Papers by Keyword: Homology Modeling

Abstract: CD36 is a class B scavenger receptor, which is on the surface of many cells such as platelets, macrophages, endothelial and smooth muscle cells. CD36 has been shown to play a critical role in the development of atherosclerosis by its capacity to adhere oxidized low density lipoproteins (OxLDL). It’s very valuable to find out the antagonists for CD36, but the three-dimensional protein structure of CD36 has not been determined and there are no template structures in the PDB library, which greatly prevents the antagonist discovery from structure-based drug discovery. The aim of the present study is to predict the three-dimensional structure using computational methods by I-TASSER.

Abstract: Activated toxins interact with α-amylase receptor on the brush border membrane vesicle (BBMV) of the midgut epithelium, which activates intracellular oncotic pathways and leads to cell death. In order to decipher the mechanism of process how toxins interact with their receptors, it is essential to investigate their three-dimensional structure. The three-dimensional structure of α-amylase was constructed by homology modeling, based on crystal structure of Bacillus cereus oligo-1,6-glucosidase and the model was further evaluated using PROSA energy and ERRAT. The substrate binding pocket responsible for the interactions with toxins was predicted and analyzed, and the important role of binding of toxin to binding pocket on α-amylase was discussed in the aspect of Cry4Ba and Cry11Aa toxicity.

Abstract: The interaction between Rdlβ5 GABA receptors of house fly before and after mutation and AVM was considered as the reason that AVM cause the insect death and investigated with Sybylx1.1 software. The docking results showed that the hydrogen bond and hydrophobic interaction played an important role among the complexes of Rdlβ5 GABA receptor and avermectin. Hydrogen bond of 2.217 Å formed between B/Ser58 of GABA receptor and atom O42 of avermectin before mutation, 1.953 Å hydrogen bond formed between A/Gln6 of GABA receptor and hydroxyl (C₇) of avermectin after mutation. In addition, our results indicated that the binding free energy (ΔE) of AVM and GABA receptors increased 3.59 kcal mol⁻¹ after mutation, which was consistent with the experimental phenomenon of the insecticidal resistance to AVM.

Abstract: TbpA is a highly conserved transmembrane protein that may serve as a channel for transport of iron across the outer membrane, which is required for transferrin utilization and is responsible for removing the iron from transferrin and for transporting iron across the outer membrane in a TonB-dependent manner. In the present study, a 3D homology modeling of TbpA from Actinobacillus pleuropneumoniae (App) L20 strain, based upon the Crystal structure of the hemehemoglobin outer membrane transporter ShuA from Shigella dysenteriae (PDB code: 3fhh) was performed using bioinformatics tools, as no experimental 3D structures. The program VERIFY 3D assessed the quality of the predicted structure of TbpA with acceptable scores. All the results converged to the fact that the predicted 3-Dimenrsional structure of TbpA is of good quality with acceptable scores.

Abstract: α-Glucosidases play critical role both in primary metabolism and in glycoconjugate biosynthesis and processing. In this paper, the reasonable three-dimensional molecular model of AglA was generated by homology modeling. This modeled protein is divided into five major structural domains, and the catalytic domain is classical (β/α) 8 barrel with the active site pocket positioned at its C-terminal side. With analyses of conserved residues and overlay of homology structures, the residues Tyr 662, Tyr527, Glu521, His238 and Tyr235 was predicted as the main substrate binding sites, and residues Asp490, Glu493 and Asp660 were deduced to be the acid/base catalytic residues.

Abstract: Estrogen-related receptors (ERRs), orphan nuclear receptors, share a significant amino acid sequence homology with estrogen receptors (ERs), yet their ligands do not respond in the same manner. In fact, some of the ligands that are known as agonists of ERs show antagonistic effect in ERRs. Accordingly, the current study investigated the structures of the ligand-binding domains using homology model building and docking studies. The results showed clear differences between the ligand-binding pockets of ERRs and ERs, thereby providing structural insights into the activities related to the ligands.