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Journal of Molecular Graphics & Modelling

Margarita G Ilyina, Edward M Khamitov, Akhat G Mustafin, S L Khursan
Relative stabilities of the N1/N3/О5/О6 anions of 42 substituted uracils in gas phase and aqueous solutions have been theoretically studied using approximation IEFPCM (SMD) - TPSS/aug-cc-pVTZ. The specific solvation of uracil and its anions has been simulated with the first hydrate shell made up with 5 water molecules. The nonspecific solvation has been accounted in terms of the SMD model. We have found a series of relative stability under conditions of both specific and nonspecific hydration. The series is ranked according to the increase of the relative stability of the N3 anion...
November 11, 2017: Journal of Molecular Graphics & Modelling
Kai Zhao, Xin Zhou, Ming Ding
Oncogenic BRAF V600E mutation confers constitutive activation for the kinase and is closely related to the pathogenesis of metastasic bowel cancer (MBC). Here, the V600E-induced conformational change in MBC BRAF kinase domain is characterized systematically at structural, energetic and dynamic levels. The mutation is observed to cause a conformational conversion of the kinase's activation loop from DFG-out to DFG-in, thus activating the kinase. Electrostatic force is primarily responsible for the conformational conversion and stabilization of DFG-in associated with the mutation...
November 9, 2017: Journal of Molecular Graphics & Modelling
Ayyappa Kumar Sista Kameshwar, Richard Barber, Wensheng Qin
Extrinsic catalytic properties of laccase enable it to oxidize a wide range of aromatic (phenolic and non-phenolic) compounds which makes it commercially an important enzyme. In this study, we have extensively compared and analyzed the physico-chemical, structural and functional properties of white, brown and soft rot fungal laccases using standard protein analysis software. We have computationally predicted the three-dimensional comparative models of these laccases and later performed the molecular docking studies using the lignin model compounds...
November 8, 2017: Journal of Molecular Graphics & Modelling
Mohd Riyaz, Sarita Yadav, Neetu Goel
The catalytic oxidation of CO by molecular oxygen (O2) over graphene, epoxy functionalized graphene and sulphur doped graphene surface is investigated theoretically by employing dispersion corrected Density Functional Theory. The adsorption of O2 and CO molecules over the pristine, functionalized and doped graphene surface has been compared. The channel for oxidation of CO to CO2 is elucidated in detail in the presence of aqueous solvent. Computations suggest that catalytic cycle of CO oxidation is initiated through the ER-mechanism, with the formation of a carbonate intermediate, the second pre-adsorbed CO reacts with the carbonate intermediate through LH-mechanism whereby, two CO2 molecules are released and adsorption surface becomes available for the subsequent reaction...
November 7, 2017: Journal of Molecular Graphics & Modelling
C Pitchumani Violet Mary, S Vijayakumar, R Shankar
Curcumin, a well-documented phytochemical compound used to treat various diseases because of its more tolerability in the human body and has no side effects. The present study describes the metal chelating ability of Curcumin for Mn(2+), Fe(2+) and Zn(2+) metal ions and their antioxidant properties using density functional theory in both gas and DMSO solvent phases. Results reveal that the carbonyl group at diketo moiety is destabilized due to the metal ion coordination. The interaction energies reveal that CurEN-Zn(2+) are the most stable rather than the CurEN-Mn(2+) and CurEN-Fe(2+) complexes...
November 1, 2017: Journal of Molecular Graphics & Modelling
Ali Hajiebrahimi, Younes Ghasemi, Amirhossein Sakhteman
With the growing number of labor-intensive data in the pharmaceutical industries and public domain for protein-ligand complexes, a significant challenge is still remaining in managing and leveraging this vast information. Here, a standalone application is presented for analysis, organization, and illustration of structural data and molecular interactions for exploiting 3D-structures into simple 1D fingerprints. The utility of the approach was shown in unraveling a feasible solution for post-processing of docking results in parallel with providing fruitful analysis for users in order to investigate molecular interactions...
November 1, 2017: Journal of Molecular Graphics & Modelling
Xinhua Cao, Mingxiao Di, Jun Wang
Azoreductase from Shewanella oneidensis MR-1 (soAzoR) possesses great potential in cleaving azo bond of azo dyes during degradation progress. However, detailed information on interaction of soAzoR with either prosthetic group or substrate remains unavailable, mainly due to the absence of crystallization of soAzoR. In order to unravel these mechanisms, we firstly built the tertiary structure of soAzoR and then computationally predicted the binding mode of FMN, NADH and a model dye, methyl red (MR). Ten residues of soAzoR, which are predicted to participate in ligands binding, were separately substituted for either alanine or phenylalanine to confirm their function...
October 31, 2017: Journal of Molecular Graphics & Modelling
Olivier Holtomo, Mama Nsangou, Jean Jules Fifen, Ousmanou Motapon
DFT methods including B3LYP, B3PW91 and M05-2x associated to 6-31+G(d,p) were used for the structural and antioxidant potency studies of phenylethyl-3,4-dihydroxy-hydrocinnamate (PDH). Solvents were employed according to their protric and aprotic character. So, calculated structures agree with the experimental data. O4H4 is propitious to scavenge radicals whatever the medium except in water where O3H3 and O4H4 are competitive. The explicit solvents of dichloromethane (DCM) and water present a disparity of OH bond dissociation enthalpy and free energy (BDE and BDFE)...
October 28, 2017: Journal of Molecular Graphics & Modelling
Xuemei Jin, Kyungro Lee, Nam Hee Kim, Hyun Sil Kim, Jong In Yook, Jiwon Choi, Kyoung Tai No
Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery...
October 27, 2017: Journal of Molecular Graphics & Modelling
Ya-Jyun Chen, Bo-Yen Huang, Chia-Ning Yang
Oxygen homeostasis in normal and tumor cells is mediated by hypoxia-inducible factors (HIFs), which are active as heterodimer complexes, such as HIF-2α-aryl hydrocarbon receptor nuclear translocator (ARNT) and HIF-1α-ARNT. A series of mutations on the interfaces between HIF-2α and ARNT and on the domain-domain interface within HIF-2α has been reported to exert varying effects on HIF-2α-ARNT dimerization. In the present study, molecular dynamic simulations were conducted to evaluate HIF-2α mutations, namely R171A, V192D, and R171A/V192D, which are not involved in the interaction with ARNT but impede HIF-2α-ARNT dimerization...
October 18, 2017: Journal of Molecular Graphics & Modelling
Mohammad Jafar Momeni, Chandra Chowdhury, Morteza Mousavi-Khoshdel
In this contribution, we explore Li adsorption and diffusion on defective silicenes using first principles calculations. Defect formation energy (Ef) values showed that silicenes with 5105 and 5559 vacancy defects (Si-5559 and Si-5105) are likely to form during the fabrication process and Ef values are about one-third of graphenes. Calculation of Li adsorption energy indicated that Si-5559 and Si-5105 are better than pristine silicene for Li dispersion in the half-lithiated state. The diffusion barrier of Li on the surface of Si-5559 and Si-5105 and in the proximity of defected zone were obtained to be 0...
October 18, 2017: Journal of Molecular Graphics & Modelling
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Sergey Vladimirovich Lelevich
This study is on the analysis of ethanol binding sites on 3D structures of nonredundant proteins from the Protein Data Bank. The only one amino acid residue that is significantly overrepresented around ethanol molecules is Tyr. There are usually two or more Tyr residues in the same ethanol binding site, while residues of Thr, Asp and Gln are underrepresented around them. Residues of Ala and Pro are significantly underrepresented in ethanol binding surfaces. Several residues (Phe, Val, Pro, Ala, Arg, His, Ser, Asp) bind ethanol significantly more frequent if they are not included in beta strands...
October 18, 2017: Journal of Molecular Graphics & Modelling
Z Ghanbari, M R Housaindokht, M R Bozorgmehr, M Izadyar
The role of the anions in transferrin chemistry highlights the importance of the anion binding site in transferrin family. A synergistic anion as carbonate is an anion that is required for iron binding by transferrin while non-synergistic anions do not act as the synergistic anions to promote iron binding, but affect the iron binding and release. Some questions remain unclear about the difference between synergistic and non-synergistic anion functions. In the present work, molecular dynamic simulation techniques were employed in order to gain access into a molecular level understanding of the iron binding site of the human serum transferrin during the synergistic and non-synergistic anion binding...
October 18, 2017: Journal of Molecular Graphics & Modelling
Shymaa Abdullah Damfo, Pedro Reche, Derek Gatherer, Darren R Flower
Malaria is a global health burden, and a major cause of mortality and morbidity in Africa. Here we designed a putative malaria epitope ensemble vaccine by selecting an optimal set of pathogen epitopes. From the IEDB database, 584 experimentally-verified CD8+ epitopes and 483 experimentally-verified CD4+ epitopes were collected; 89% of which were found in 8 proteins. Using the PVS server, highly conserved epitopes were identified from variability analysis of multiple alignments of Plasmodium falciparum protein sequences...
October 12, 2017: Journal of Molecular Graphics & Modelling
Alexey V Sulimov, Danil C Kutov, Ekaterina V Katkova, Ivan S Ilin, Vladimir B Sulimov
Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs...
October 12, 2017: Journal of Molecular Graphics & Modelling
Kalyanashis Jana, Tusar Bandyopadhyay, Bishwajit Ganguly
Acid suppressant SCH28080 and its derivatives reversibly reduce acid secretion activity of the H(+),K(+)-ATPase in a K(+) competitive manner. The results on homologation of the SCH28080 by varying the linker chain length suggested the improvement in efficacy. However, the pharmacokinetic studies reveal that the hydrophobic nature of the CH2 linker units may not help it to function as a better acid suppressant. We have exploited the role of linker unit to enhance the efficacy of such reversible acid suppressant drug molecules using hetero linker, i...
October 12, 2017: Journal of Molecular Graphics & Modelling
Jaime Rubio-Martinez, M Santos Tomas, Juan J Perez
In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked...
October 12, 2017: Journal of Molecular Graphics & Modelling
Ramachandran Gnanasekaran
Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways...
October 8, 2017: Journal of Molecular Graphics & Modelling
Yunyun Liang, Shengli Zhang
Structural class is an important attribute of protein, which plays an important role in both the experiment and theoretical research of protein science. Prediction of protein structural classes has been a challenging task, specifically for low-similarity datasets. In this paper, we develop a feature extraction method PSSS-SOMA-PSSM by incorporating two different modes of evolutionary information into Chou's general pseudo amino acid composition (PseAAC) based on predicted secondary structure sequence (PSSS) and position-specific scoring matrix (PSSM)...
October 7, 2017: Journal of Molecular Graphics & Modelling
Madeline L Galbraith, Jeffry D Madura
Poly(n-isopropylacrylamide), PNIPAM, is a thermo-responsive polymer that has been thoroughly studied for its many applications, such as drug delivery and actuators. Below the lower critical solution temperature (LCST), PNIPAM is well hydrated in the elongated conformation. The transition occuring at the LCST results in a less hydrated collapsed state above the LCST. This volume phase transition is dependent upon the hydration of the polymer and its hydrophobicity. Some research has been done on potential modifications of PNIPAM for applications, but until now there has not been a study of the hydration properties as a function of hydrophobicity...
October 6, 2017: Journal of Molecular Graphics & Modelling
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