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Journal of Molecular Graphics & Modelling

Hujun Shen, Mingsen Deng, Yachao Zhang
Recent crystal structures of RNA-dependent RNA polymerase (3D(pol)) from Coxsackievirus B3 (CVB3) revealed that a tyrosine mutation at Phe364 (F364Y) resulted in structures with open active site whereas a hydrophobic mutation at Phe364 (F364A) led to conformations with closed active site. Besides, the crystal structures showed that the F364W mutation had no preference between the open and closed active sites, similar to wild-type. In this paper, we present a molecular dynamics (MD) study on CVB3 3D(pol) in order to address some important questions raised by experiments...
September 12, 2017: Journal of Molecular Graphics & Modelling
Yuan-Chun Hu, Wei-Lu Ding, Xing-Liang Peng, Ze-Sheng Li
We have theoretically designed two D-A-π-A dyes 3 and 4 based on the efficient references 1 and 2 by introducing an extra electron donor unit (D2). Via calculating the electronic structures of isolated dyes, we obtain that dyes 3 and 4 possess stronger light-harvesting efficiency imparted by the fluorescence energy transfer of D2 part, maintain comparable lifetime of excited states, and shorten the electron injection time significantly with regard to 1 and 2. Meanwhile, dye 3 positively shifts the edge of virtual states of TiO2 in a larger extent compared to its counterparts...
September 8, 2017: Journal of Molecular Graphics & Modelling
Pratishtha Singh, Anjali Ganjiwale, Allyn C Howlett, Sudha M Cowsik
Cannabinoid Receptor Interacting Protein isoform 1b (CRIP1b) is known to interact with the CB1 receptor. Alternative splicing of the CNRIP1 gene produces CRIP1a and CRIP1b with a difference in the third exon only. Exons 1 and 2 encode for a functional domain in both proteins. CRIP1a is involved in regulating CB1 receptor internalization, but the function of CRIP1b is not very well characterized. Since there are significant identities in functional domains of these proteins, CRIP1b is a potential target for drug discovery...
September 6, 2017: Journal of Molecular Graphics & Modelling
Palak Patel, Krupali Parmar, Vivek K Vyas, Dhaval Patel, Mili Das
Human islet amyloid polypeptide (hIAPP) is a natively unfolded polypeptide hormone of glucose metabolism, which is co-secreted with insulin by the β-cells of the pancreas. In patients with type 2 diabetes, IAPP forms amyloid fibrils because of diabetes-associated β-cells dysfunction and increasing fibrillation, in turn, lead to failure of secretory function of β-cells. This provides a target for the discovery of small organic molecules against protein aggregation diseases. However, the binding mechanism of these molecules with monomers, oligomers and fibrils to inhibit fibrillation is still an open question...
September 6, 2017: Journal of Molecular Graphics & Modelling
Nathaniel R Gunby, Sarah L Masters, Deborah L Crittenden
Molecular properties depend on molecular structure, so the first step in any computational chemistry investigation is to generate all thermally accessible conformers. Typically it is necessary to make a trade-off between the number of conformers to be explored and the accuracy of the method used to calculate their energies. Ab initio potential energy surface scans can, in principle, be applied to any molecule, but their conformational cost scales poorly with both molecular size and dimensionality of the search space...
September 6, 2017: Journal of Molecular Graphics & Modelling
Farhad Jahanfar, Hamed Hamishehkar
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. The ARMS2 gene encodes a putative small (11kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of the A69S mutation, we performed a detailed analysis of the ARMS2 sequence with a broad set of bioinformatics tools...
September 6, 2017: Journal of Molecular Graphics & Modelling
Abolfazl Azizi, Ali Ebrahimi
The interaction between positively charged aromatic groups (π(+)-π(+)) is characterized by stacked pyridinium ion derivatives X-PyH(+)||X-PyH(+) (XH, NH2, OH, CN, F, Br and Cl) at the M06-2X/6-311++G(d,p) level of theory in the presence of three solvents. The results indicate the formation of π(+)-π(+) stacking in a dielectric solvent can be due to the significant stability of the charge-charge repulsion forces. The trend in the absolute value of stacking interaction energy |ΔEπ(+)⋯π(+)| with respect to the solvent is formamide>water>acetone...
September 4, 2017: Journal of Molecular Graphics & Modelling
Akbar Omidvar
The activation of the O2 molecule and yielding two separated O atoms is an essential step for the oxygen reduction reaction processes. Dissociation of the strong bond in the O2 often involves large activation barriers on metal particles used as catalysts. Here, the catalytic activity for the O2 dissociation of the transition metals (Fe, Co, Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au) deposited on the BN nanocluster have been studied theoretically using density functional theory. The following outcomes can be derived from our calculations: (1) The strong interaction between the Fe and Ni metal atoms and boron atom in BN nanocluster suggests that these transition metals deposited on BN nanocluster should be stable under high temperatures...
September 4, 2017: Journal of Molecular Graphics & Modelling
Laura Domicevica, Heidi Koldsø, Philip C Biggin
P-glycoprotein (P-gp) can transport a wide range of very different hydrophobic organic molecules across the membrane. Its ability to extrude molecules from the cell creates delivery problems for drugs that target proteins in the central nervous system (CNS) and also causes drug-resistance in many forms of cancer. Whether a drug will be susceptible to export by P-gp is difficult to predict and currently this is usually assessed with empirical and/or animal models. Thus, there is a need to better understand how P-gp works at the molecular level in order to fulfil the 3Rs: Refinement, reduction and replacement of animals in research...
September 2, 2017: Journal of Molecular Graphics & Modelling
Yinguang Zhang, Yongwang Zhang, Yuxiang Zhang
Human sacum is regulatory adaptor protein involved in cellular signaling network of colorectal cancer. Molecular evidence suggests that the protein is integrated into oncogenic signaling network by binding to SH3-containing proteins through its proline-rich motifs. In this study, we have performed a transcriptome-wide analysis and identification of sacum-binding partners in the genome profile of human colorectal cancer. The sacum-binding potency of SH3-containing proteins found in colorectal cancer was investigated by using bioinformatics modeling and intermolecular binding analysis...
September 2, 2017: Journal of Molecular Graphics & Modelling
B G de Sousa, J I N Oliveira, E L Albuquerque, U L Fulco, V E Amaro, C A G Blaha
Many species of bacteria involved in degradation of n-alkanes have an important constitutional metabolic enzyme, the alkane hydroxylase called AlkB, specialized in the conversion of hydrocarbons molecules that can be used as carbon and/or energy source. This enzyme plays an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. A number of these enzymes has been biochemically characterized in detail because the potential of alkane hydroxylases to catalyse high added-value reactions is widely recognized...
September 1, 2017: Journal of Molecular Graphics & Modelling
Mehdi D Esrafili, Fahimeh Sharifi, Leila Dinparast
Today, the global greenhouse effect of carbon dioxide (CO2) is a serious environmental problem. Therefore, developing efficient methods for CO2 capturing and conversion to valuable chemicals is a great challenge. The aim of the present study is to investigate the catalytic activity of Pt- or Ni-doped graphene for the hydrogenation of CO2 by a hydrogen molecule. To gain a deeper insight into the catalytic mechanism of this reaction, the reliable density functional theory calculations are performed. The adsorption energies, geometric parameters, reaction barriers, and thermodynamic properties are calculated using the M06-2X density functional...
August 28, 2017: Journal of Molecular Graphics & Modelling
S Sahmani, M M Aghdam, M Bahrami
Understanding the size-dependent behavior of structures at nanoscale is essential in order to have an effective design of nanosystems. In the current investigation, the surface elasticity theory is extended to study the nonlinear buckling and postbuckling response of axially loaded silicon cylindrical naoshells. Thereby, an efficient size-dependent shear deformable shell model is developed including the size effect of surface free energy. A boundary layer theory of shell buckling in conjunction with a perturbation-based solution methodology is employed to predict the size dependency in the buckling loads and postbuckling behavior of silicon nanoshells having various thicknesses...
August 24, 2017: Journal of Molecular Graphics & Modelling
Zhe Ju, Jian-Jun He
As one of the most important and common histones post-translational modifications, crotonylation plays a key role in regulating various biological processes. The accurate identification of crotonylation sites is crucial to elucidate the underlying molecular mechanisms of crotonylation. In this study, a novel bioinformatics tool named CKSAAP_CrotSite is developed to predict crotonylation sites. The highlight of CKSAAP_CrotSite is to adopt the composition of k-spaced amino acid pairs as input encoding, and the support vector machine is employed as the classifier...
August 24, 2017: Journal of Molecular Graphics & Modelling
Carolyn Readmond, Chun Wu
Currently, Vorapaxar is the only recently FDA-approved antiplatelet drug targeting Protease-activated receptor 1 (PAR1). However, a novel antagonist, F16357, has been shown to prevent painful bladder syndrome, also known as interstitial cystitis (IC). Unfortunately, there is no high resolution structure of the F16357-receptor complex, hindering its optimization as a therapeutic agent. In this study, we used docking and molecular dynamic (MD) simulations to investigate the detailed interactions between F16357 and PAR1 at a molecular level...
August 24, 2017: Journal of Molecular Graphics & Modelling
Nguyen Minh Tam, Minh Tho Nguyen, Son Tung Ngo
The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R=0...
August 24, 2017: Journal of Molecular Graphics & Modelling
Nahid Hesabi, Ali Ebrahimi, Alireza Nowroozi
Some biological activities of quinones can be attributed to the H-bonding ability of acceptor oxygen atoms. According to the results obtained from the quantum mechanical calculations performed on a wide variety of complexes between the 1,4-benzoquinone (BQ) derivatives and HF molecules, the interplay between H-bonds and individual H-bond interaction energies (EHB) can be affected by the substituents placed on the six-membered ring of BQ. The total binding energies of complexes become more negative by the electron donating substituents (EDSs) while the changes are reversed by the electron withdrawing substituents (EWSs)...
August 19, 2017: Journal of Molecular Graphics & Modelling
Pratibha Singh, Priti Talwar
Recently, a new signaling complex Death Associated Protein Kinase 1 (DAPK1) ̶ N-methyl-D-aspartate receptor subtype 2B (NMDAR2B or NR2B) engaged in the neuronal death cascade was identified and it was found that after stroke injury, N-methyl-D-aspartate glutamate (NMDA) receptors interact with DAPK1 through NR2B subunit and lead to excitotoxicity via over-activation of NMDA receptors. An acute brain injury, such as stroke, is a serious life-threatening medical condition which occurs due to poor blood supply to the brain and further leads to neuronal cell death...
August 18, 2017: Journal of Molecular Graphics & Modelling
Pravin Kumar, Shashwati Ghosh Sachan, Raju Poddar
Improving the industrial enzyme for better yield of the product is important and a challenging task. One of such important industrial enzymes is microbial Hydroxycinnamoyl-CoA hydratase-lyase (HCHL). It converts feruloyl-CoA to vanillin. We place our efforts towards the improvement of its catalytic activity with comprehensive computational investigation. Catalytic core of the HCHL was explored with molecular modeling and docking approaches. Site-directed mutations were introduced in the catalytic site of HCHL in a sequential manner to generate different mutants of HCHL...
August 18, 2017: Journal of Molecular Graphics & Modelling
Nguyen Quoc Thai, Hoang Linh Nguyen, Huynh Quang Linh, Mai Suan Li
The treatment of many diseases may require drugs that are capable to attack multiple targets simultaneously. Obviously, the virtual screening of multi-target drug candidates is much more time consuming compared to the single-target case. This, in particular, concerns the last step of virtual screening where the binding free energy is computed by conventional molecular dynamics simulation. To overcome this difficulty we propose a simple protocol which is relied on the fast steered molecular dynamics simulation and on available experimental data on binding affinity of reference ligand to a given target...
August 18, 2017: Journal of Molecular Graphics & Modelling
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