We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman ...

in this research, structural and electronic properties of zncdn-1ten clusters (n=1-10) have been studied by formalism of density functional theory and using the projector augmented wave within local density approximation. the structural properties (such as bond length/angle and coordination number), electronic and optical properties (such as binding energy, kohn-sham spectrum and partial charge...

Protein backbone helical structures have the same values of dihedral angles φ and ψ from unit to unit and thus, can be uniquely determined by a pair (φ,ψ). We focus our attention on two types of protein secondary structure αand 310-helices stabilized by 1-5 and 1-4 hydrogen bonding pattern respectively. Even though both αand 310-helices each represent a group of helices, various studies show th...

Chain Fold It is a usual way to tabulate the torsion (dihedral) angles for each residue to reconstruct protein structure using standard covalent bond length and angles. The backbone can be further represented by virtual bond between Cα-atoms. The mainchain is fully described by the virtual dihedral angle αi defined by four successive Cα atoms and the virtual bond angle. This description is used...

Background: Various forms of the so-called loop closure problem are crucial to protein structure prediction methods. Given an Nand a C-terminal end, the problem consists of finding a suitable segment of a certain length that bridges the ends seamlessly. In homology modelling, the problem arises in predicting loop regions. In de novo protein structure prediction, the problem is encountered when ...

We have performed ab initio calculations on the model cluster (OH)3Ge±O±Ge(OH)3 in order to re®ne the relationships between O quadrupolar coupling parameters and the local structure around the bridging oxygen. From these calculations the trend in the bridging oxygen O quadrupolar coupling constant, Cq, and asymmetry parameter, gq, with changing Ge±O±Ge angle was found to be similar to previousl...