A comprehensive description of the energetic, conformational, and vibrational features of the two amino acids (AAs) with polar side chains, i.e., serine and threonine, in aqueous environment, is provided. To adequately analyze the side chain conformational flexibility of these amino acids, we resorted to quantum mechanical calculations with the use of density functional theory, which allowed the determination of the energetic features of these AAs through 236 clusters. Each cluster contains a zwitterionic AA surrounded by seven explicit water molecules. The obtained data could evidence the effect of the side chain conformational angle (χ1 and χ2) as well as the location of water molecules on the energy landscapes of both AAs. Four of the lowest energy clusters of each AA, which give rise to distinct side chain conformations, were selected in order to reproduce the FT-IR and Raman spectra recorded in aqueous solutions and to assign the vibrational modes responsible of the main observed bands.
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7 August 2011
Research Article|
August 01 2011
Energy maps, side chain conformational flexibility, and vibrational features of polar amino acids L-serine and L-threonine in aqueous environment
Belén Hernández;
Belén Hernández
1Groupe de Biophysique Moléculaire, UFR SMBH,
Université Paris
13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Fernando Pflüger;
Fernando Pflüger
1Groupe de Biophysique Moléculaire, UFR SMBH,
Université Paris
13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Alain Adenier;
Alain Adenier
2
Université Paris Diderot
, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 75013 Paris, France
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Mama Nsangou;
Mama Nsangou
3Département des Sciences Physiques,
Ecole Normale Supérieure de Maroua
, B.P. 46, Maroua, Cameroun
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Sergei G. Kruglik;
Sergei G. Kruglik
4
Université Pierre et Marie Curie Paris 06
, Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), 75252 Paris, France
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Mahmoud Ghomi
Mahmoud Ghomi
a)
1Groupe de Biophysique Moléculaire, UFR SMBH,
Université Paris
13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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a)
Author to whom correspondence should be addressed. Electronic mail: mahmoud.ghomi@univ-paris13.fr.
J. Chem. Phys. 135, 055101 (2011)
Article history
Received:
March 18 2011
Accepted:
July 11 2011
Citation
Belén Hernández, Fernando Pflüger, Alain Adenier, Mama Nsangou, Sergei G. Kruglik, Mahmoud Ghomi; Energy maps, side chain conformational flexibility, and vibrational features of polar amino acids L-serine and L-threonine in aqueous environment. J. Chem. Phys. 7 August 2011; 135 (5): 055101. https://doi.org/10.1063/1.3617415
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