جستجوی مقالات مرتبط با کلیدواژه "molecular dynamic simulation" در نشریات گروه "شیمی"

CP47 is one of the essential components of photosystem II (PSII) in green plants, green algae, and cyanobacteria; which is involved in the light reactions of photosynthesis. Various studies have shown that the binding of the extrinsic protein of 33 kDa (PsbO) to the large extrinsic loop of CP47 (E loop) is an essential photoautotrophic activity of the PSII complex. Moreover, the deletion of the amino acids between Gly-351 and Thr-365 within loop E failed to assemble stable PSII centers. In this study, using computational methods, the effect of Phenylalanine (Phe) mutation at position 363 on Synechocystis sp. PCC 6803 CP47 was investigated and then the mutant model was compared with the native one. Because the experimental 3D structure of Synechocystis sp. PCC 6803 CP47 and PsbO proteins are not available in the Protein Data Bank (PDB), the 3D structure of these proteins was modeled by homology modeling. After refining and energy minimization, the quality of protein geometry was assessed by different criteria such as PROCHECK and ProSA. Then, structural analysis of mutant and native models was performed with Molecular Dynamic (MD) simulation and docking method. The analysis of results obtained from MD simulation shows that F363R mutation affects the flexibility of some regions and especially leads to an increase in mutation region and changes the conformation of CP47. In addition, the results of docking studies indicate that F363R mutation can decrease buried surface area (BSA) at the interface region and decrease the binding energy of CP47 and PsbO. These data reinforce our hypothesis that an increase of flexibility at the position of F363 in the large extrinsic loop of CP47 may be an important factor in reducing interaction between CP47 and PsbO extrinsic protein and then water oxidation. oxidation.

TRPV1 are ion channels capable of sensing different stimuli, integrating and translating them into signal language. TRPV1 antagonists have attracted much attention for the treatment of various diseases related to the management of pain physiology and neurogenic inflammation, such as anti-inflammatory, antineoplastic, and anti-nociceptive effects. Here, we performed a 3D-QSAR, molecular docking, and MD simulations on a novel series of indole triazole derivatives as antagonists of TRPV1. The aim was to design novel potent TRPV1 antagonists with strong inhibitory activity. The significant 3D-QSAR models showed a good correlation between experimental and predicted activity. CoMSIA was used to construct the best 3D QSAR model using the PLS method showing correlative and predictive ability (R2=0.985. Q2=0.788. SEE=0.105). Electrostatic, steric, and hydrophobic fields play an important role in the variation of biological activity. Molecular Docking analysis was used to validate the 3D-QSAR methods and to explain the binding site and interactions between the ligands and the receptor. Based on these results, a novel series of compounds were predicted. The pharmacokinetic properties of predicted compounds were analyzed by drug-likeness and ADMET prediction. The best-docked compounds were subjected to MD simulation to affirm the final candidate molecules' conformational to confirm their dynamic behavior and stability.