The Fastest Simulation of Protein Folding Based on Torsion Angles

Backgrounds: Enormous number of possible conformations in the protein structure simulation have led molecular dynamics researchers to be frustrated until now. Some methods with defects ended their experiments into failure. This made them fail to determine the structure and function of folded protein in stable state with the lowest potential energy. This apparently exist in nature. The purpose of resolving a protein folding pathway that follows protein backbone residues torsional inertia was accomplished. Results A new method, torsion angle modeling, was adopted focused on the rotation of dihedral angles. The potential energy was calculated by rotating torsion angles of the peptide with 8 residues. It was found that when moving in the order of torsional inertia, 8 residues swivel in sequence. Six passes were repeated to find the lowest value. Conclusion The protein backbone torsion angle plays very important role in predicting protein structure. Actually it was thousand times faster or more than others to get the obvious pathway.

Structural and Functional Analyses of PolyProline-II helices in Globular Proteins

PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which the constituent residues have the backbone torsion angle (φ,ψ) values of (-75°, 145°) and take up extended left handed conformation, lacking any intra-helical hydrogen bonds. They are found to occur very frequently in protein structures with their number exceeding that of π-helices, though it is considerably less than that of α-helices and β-strands. A relatively new procedure, ASSP, for the identification of regular secondary structures using Cα trace identifies 3597 PPII helices in 3582 protein chains, solved at resolution ≤ 2.5Å. Taking advantage of this significantly expanded database of PPII-helices, we have analyzed the functional and structural roles of PPII helices as well as determined the amino acid propensity within and around them. Though Pro residues are highly preferred, it is not a mandatory condition for the formation of PPII-helices, since ~40% PPII-helices were found to contain no Proline residues. Aromatic amino acids are avoided within this helix, while Gly, Asn and Asp residues are preferred in the proximal flanking regions. These helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0ű0.1Å respectively. A majority (~72%) of PPII-helices were found to occur in conjunction with α-helices and β-strands, and serve as linkers as well. The analysis of various intra-helical non-bonded interactions revealed frequent presence of C-H...O H-bonds. PPII-helices participate in maintaining the three-dimensional structure of proteins and are important constituents of binding motifs involved in various biological functions.