Atomic determinants for inducing β conformation in protein structure

Statistical analysis on existing structural files of proteins indicates that 400 possible dipeptides are differentlydistributed in defined structural classes of proteins. We took 12 favorable dipeptides for beta conformation along with12 dipeptides that are not significantly found in this conformation. The structures were geometrically optimized at DFTlevel (B3LYP 6-311++g**) and their physico chemical properties including bond lengths, bond angles, torsion anglesand charge distribution on specific atoms were calculated by Gaussian 09 program. For mimicking the beta sheetsecondary structure, in our peptide model; the φ and ψ torsion angles were constraint to β conformation. The output ofthe computational study was statistically compared using T-test analysis and it was found that the bond lengths of N-Hand Cα1-C1 are significantly different in two datasets. It was also revealed that bond angles including C1-N1-H2 andH2-N2-Cα2 are different in two groups. However, there was no significant difference in specifying torsion angles forthe planarity of peptide plane.

Keywords:

Protein , Dipeptide , Conformation , DFT , Gaussian