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Number of results

Journal

2010 | 8 | 3 | 566-575

Article title

Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

Content

Title variants

Languages of publication

EN

Abstracts

EN
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. [...]

Publisher

Journal

Year

Volume

8

Issue

3

Pages

566-575

Physical description

Dates

published
1 - 6 - 2010
online
25 - 4 - 2010

Contributors

  • Department of Chemistry. Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco, 917 - 5700, San Luis, Argentina
  • Department of Chemistry. Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco, 917 - 5700, San Luis, Argentina
author
  • Department of Chemistry. Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco, 917 - 5700, San Luis, Argentina
  • Department of Chemistry. Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco, 917 - 5700, San Luis, Argentina

References

  • [1] S.S. Zimmerman, M.S. Pottle, G. Némethy, H.A. Scheraga, Macromolecules 10, 1 (1977) http://dx.doi.org/10.1021/ma60055a001[Crossref]
  • [2] K.T. O’Neil, W.F. DeGrado, Science 250, 646 (1990) http://dx.doi.org/10.1126/science.2237415[Crossref]
  • [3] M.J. Rooman, J.P.A. Kocher, S.J. Wodak, Biochemistry 31, 10226 (1992) http://dx.doi.org/10.1021/bi00157a009[Crossref]
  • [4] M. Blaber, X.J. Zhang, B.W. Matthews, Science 260, 1637 (1993) http://dx.doi.org/10.1126/science.8503008[Crossref]
  • [5] C. Brooks, D.A. Case, Chem. Rev. 93, 2487 (1993) http://dx.doi.org/10.1021/cr00023a008[Crossref]
  • [6] A.G. Street, S.L. Mayo, Proc. Natl. Acad. Sci. U.S.A. 96, 9074 (1999) http://dx.doi.org/10.1073/pnas.96.16.9074[Crossref]
  • [7] P. Koehl, V. Levitt, Proc. Natl. Acad. Sci. U.S.A. 96, 12524 (1999) http://dx.doi.org/10.1073/pnas.96.22.12524[Crossref]
  • [8] G. Chasse et al., J. Mol. Struct. (THEOCHEM) 537, 319 (2001) http://dx.doi.org/10.1016/S0166-1280(00)00687-4[Crossref]
  • [9] H. Valdés, K. Pluhácková, M. Pitonák, J. Rezác, P. Hobza. Phys. Chem. Chem. Phys. 10, 2747, (2008) http://dx.doi.org/10.1039/b719294k[Crossref]
  • [10] S. Anishetty, G. Pennathur, R. Anishetty. BMC Struct. Biol. 2, 9 (2002) http://dx.doi.org/10.1186/1472-6807-2-9[Crossref]
  • [11] G. Duan, V.H. Smith, Jr., D. Weaver, Chem. Phys. Lett. 310, 323 (1999) http://dx.doi.org/10.1016/S0009-2614(99)00804-0[Crossref]
  • [12] J.B.O. Mitchell, C.L. Nandi, I.K. McDonald, J.M. Thornton, J. Mol. Biol. 239, 315 (1994) http://dx.doi.org/10.1006/jmbi.1994.1370[Crossref]
  • [13] M.M. Flocco, S.L. Mowbray, J. Mol. Biol. 235, 709 (1994) http://dx.doi.org/10.1006/jmbi.1994.1022[Crossref]
  • [14] F. Nardi, G.A. Worth, R.C. Wade, Folding and Design 2, S62 (1997) http://dx.doi.org/10.1016/S1359-0278(97)00066-7[Crossref]
  • [15] J.B.O. Mitchell et al., Nature 366, 413 (1993) http://dx.doi.org/10.1038/366413a0[Crossref]
  • [16] G. Tóth, C.R. Watts, R.F. Murphy, S. Lovas, Proteins: Struct. Funct. Genet. 43, 373 (2001) http://dx.doi.org/10.1002/prot.1050[Crossref]
  • [17] D. Reha et al., Chem. Eur. J. 11, 6803 (2005) http://dx.doi.org/10.1002/chem.200500465[Crossref]
  • [18] H. Valdés, D. Reha, P. Hobza, J. Phys. Chem. B 110, 6385 (2006) http://dx.doi.org/10.1021/jp057425y[Crossref]
  • [19] J. Cerný, P. Jurecka, P. Hobza, H. Valdés, J. Phys. Chem. A 111, 1146 (2007) http://dx.doi.org/10.1021/jp066504m[Crossref]
  • [20] D. Toroz, T. van Mourik, Mol. Phys. 105, 209 (2007) http://dx.doi.org/10.1080/00268970601138762[Crossref]
  • [21] L.F. Holroyd, T. van Mourik, Chem. Phys. Lett. 442, 42 (2007) http://dx.doi.org/10.1016/j.cplett.2007.05.072[Crossref]
  • [22] T. van Mourik, P.G. Karamertzanis, S.L. Price, J. Phys. Chem. A 110, 8 (2006) http://dx.doi.org/10.1021/jp0563181[Crossref]
  • [23] M.R. Peterson, I.G. Csizmadia, J. Am. Chem. Soc. 100, 6911 (1978) http://dx.doi.org/10.1021/ja00490a023[Crossref]
  • [24] M.R. Peterson, I.G. Csizmadia, Prog. Theor. Org. Chem. 3, 190 (1982)
  • [25] M.F. Masman, S. Lovas, R.M. Murphy, R.D. Enriz, A.M. Rodríguez, J. Phys. Chem. A. 111, 10682 (2007) http://dx.doi.org/10.1021/jp0716886[Crossref]
  • [26] A.M. Rodríguez, J.C.P. Koo, D. Rojas, N. Peruchena, R.D. Enriz, Inter. J. Quant. Chem. 106, 1580 (2006) http://dx.doi.org/10.1002/qua.20883[Crossref]
  • [27] M.W. Klipfel et al., J. Phys. Chem. A. 107, 5079 (2003) http://dx.doi.org/10.1021/jp030111v[Crossref]
  • [28] M.F. Masman et al., Eur. Phys. J. D. 20, 531 (2002) http://dx.doi.org/10.1140/epjd/e2002-00150-y[Crossref]
  • [29] V. Pichon-Pesme, H. Lachekar, M. Souhassou, C. Lecomte, Acta Cryst. B56, 728 (2000)
  • [30] A. Liwo et al., Biopolymers 38, 157 (1996) http://dx.doi.org/10.1002/(SICI)1097-0282(199602)38:2<157::AID-BIP3>3.0.CO;2-U[Crossref]
  • [31] D.R. Ripoll, H.A. Scheraga, Biopolymers 27, 1283 (1988) http://dx.doi.org/10.1002/bip.360270808[Crossref]
  • [32] D.R. Ripoll, H.A. Scheraga, Biopolymers 30, 165 (1990) http://dx.doi.org/10.1002/bip.360300116[Crossref]
  • [33] H.A. Scheraga, D.R. Ripoll, A. Liwo, C. Czaplewski, User Guide ECEPPAK and ANALYZE Programs.
  • [34] G. Némethy et al., J. Phys. Chem. 96, 6472 (1992) http://dx.doi.org/10.1021/j100194a068[Crossref]
  • [35] J. Vila, R.L. Williams, M. Vásquez, H.A. Scheraga, Proteins: Struct. Funct. Genet. 10, 199 (1991) http://dx.doi.org/10.1002/prot.340100305[Crossref]
  • [36] R.L. Williams, J. Vila, G. Perrot, H.A. Scheraga, Proteins: Struct. Funct. Genet. 14, 110 (1992) http://dx.doi.org/10.1002/prot.340140112[Crossref]
  • [37] M.F. Masman et al., Eur. J. Med. Chem. 44, 212 (2009) http://dx.doi.org/10.1016/j.ejmech.2008.02.019[Crossref]
  • [38] M.J. Frisch et al., Gaussian 03, Revision B.05, Gaussian Inc. (Pittsburgh PA, 2003)
  • [39] W.J. Hehre, L. Radom, P.V.R. Schleyer, J.A. Pople, Ab Initio Molecular Theory (John Wiley & Sons, New York, 1986)
  • [40] C.C.J. Roothaan, Rev. Mod. Phys. 23, 69 (1951) http://dx.doi.org/10.1103/RevModPhys.23.69[Crossref]
  • [41] W.J. Hehre, R. Ditchfield, J.A. Pople, J. Chem. Phys. 56, 2257 (1972) http://dx.doi.org/10.1063/1.1677527[Crossref]
  • [42] P.C. Hariharan, J.A. Pople, Mol. Phys. 27, 209 (1974) http://dx.doi.org/10.1080/00268977400100171[Crossref]
  • [43] T.H. Dunning, Jr., J. Chem. Phys. 90, 1007 (1989) http://dx.doi.org/10.1063/1.456153[Crossref]
  • [44] R.A. Kendall, T.H. Dunning, Jr., R.J. Harrison, J. Chem. Phys. 96, 6796 (1992) http://dx.doi.org/10.1063/1.462569[Crossref]
  • [45] E.G. Robertson, J.P. Simons, Phys. Chem. Chem. Phys. 3, 1 (2001) http://dx.doi.org/10.1039/b008225m[Crossref]
  • [46] H. Valdes, V. Spiwok, J. Rezac, D. Reha, A.G. Abo- Riziq, M.S. de Vries, P. Hobza. Chem. Eur. J. 14, 4886 (2008) http://dx.doi.org/10.1002/chem.200800085[Crossref]

Document Type

Publication order reference

Identifiers

YADDA identifier

bwmeta1.element.-psjd-doi-10_2478_s11532-010-0015-1
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