Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

Abstract

Protein structure modeling using a homologous template is one of many routines that accompany the molecular dynamics simulation for biological material. There are currently two protocols of protein modeling available in Accelrys Discovery Studio 2.1, Build Mutants and Build Homology Modeling protocols. Both are template-based modeling, but with a different process. In this study, two different templates, 3CKZ and 274Y, have been used to see how much the differences will be made by those two protocols if the templates has significant percentage of identity. Evaluation of structure models has been performed using DOPE score, 3D-profile, and PROCHECK. The results indicated that Build Mutants Protocols produces more stable structures but has a low reliability values and low quality of stereochemistry when using a template that has a lower percentage of identity. The results also yield more stable, reliable, and higher percentage of residues in most favoured and additionally allowed region for the usage of Build Homology Modeling Protocol on both templates. These observations suggest that Build Homology Modeling protocol is recommended for protein modeling

Preparation of Ractopamine Single-Chain Variable Fragment and Development of icELISA Based on Immunomagnetic Beads

“…In general, the PDF function in DS is used to evaluate geometrical properties such as the bond angle, bond length, and dihedral angle in protein conformations, and the PDF physical energy, dope fraction, and total PDF energy are used to evaluate the conformational model quality and confidence. The smaller the PDF function value, the better the model built; the lower the PDF total energy value, the better the optimized model; and the lower the dope score, the more reliable the model quality. , The results of specific template alignments and optimization are shown in Table S4, and the results of homology modeling are shown in Figure A. Ramachandran plots and profile-3D were used to evaluate the reasonable conformation of amino acids in the models, and the results are shown in Figure B,C.…”

“…The smaller the PDF function value, the better the model built; the lower the PDF total energy value, the better the optimized model; and the lower the dope score, the more reliable the model quality. 27,28 The results of specific template alignments and optimization are shown in Table S4, and the results of homology modeling are shown in Figure 6A. Ramachandran plots and profile-3D were used to evaluate the reasonable conformation of amino acids in the models, and the results are shown in Figure 6B,C.…”

Molecular Dynamics Simulation of the Allosteric Regulation of eIF4A Protein from the Open to Closed State, Induced by ATP and RNA Substrates

“…Ser1–Ser10, Arg352–Arg355) in this model were repaired using the loop search method in the Swiss-Pdb Viewer ( http://spdbv.vital-it.ch/ ). Based on the X-ray crystal structure of the human eIF4AIII+ADPNP+RNA complex with a closed conformation (PDB entry 2J0S (A chain)), we build the closed structure of the yeast eIF4A protein bound by ATP and RNA substrates by using the homology modeling technologies in the “Build Mutants protocol” of the Discovery Studio v.2.1 (DS 2.1, 2008) (assigned as ATP+RNA+C-eIF4A model) [40] , which is shown in Figure 1 . The human eIF4AIII protein shares 62% amino acid sequence identity with the yeast eIF4A protein [18] , with highly identical conserved motifs (see Figure S1 ).…”