Abstract
The potential energy surface (PES) of tyrosyl-glycyl-glycine (YGG) tripeptide in solution was explored using EDMC (Electrostatically Driven Monte Carlo) and in the gas-phase by means of ab initio quantum chemical calculations. The theoretical computational analysis revealed that this tripeptide possesses a significant molecular flexibility. A C7 backbone conformation was the most energetically preferred for the central Gly residue, using both methodologies. Some new stable conformers that have not been previously reported were identified in the gas phase as well. This study points out the interplay of backbone and side-chain contributions in determining the relative stabilities of energy minima. In addition, the peptide backbone of YGG was compared with other small peptides containing aromatic side-chains (Phe-Gly-Gly and Trp-Gly-Gly). The comparison with experimental X-ray results was also satisfactory.
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S.S. Zimmerman, M.S. Pottle, G. Némethy, H.A. Scheraga, Macromolecules 10, 1 (1977)
K.T. O’Neil, W.F. DeGrado, Science 250, 646 (1990)
M.J. Rooman, J.P.A. Kocher, S.J. Wodak, Biochemistry 31, 10226 (1992)
M. Blaber, X.J. Zhang, B.W. Matthews, Science 260, 1637 (1993)
C. Brooks, D.A. Case, Chem. Rev. 93, 2487 (1993)
A.G. Street, S.L. Mayo, Proc. Natl. Acad. Sci. U.S.A. 96, 9074 (1999)
P. Koehl, V. Levitt, Proc. Natl. Acad. Sci. U.S.A. 96, 12524 (1999)
G. Chasse et al., J. Mol. Struct. (THEOCHEM) 537, 319 (2001)
H. Valdés, K. Pluhácková, M. Pitonák, J. Rezác, P. Hobza. Phys. Chem. Chem. Phys. 10, 2747, (2008)
S. Anishetty, G. Pennathur, R. Anishetty. BMC Struct. Biol. 2, 9 (2002)
G. Duan, V.H. Smith, Jr., D. Weaver, Chem. Phys. Lett. 310, 323 (1999)
J.B.O. Mitchell, C.L. Nandi, I.K. McDonald, J.M. Thornton, J. Mol. Biol. 239, 315 (1994)
M.M. Flocco, S.L. Mowbray, J. Mol. Biol. 235, 709 (1994)
F. Nardi, G.A. Worth, R.C. Wade, Folding and Design 2, S62 (1997)
J.B.O. Mitchell et al., Nature 366, 413 (1993)
G. Tóth, C.R. Watts, R.F. Murphy, S. Lovas, Proteins: Struct. Funct. Genet. 43, 373 (2001)
D. Reha et al., Chem. Eur. J. 11, 6803 (2005)
H. Valdés, D. Reha, P. Hobza, J. Phys. Chem. B 110, 6385 (2006)
J. Cerný, P. Jurecka, P. Hobza, H. Valdés, J. Phys. Chem. A 111, 1146 (2007)
D. Toroz, T. van Mourik, Mol. Phys. 105, 209 (2007)
L.F. Holroyd, T. van Mourik, Chem. Phys. Lett. 442, 42 (2007)
T. van Mourik, P.G. Karamertzanis, S.L. Price, J. Phys. Chem. A 110, 8 (2006)
M.R. Peterson, I.G. Csizmadia, J. Am. Chem. Soc. 100, 6911 (1978)
M.R. Peterson, I.G. Csizmadia, Prog. Theor. Org. Chem. 3, 190 (1982)
M.F. Masman, S. Lovas, R.M. Murphy, R.D. Enriz, A.M. Rodríguez, J. Phys. Chem. A. 111, 10682 (2007)
A.M. Rodríguez, J.C.P. Koo, D. Rojas, N. Peruchena, R.D. Enriz, Inter. J. Quant. Chem. 106, 1580 (2006)
M.W. Klipfel et al., J. Phys. Chem. A. 107, 5079 (2003)
M.F. Masman et al., Eur. Phys. J. D. 20, 531 (2002)
V. Pichon-Pesme, H. Lachekar, M. Souhassou, C. Lecomte, Acta Cryst. B56, 728 (2000)
A. Liwo et al., Biopolymers 38, 157 (1996)
D.R. Ripoll, H.A. Scheraga, Biopolymers 27, 1283 (1988)
D.R. Ripoll, H.A. Scheraga, Biopolymers 30, 165 (1990)
H.A. Scheraga, D.R. Ripoll, A. Liwo, C. Czaplewski, User Guide ECEPPAK and ANALYZE Programs.
G. Némethy et al., J. Phys. Chem. 96, 6472 (1992)
J. Vila, R.L. Williams, M. Vásquez, H.A. Scheraga, Proteins: Struct. Funct. Genet. 10, 199 (1991)
R.L. Williams, J. Vila, G. Perrot, H.A. Scheraga, Proteins: Struct. Funct. Genet. 14, 110 (1992)
M.F. Masman et al., Eur. J. Med. Chem. 44, 212 (2009)
M.J. Frisch et al., Gaussian 03, Revision B.05, Gaussian Inc. (Pittsburgh PA, 2003)
W.J. Hehre, L. Radom, P.V.R. Schleyer, J.A. Pople, Ab Initio Molecular Theory (John Wiley & Sons, New York, 1986)
C.C.J. Roothaan, Rev. Mod. Phys. 23, 69 (1951)
W.J. Hehre, R. Ditchfield, J.A. Pople, J. Chem. Phys. 56, 2257 (1972)
P.C. Hariharan, J.A. Pople, Mol. Phys. 27, 209 (1974)
T.H. Dunning, Jr., J. Chem. Phys. 90, 1007 (1989)
R.A. Kendall, T.H. Dunning, Jr., R.J. Harrison, J. Chem. Phys. 96, 6796 (1992)
E.G. Robertson, J.P. Simons, Phys. Chem. Chem. Phys. 3, 1 (2001)
H. Valdes, V. Spiwok, J. Rezac, D. Reha, A.G. Abo- Riziq, M.S. de Vries, P. Hobza. Chem. Eur. J. 14, 4886 (2008)
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Barrera Guisasola, E.E., Masman, M.F., Enriz, R.D. et al. Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring. cent.eur.j.chem. 8, 566–575 (2010). https://doi.org/10.2478/s11532-010-0015-1
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DOI: https://doi.org/10.2478/s11532-010-0015-1