Polyalanine gas phase acidities determination and conformational space analysis by genetic algorithm assessment

ISSN: 2410-9649 Bourjila et al / Chemistry International 2(3) (2016) 145-157 iscientic.org. 146 www.bosaljournals/chemint/ [email protected] Several factors may influence the convergence of these polypeptides towards the equilibrium structures, the diversity and the multiplication in dihedral angles (HSCC, HNCC, OCCN, HNCO, CNCC, CCNC,...) vary and depends upon the nature of S,O and N heteroatoms, the acidic hydrogen of the thiol group and the hydrogen of the amine and the amide (Figure 1). Studies in model systems with different force fields have shown that the method of molecular mechanics MM is able to properly model the energies of polypeptides (Beachy et al., 1997). For large polypeptides, the MM is not able to accurately model the intramolecular interactions (Beachy et al., 1997). An alternative to this method could be the use of semi empirical procedures, AM1 in this case (Dewar et al., 1985), to account for electronic effects. Furthermore, an important factor to take into account is the choice of the PES scanning technique. This must indeed be able to locate the global minimum without 'getting caught' by local minima in the PES area surrounding the starting structure. Several research techniques can be used. The MNC genetic algorithm, developed and reported, allows after a sequence of steps (selection, crossover, mutation and substitution) to explore and exploit a very large conformational search space to converge directly to the proper equilibrium structures. The acidity of an isolated amino acid is the most important thermochemical property which influences the structure, the reactivity, folding proteins and peptides as well (Ren et al., 2009). In solution form, the chemistry of this factor may be affected by the solvent; hence the concept of gas phase chemistry where solvent effect is eliminated is required. Acidity of a peptide of an amino acid depends primarily on its position along the peptide chain. A residue located in the N-terminal of a helix is more acidic than the C-terminal one (Ren et al., 2009; Morisheti et al., 2010). The acidity of the isolated amino acids is widely studied in recent years (Jones et al., 2007), while information on the acidity in the gas phase of neutral peptides is still rare (Morisheti et al., 2010). The acidity in the gas phase of the studied polypeptides is due to the acidity of the cysteine residue which contains acid thiol site. Therefore, the theoretically study of the equilibrium structures, the acidity in the gas phase and its variation as a function of the position of the cysteine and . H N H H C