. 24. Milner-White, E.J., Bell, L.H. & Maccallum, P.H. (1992) Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides. Different puckers are favored in certain situations. J. Mol. Biol. 228, 725-734.
25. 25. Tanaka, S. & Scheraga, H.A. (1974) Calculation of conformational properties of oligomers of L-proline. Macromolecules 7, 698-705.
26. 26. Thomasson, K.A. & Applequist, J. (1990) Bond-optimized ring closure for proline: comparison of conformations and semiempirical energies with small molecule X-ray structures. Biopolymers 30, 437-450.
27. 27. Schmidt, J.M., Brüschweiler, R., Ernst, , R.R., Dunbrack Jr, R.L., Joseph, D. & Karplus, M. (1993) Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the CHARMM force field. J. Am. Chem. Soc. 115, 8747-8756.
28. 28. Grathwohl, C. & Wüthrich, K. (1981) NMR studies of the rates of proline cis-trans isomerization in oligopeptides. Biopolymers 20, 2623-2633.
29. 29. Yao, J., Feher, V.A., Espejo, B.F., Reymond, M.T., Wright, P.E. & Dyson, H.J. (1994) Stabilization of a Type VI turn in a family of linear peptides in water solution. J. Mol. Biol. 243, 736-753.
30. 30. Kang, Y.K., Han, S.J. & Jhon, J.S. (1998) Proline puckering and cis-trans isomerization of proline-containing peptides. In: Frontiers of Peptide Science, Proceedings of the 15th American Peptide Symposium (Tam, J.P., Kaumaya, P.T.P., eds), Kluwer Academic Publishers, Dordrecht, The Netherlands, in press.
31. 31. Han, S.J., Jhon, J.S. & Kang, Y.K. (1997) Pyrrolidine puckering and imide cis-trans isomerization of Ac-X-Pro-NHMe dipeptides. Bull. Korean Chem. Soc. 18, 899-902.
32. 32. IUPAC-IUB Commission on Biochemical Nomenclature (1970) Abbreviations and symbols for the description of the conformation of polypeptide chains. Biochemistry 9, 3471-3479.
33. 33. Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S. & 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.
34. 34. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986) An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7, 230-252.
35. 35. Scheraga, H.A. (1992) Predicting three-dimensional structures of oligopeptides. In Reviews in Computational Chemistry. (Lipkowits, K.B., Boyd, D.B., eds), VCH, New York pp. 73-142.
36. 36. Gibson, K.D. & Scheraga, H.A. (1997) Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. J. Comput. Chem. 18, 403-415.
37. 37. Kang, Y.K., No, K.T. & Scheraga, H.A. (1996) Intrinsic torsional potential parameters for conformational analysis of peptides and proteins. J. Phys. Chem. 100, 15588-15598.
38. 9. J. Biomol. Struct. Dyn. 7, 391-419.
39. 39. Roterman, I.K., Lambert, M.H., Gibson, K.D. & Scheraga, H.A. (1989) A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. φ-ψ maps for N-acetyl alanine N′-methyl amide: comparisons, contrasts and simple experimental tests. J. Biomol. Struct. Dyn. 7, 421-453.
40. 40. Gay, D.M. (1983) Subroutines for unconstrained minimization using a model/ trust-region approach. ACM Trans. Math. Software 9, 503-524.
41. 41. Zimmerman, S.S., Pottle, M.S., Némethy, G. & Scheraga, H.A. (1977) Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules 10, 1-9.
42. 42. Vásquez, M., Némethy, G. & Scheraga, H.A. (1983) Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid. Macromolecules 16, 1043-1049.
43. 43. Zimmerman, S.S. & Scheraga, H.A. (1977) Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N′-methylamides of Pro-X and X-Pro dipeptides. Biopolymers 16, 811-843.
44. 44. Schimmel, P.R. & Flory, P.J. (1968) Conformational energies and configurational statistics of copolypeptides containing L-proline. J. Mol. Biol. 34, 105-120.
45. 45. Yao, J., Brüschweiler, R., Dyson, H.J. & Wright, P.E. (1994) Differential side chain hydration in a linear peptide containing a Type VI turn. J. Am. Chem. Soc. 116, 12051-12052.
46. 46. Richardson, J.S. & Richardson, D.C. (1989) Principles and patterns of protein conformation. In Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G.D., ed), Plenum Press, New York pp. 1-98.
47. 47. Richardson, J.S. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167-339.