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Journal of Biomolecular Structure & Dynamics

Takahide Okuyama, Ryosuke Yamagishi, Jiro Shimada, Masaaki Ikeda, Yayoi Maruoka, Hiroki Kaneko
Oct4 is a master regulator of the induction and maintenance of cellular pluripotency, and has crucial roles in early stages of differentiation. It is the only factor that cannot be substituted by other members of the same protein family to induce pluripotency. However, although Oct4 nuclear transport and delivery to target DNA are critical events for reprogramming to pluripotency, little is known about the molecular mechanism. Oct4 is imported to the nucleus by the classical nuclear transport mechanism, which requires importin α as an adaptor to bind the nuclear localization signal (NLS)...
February 6, 2017: Journal of Biomolecular Structure & Dynamics
Suniba Shuaib, Bhupesh Goyal
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β42 (Aβ42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ42...
February 6, 2017: Journal of Biomolecular Structure & Dynamics
Mohammad Furkan, Asim Rizvi, Md Tauqir Alam, Aabgeena Naeem
Catalase, a ubiquitous enzyme of the free radical scavenging machinery unfolds and aggregates in the presence of 2, 2, 2, triflouroethanol (TFE). Catalase molecule aggregates at 50% TFE as evident by high thioflavin T fluorescence, shifted congo red absorbance, change in circular dichroism and soret spectra. TEM images confirmed the nature of catalase aggregates to be oligomers. Organic solvent induced aggregation of catalase is prevented by presence of peroxidase (another enzyme of the free radical scavenging machinery)...
February 2, 2017: Journal of Biomolecular Structure & Dynamics
Ramesh Prasad, Prosenjit Sen
Tissue factor (TF)-mediated factor VII (FVII) activation and subsequent proteolytic TF-FVIIa binary complex formation is the key step initiating the coagulation cascade, with implications in various homeostatic and pathologic scenarios. TF binding allosterically modifies zymogen-like free FVIIa to its highly catalytically active form. As the result of unresolved crystal structure of the full-length TF1-263-FVIIa binary complex and free FVIIa, allosteric alterations in FVIIa following its binding to full-length TF and the consequences of these on function are not entirely clear...
February 2, 2017: Journal of Biomolecular Structure & Dynamics
Roohollah Ghobadi, Adeleh Divsalar, Ali Reza Harifi-Mood, Ali Akbar Saboury
Successful clinical experience of using cisplatin and its derivatives in cancer therapy has encouraged scientists to synthesize new metal complexes with the aim of interacting with special targets such as proteins In this regard, biological effects of [Pt(FIP)(Phen)](NO3)2 compound which contains a novel phen-imidazole ligand, FIP, was investigated on bovine liver Catalase (BLC) structure and function. Various spectroscopic methods such as UV-visible, fluorescence, and circular dichroism (CD) were applied at two temperatures of 25 and 37 °C for kinetics and structural studies...
February 2, 2017: Journal of Biomolecular Structure & Dynamics
Massoud Saidijam, Sonia Azizpour, Simon G Patching
We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1,551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition...
February 2, 2017: Journal of Biomolecular Structure & Dynamics
Pedro Josué Trejo-Soto, Alicia Hernández-Campos, Antonio Romo-Mancillas, José L Medina-Franco, Rafael Castillo
The AKT isoforms are a group of key kinases that play a critical role in tumorigenesis. These enzymes are overexpressed in different types of cancers, such as breast, colon, prostate, ovarian and lung. Because of its relevance the AKT isoforms are attractive targets for the design of anticancer molecules. However, it has been found that AKT1 and AKT3 isoforms have a main role in tumor progression and metastasis; thus, the identification of AKT isoforms specific inhibitors seems to be a challenge. Previously, we identified an ATP binding pocket pan-AKT inhibitor, this compound is a 2,4,6-trisubstituted pyridine (compound 11), which represents a new interesting scaffold for the developing of AKT inhibitors...
February 2, 2017: Journal of Biomolecular Structure & Dynamics
C Pitchumani Violet Mary, R Shankar, S Vijayakumar
Computational studies on the interaction of novel inhibitor compounds with the Cathepsin K protease has been performed to study the inhibition properties of the inhibitor compounds. The quantum chemical calculations have been performed to analyze the molecular geometries, structural stability, reactivity, nature of interaction and the charge transfer properties using B3LYP level of theory by implementing 6-311g(d,p) basis set. The calculated C-S and N-H...N bond lengths of the inhibitor-triad complexes are found to agree well with the previous literature results...
February 2, 2017: Journal of Biomolecular Structure & Dynamics
Saikiran Reddy Peddi, Sree Kanth Sivan, Vijjulatha Manga
The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔGbind and experimental pIC50 values...
February 1, 2017: Journal of Biomolecular Structure & Dynamics
Garima Sharma, S Vasanth Kumar, Habibah A Wahab
A series of dimeric naphthoquinones containing natural 2-hydroxy-1-4-naphthoquinone moiety was designed, synthesized, and evaluated against neuraminidase of H5N1 virus. p-hydroxy derivatives showed higher inhibition when compared to p-halogenated compounds. Molecular docking studies conducted with H5N1 neuraminidase clearly demonstrated different binding modes of the most active compound onto the open and closed conformations of loop 150. The results thus provide not only evidences of a novel scaffold evaluated as inhibitor, but also a rational explanation involving molecular modeling and the role of loop 150 in the binding...
February 1, 2017: Journal of Biomolecular Structure & Dynamics
Vikrant Kumar Sinha, Om Prakash Sharma, Muthuvel Suresh Kumar
Serine protease cleaved Complement component 4 (C4) at sessile loop, which is significant for completion of lectin and classical complement pathways at the time of infections. The co-crystalized structure of C4 with Mannose-binding protein-associated serine protease 2 (MASP2) provided the structural and functional aspects of its interaction and underlined the C4 activation by MASP2. The same study also revealed the significance of Complement control protein (CCP) domain through mutational study, where mutated CCP domain led to the inhibition of C4 activation...
January 29, 2017: Journal of Biomolecular Structure & Dynamics
Yury N Vorobjev, Harold A Scheraga, Jorge A Vila
A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water. The accuracy of the proposed method of calculation of pKa values is estimated from a test set of experimental pKa data for 297 ionizable residues from 34 proteins...
January 29, 2017: Journal of Biomolecular Structure & Dynamics
Ramin Ekhteiari Salmas, Serdar Durdagi, Mehmet Fuat Gulhan, Merve Duruyurek, Huda I Abdullah, Zeliha Selamoglu
The objective of the present study was to evaluate the effects of propolis, pollen, and caffeic acid phenethyl ester (CAPE) on tyrosine hydroxylase (TH) activity and total RNA levels of Nω-nitro-L-arginine methyl ester (L-NAME) inhibition of nitic oxide synthase in the heart, adrenal medulla, and hypothalamus of hypertensive male Sprague dawley rats. The TH activity in the adrenal medulla, heart, and hypothalamus of the rats was significantly increased in the L-NAME group versus control (P<0.05). Treatment with L-NAME led to a significant increase in blood pressure (BP) in the L-NAME group compared to control (P<0...
January 29, 2017: Journal of Biomolecular Structure & Dynamics
Sk Abdul Amin, Sonam Bhargava, Nilanjan Adhikari, Shovanlal Gayen, Tarun Jha
Phosphodiesterase 1 (PDE1) is a potential target for a number of neurodegenerative disorders such as Schizophrenia, Parkinson's and Alzheimer's diseases. A number of pyrazolo[3,4-d]pyrimidine PDE1 inhibitors were subjected to different molecular modeling techniques [such as regression-based quantitative structure-activity relationship (QSAR): multiple linear regression (MLR), support vector machine (SVM) and artificial neural network (ANN); classification-based QSAR: Bayesian modeling and Recursive partitioning; Monte Carlo based QSAR; Open3DQSAR; pharmacophore mapping and molecular docking analyses] to get a detailed knowledge about the physicochemical and structural requirements for higher inhibitory activity...
January 29, 2017: Journal of Biomolecular Structure & Dynamics
Neeraj Dohare, Abbul Bashar Khan, Neha Maurya, Sonu Thakur, Fareeda Athar, Prashant Singh, Rajan Patel
No abstract text is available yet for this article.
January 24, 2017: Journal of Biomolecular Structure & Dynamics
Zeinab Tavassoli, Majid Taghdir, Bijan Ranjbar
One way to control hypertension is inactivation of the Renin- Angiotensin- Aldosterone System (RAAS). Inhibition of renin as a rate-limiting step of this system is an effective way to stop up RAAS. It has been proved that soyasaponin I, an herbal compound obtained from soybeans, has anti-hypertensive effect via renin inhibition, so it has the potential of being an anti-hypertensive drug. Herein, some theoretical approaches such as Docking Simulation, Molecular Dynamics (MD) Simulation and MMPBSA analysis have been used to study how soyasaponin I inhibits renin at the structural level...
January 19, 2017: Journal of Biomolecular Structure & Dynamics
Amartya Roy, Paromita Seal, Jyotirmoy Sikdar, Sanghamitra Banerjee, Rajen Haldar
Linezolid, one of the reserve antibiotic of oxazolidinone class has wide range of antimicrobial activity. Here we have conducted a fundamental study concerning the dynamics of its interaction with bovine serum albumin (BSA), and the post binding modification of the later by employing different spectroscopic (absorption, fluorescence and circular dichroism (CD) spectroscopy) and molecular docking tools. Gradual quenching of the tryptophan (Trp) fluorescence upon addition of linezolid to BSA confirms their interaction...
January 19, 2017: Journal of Biomolecular Structure & Dynamics
Fatemeh Khosravi, Hassan Mansouri-Torshizi
Four Co(III)-, Cu(II)-, Zn(II)- and Pd(II)- based potent antibacterial complexes of formula K3[Co(ox)3].3H2O (I), [Cu(bpy)2Cl]Cl.5H2O (II), [Zn(bpy)3]Cl2 (III) and [Pd(bpy)2](NO3)2 (IV) (where ox is oxalate and bpy is 2,2'-bipyridine) were synthesized. They were characterized by elemental analyses, molar conductance measurements, UV-Vis, FT-IR, (1)H NMR and (13)C NMR spectra. These metal complexes were ordered in three combination series of I+II, I+II+III and I+II+III+IV. Antibacterial activity was tested for each of these four metal complexes and their combinations against gram positive and gram negative bacteria...
January 16, 2017: Journal of Biomolecular Structure & Dynamics
Indrani Bera, Mrinal Vishwas Marathe, Pavan V Payghan, Nanda Ghoshal
Opioid agonists are used clinically for the treatment of acute and chronic pain, however, their clinical use is limited due to the presence of undesired side effects. Dual agonists, simultaneously targeting mu and kappa opioid receptors, show fewer side effects than that of selective agonists. In the present work, 2D- and 3D- Quantitative Structure Activity Relationship studies were performed on a series of aminomorphinan derivatives as dual agonists, using a wide range of descriptors. The aim of the study was to identify the structural requirements for the activity of these compounds towards mu and kappa opioid receptors and using the models, with best external predictability, for predicting the activities of new hits obtained from shape based virtual screening of drug like compounds from ZINC database...
January 16, 2017: Journal of Biomolecular Structure & Dynamics
Prabu Manoharan, Kiranmai Chennoju, Nanda Ghoshal
More than 100 years of research on Alzheimer's disease didn't yield a potential cure for this dreadful disease. Poor Blood Brain Barrier (BBB) permeability and P-glycoprotein binding of BACE1 inhibitors are the major causes for the failure of these molecules during clinical trials. The design of BACE1 inhibitors with a balance of sufficient affinity to the binding site and little or no interaction with P-glycoproteins is indispensable. Identification and understanding of protein-ligand interactions are essential for ligand optimization process...
January 12, 2017: Journal of Biomolecular Structure & Dynamics
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