Conformational analysis of endomorphin-1 by molecular dynamics methods

Journal of Peptide Research

Volumn 62, Issue 4, 2003, Pages 145-157

  Leitgeb, B ^a   Szekeres, A ^b   Toth G ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b UNIVERSITY OF SZEGED   (Hungary)

Author keywords

turns; Bifurcation and inverse bifurcation; C terminal turns and inverse turns; Conformational analysis; Endomorphin 1; Intramolecular H bonds; Molecular dynamics; N terminal inverse turns; Simulated annealing

Indexed keywords

AMIDE; AMINE; ENDOMORPHIN 1; MU OPIATE RECEPTOR AGONIST; PEPTIDE; PHENYLALANINE; TETRAPEPTIDE; TRYPTOPHAN; TYROSINE; TYROSYLPROLINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; ATOMIC PARTICLE; BETA CHAIN; CHEMICAL BOND; CIS ISOMER; EXPERIMENTAL MODEL; HYDROGEN BOND; ISOMER; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SIMULATION; TRANS ISOMER;

AMINO ACIDS, CYCLIC; CLUSTER ANALYSIS; COMPUTER SIMULATION; HYDROGEN BONDING; ISOMERISM; MODELS, MOLECULAR; OLIGOPEPTIDES; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 0141504412     PISSN: 1397002X     EISSN: None     Source Type: Journal    
DOI: 10.1034/j.1399-3011.2003.00084.x     Document Type: Article

References (22)

1. Zadina, J.E., Hackler, L., Ge, L.J. & Kastin, A.J. (1997) A potent and selective endogenous agonist for the μ-opiate receptor. Nature 386, 499-502.
2. Podlogar, B.L., Paterlini, G., Ferguson, D.M., Leo, G.C., Demeter, D.A., Brown, F.K. & Reitz, A.B. (1998) Conformational analysis of the endogenous μ-opioid agonist endomorphin-1 using NMR spectroscopy and molecular modeling. FEBS Lett. 439, 13-20.
3. Fiori, S., Renner, C., Cramer, J., Pegoraro, S. & Moroder, L. (1999) Preferred conformation of endomorphin-1 in aqueous and membrane-mimetic environments. J. Mol. Biol. 291, 163-175.
4. Schwyzer, R. (1977) ACTH: a short introductory review. Ann. N. Y. Acad. Sci. 297, 3-26.
5. 1H NMR spectroscopy and molecular modeling calculation. J. Pept. Res. 58, 399-412.
6. Eguchi, M., Shen, R.Y.W., Shea, J.P., Lee, M.S. & Kahn, M. (2002) Design, synthesis, and evaluation of opioid analogues with non-peptidic β-turn scaffold: enkephalin and endomorphin mimetics. J. Med. Chem. 45, 1395-1398.
7. Keller, M., Boissard, C., Patiny, L., Chung, N.N., Lemieux, C., Mutter, M. & Schiller, P.W. (2001) Pseudoproline-containing analogues of morphiceptin and endomorphin-2: evidence for a Cis Tyr-Pro amide bond in the bioactive conformation. J. Med. Chem. 44, 3896-3903.
8. Leitgeb, B., Ötvös, F. & Tóth, G. (2003) Conformational analysis of endomorphin-2 by molecular dynamics methods. Biopolymers 68, 497-511.
9. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham III, T.E., DeBolt, S., Ferguson, D., Scibel, G. & Kollman, P.A. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91, 1-41.
10. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. & Kollman, P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
11. INSIGHT/DISCOVER: Biosym Technologies, Scranton Road, San Diego, USA.
12. Zimmerman, S.S., Pottle, M.S., Némethy, G. & Sheraga, H.A. (1977) Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules 10, 1-9.
13. Vass, E., Holly, S., Majer, Zs., Samu, J., Laczkó, I. & Hollósi, M. (1997) FTIR and CD spectroscopic of H-bonded folded polypeptide structures. J. Mol. Struct. 408/409, 47-56.
14. Vass, E., Kurz, M., Konat, R.K. & Hollósi, M. (1998) FTIR and CD spectroscopic studies on cyclic penta-and hexa-peptides. Detailed examination of hydrogen bonding in β- and γ-turns determined by NMR. Spectrochimica Acta Part A 54, 773-786.
15. Venkatachalam, C. (1968) Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6, 1425-1436.
16. Lewis, P., Momany, F. & Sheraga, H. (1973) Chain reversals in proteins. Biochem. Biophys. Acta 303, 211-229.
17. Rose, G.D., Gierasch, L.M. & Smith, J.A. (1985) Turns in peptides and proteins. Adv. Protein. Chem. 37, 1-109.
18. Némethy, G. & Printz, M.P. (1972) Macromolecules 5, 755-758.
19. Alkorta, I., Suarez, M.L., Herranz, R., Muniz, R.G. & Garcia-López, M.T. (1996) Similarity study on peptide γ-turn conformation mimetics. J. Mol. Model. 2, 16-25.
20. Milner-White, E.J., Ross, B.M., Ismail, R., Belhadj-Mostefa, K. & Poet, R. (1988) One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins. J. Mol. Biol. 204, 777-782.
21. Milner-White, E.J. (1990) Situations of gamma-turns in proteins, their relation to alpha-helices, beta-sheets and ligand binding sites. J. Mol. Biol. 216, 385-397.
22. Kelley, L.A., Gardner, S.P. & Sutcliffe, M.J. (1996) An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally-related subfamilies. Protein Eng. 9, 1063-1065.