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Abstract
At physiological conditions, a majority of biomolecules (e.g., amino acids, peptides and proteins) exist predominantly in the zwitterionic form that usually decides the biological functions. However, zwitterionic amino acids are not geometrically stable in gas phase and this seriously hampers the understanding of their structures, properties and biological functions. To this end, one of the recent research focuses is to demonstrate the stabilization effects of zwitterionic amino acids. Relative stabilities of canonical conformers are dependent on water contents, while zwitterionic stability improves monotonously and pronouncedly with increase of water contents. We find that one water molecule can render zwitterionic proline geometrically stable, and stabilities of different zwitterionic amino acids increase as glycine <proline <arginine. In addition, we have determined the numbers of water molecules required for zwitterionic proline to be energetically preferential and conformationally predominant, respectively as four and five. Five water molecules are enough to fill up the first shell of proline functional sites (carboxylic and amido), which is in line with the results of glycine. At any water content, zwitterionic formation will not be hindered kinetically because of rather low activation barriers, and the distribution of zwitterionic amino acids will be largely dependent on their thermodynamic stabilities.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1661-8) contains supplementary material, which is available to authorized users.
Highlights
Introduction of more water moleculesIntroduction of a second water molecule to proline results in a more conformational diversity, and PA, PB and PC respectively result in 8, 7 and 7 interacted structures, see Figs. 2, 3, 4 with their relative energies being listed in Table 1 and Additional file 1: Table S3
Five water molecules were found enough to fill up the first shell of proline functional sites, as in the case of glycine (Kokpol et al 1988)
PC does not represent a local minimum on the potential energy surface (PES) (Eszter et al 2003; Alln et al 2004), and so its relative stability is evaluated by fixing the N-H1 distance at 1.030 Å, with production of a higher relative energy than PB (13.1 kcal/mol)
Summary
A wide range of biomolecules (e.g., amino acids, peptides and proteins) exist predominantly in the zwitterionic form, and water molecules are essential to maintain their native conformations and physiological functions (Timasheff 1970; Rand 2004). Amino acids in gas phase consist entirely of canonical conformers (Császár 1992; Hu et al 1995; Yu et al 1995), which is totally different from the condition in aqueous solutions. This is obviously an obstacle for us to comprehend the electronic properties and biological functions of zwitterionic structures. Density functional calculations were employed to comprehend the gas-phase interaction of different proline conformers and water with a wide range of contents (n = 0–5). Afterwards, the 6-31+G(d,p) and 6-311++G (2df, 2pd) basis sets were respectively designated as bs and bs, and unless otherwise noted, all energies were reported at the B3LYP/bs2//B3LYP/bs level, which has been sufficiently validated before (Li et al 2011; Kim et al 2014; Yang et al 2009; Rankin et al 2002; Yang et al 2010; Ajitha and Suresh 2011) and in this work
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