Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations

Journal of Molecular Graphics and Modelling

Volumn 17, Issue 1, 1999, Pages 19-27

  Galzitskaya, Oxana ^a   Caflisch, Amedeo ^b  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Antamanide; Anticancer agent; Cyclic peptide; Molecular dynamics; Phakellistatin 8

Indexed keywords

ANTAMANIDE; ANTINEOPLASTIC AGENT; PEPTIDE DERIVATIVE; PHAKELLISTATIN 8; UNCLASSIFIED DRUG;

AQUEOUS SOLUTION; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DRUG CONFORMATION; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

ANTINEOPLASTIC AGENTS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDES, CYCLIC; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SOFTWARE;

EID: 0033398684     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(99)00017-0     Document Type: Article

References (25)

1. Pettit G.R., Xu J., Dorsaz A., Williams M.D., Boyd M.R., Cerny R.L. Isolation and structure of the human cancer cell growth inhibitory cyclic decapeptides phakellistatins 7, 8 and 9. Biorg. Med. Chem. Lett. 5:1995;1339-1344.
2. Herald D.L., Cascarano G.L., Pettit G.R., Srirangam J.K. Crystal conformation of the cyclic decapeptide phakellistatin 8 Comparison with antamanide . J. Am. Chem. Soc. 119:1997;6962-6973.
3. 2O. Proc. Natl. Acad. Sci. U.S.A. 76:1979;1532-1536.
4. Kessler H., Müller A., Pook K. Assignment of all proton, carbon, and nitrogen NMR signals of antamanide in chloroform solution. Liebigs Ann. Chem. 1989;903-912.
5. Mádi Z.L., Griesinger C., Ernst R.R. Conformational dynamics of proline residues in antamanide. j coupling analysis of strongly coupled spin systems based on E. COSY spectra. J. Am. Chem. Soc. 112:1990;2908-2914.
6. Kessler H., Bats J.W., Lautz J., Müller A. Conformation of antamanide. Liebigs Ann. Chem. 1989;913-928.
7. Brüschweiler R., Roux B., Blackledge M., Griesinger C., Karplus M., Ernst R.R. Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution. J. Am. Chem. Soc. 114:1992;2289-2302.
8. Brunne R.M., van Gunsteren W.F., Brüschweiler R., Ernst R.R. Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the GROMOS force field. J. Am. Chem. Soc. 115:1993;4764-4768.
9. Schmidt J.M., Brüschweiler R., Ernst R.R., Dunbrack R.L., Joseph D., Karplus M. Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the CHARMM force field. J. Am. Chem. Soc. 115:1993;8747-8756.
10. Bremi T., Brüschweiler R., Ernst R.R. A protocol for the interpretation of the side-chain dynamics based on NMR relaxation Application to phenylalanines in antamanide . J. Am. Chem. Soc. 119:1997;4272-4284.
11. Peng J.W., Schiffer C.A., Xu P., van Gunsteren W.F., Ernst R.R. Investigations of peptide hydration using NMR and molecular dynamics simulations A study of effects of water on the conformation and dynamics of antamanide . J. Biomol. NMR. 8:1996;453-476.
12. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM A program for macromolecular energy, minimization, and dynamics calculations . J. Comput. Chem. 4:1983;187-217.
13. Neria E., Fischer S., Karplus M. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105:1996;1902-1921.
14. Jorgensen W.L., Chandrasekhar J., Madura J., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:1983;926-935.
15. Brünger A., Karplus M. Polar hydrogen positions in proteins Empirical energy placement and neutron diffraction comparison . Proteins Struct. Funct. Genet. 4:1988;148-156.
16. Beglov D., Roux B. Finite representation of an infinite bulk system Solvent boundary potential for computer simulations . J. Chem. Phys. 100:1994;9050-9063.
17. Brooks C.L. III, Karplus M. Solvent effects on protein motion and protein effects on solvent motion. J. Mol. Biol. 208:1989;159-181.
18. Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical integration of the Cartesian equation of motion of a system with constraints Molecular dynamics of n-alkanes . J. Comput. Phys. 23:1977;327-341.
19. Pettit G.R., Srirangam J.K., Herald D.L., Xu J.P., Boyd M.R., Cichacz Z., Kamano Y., Schmidt J.M., Erickson K.L. Isolation and crystal structure of stylopeptide 1, a new marine Porifera cycloheptapeptide. J. Org. Chem. 60:1995;8257-8261.
20. Brüschweiler R., Blackledge M., Ernst R.R. Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution. J. Biomol. NMR. 1:1991;3-11.
21. 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.
22. Demchuk E., Bashford D., Case D.A. Dynamics of a type VI reverse turn in a linear peptide in aqueous solution. Folding Design. 2:1997;35-46.
23. 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.
24. Loewenthal R., Sancho J., Fersht A.R. Histidine-aromatic interactions in barnase. J. Mol. Biol. 224:1992;759-770.
25. Cung M.T., Vitoux B., Marraud M. Flexibility of Pro-Pro sequences IR and NMR experiments . New. J. Chem. 11:1987;503-510.