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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
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 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...
January 12, 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
Bharati Pandey, Sonam Grover, Chetna Tyagi, Sukriti Goyal, Salma Jamal, Aditi Singh, Jagdeep Kaur, Abhinav Grover
DNA gyrase is a validated target of fluoroquinolones which are key components of multidrug resistance (MDR) TB treatment. Most frequent occurring mutations associated with high level of resistance to fluoroquinolone in clinical isolates of TB patients are A90V, D94G and A90V-D94G (double mutant), present in the larger subunit of DNA Gyrase. In order to explicate the molecular mechanism of drug resistance corresponding to these mutations, molecular dynamics and mechanics approach was applied. Structure based molecular docking of complex comprised of DNA bound with Gyrase A (large subunit) and Gyrase C (small subunit) with moxifloxacin revealed high binding affinity to wild type with considerably high Glide XP docking score of -7...
January 10, 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 10, 2017: Journal of Biomolecular Structure & Dynamics
Manika Awasthi, Swati Singh, Veda P Pandey, Upendra N Dwivedi
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive accumulation of amyloid-beta (Aβ) peptides in brain. In the present study, two familial Aβ42 mutations, namely A2V (harmful) and A2T (protective) have been analyzed and compared with the wild-type (WT) by performing all-atom molecular dynamics (MD) simulations in the absence and presence of curcumin, a well known inhibitor of Aβ plaque formation. Mutant A2V was found to exhibit highest stability followed by WT and mutant A2T in the absence of curcumin...
January 5, 2017: Journal of Biomolecular Structure & Dynamics
Anu V Chandran, S Jayanthi, M Vijayan
Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from Mycobacterium tuberculosis, Mycobacterium smegmatis and Escherichia coli and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles...
January 4, 2017: Journal of Biomolecular Structure & Dynamics
Yuri N Chirgadze, Eugenia A Boshkova, Kevin P Battaile, Vitor G Mendes, Robert Lam, Tiffany S Y Chan, Vladimir Romanov, Emil F Pai, Nickolay Y Chirgadze
The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn(2+)-ion have been presented. The 152 amino acid protein consists of two similar domains with α+β topology. In both crystalline state and in solution, the protein forms a dimer with monomers related by a two-fold pseudo-symmetry rotation axis. A sequence homology search identified the protein as a member of the structural family Glyoxalase I. We have shown the enzyme possesses glyoxalase I activity in the presence of Zn(2+), Mg(2+), Ni(2+) and Co(2+), in this order of preference...
December 29, 2016: Journal of Biomolecular Structure & Dynamics
Neelam Lohani, Himanshu Narayan Singh, Moganty R Rajeswari
HMGB1 (High mobility group box 1) protein has been an attractive therapeutic target for drug designing in various human cancers and inflammatory diseases. Overexpression of HMGB1 has been associated with all the seven hallmark of cancer. Actinomycin -D (Act-D) is a classical anticancer drug that binds GC-rich DNA with high affinity to cause transcription inhibition. In the present study we utilized the 21 nucleotide G rich DNA fragment in the regulatory region of hmgb1 gene for its ability to bind with Act-D...
December 29, 2016: Journal of Biomolecular Structure & Dynamics
Madhura Pradhan, Charu Suri, Sinjan Choudhary, Pradeep Kumar Naik, Manu Lopus
Beta-sitosterol (β-SITO), a phytosterol present in many edible vegetables, has been reported to possess antineoplastic properties and cancer treatment potential. We have shown previously that it binds at a unique site (the 'SITO-site') compared to the colchicine binding site at the interface of α- and β-tubulin. In this study, we investigated the anticancer efficacy of β-SITO against invasive breast carcinoma using MCF-7 cells. Since 'isotypes' of β-tubulin show tissue-specific expression and many are associated with cancer drug resistance, using computer-assisted docking and atomistic molecular dynamic simulations, we also examined its binding interactions to all known isotypes of β-tubulin in αβ-tubulin dimer...
December 29, 2016: Journal of Biomolecular Structure & Dynamics
Tajalli Ilm Chandel, Gulam Rabbani, MohsinVahid Khan, Masihuz Zaman, Parvez Alam, Yasser E Shahein, Rizwan Hasan Khan
Isoprenaline hydrochloride is a potential cardiovascular drug helps in the smooth functioning of the heart muscles. So, we have performed the binding study of ISO with BSA. This study was investigated by UV absorption, fluorescence, synchronous fluorescence, circular dichroism, etc. The analysis of intrinsic fluorescence data showed the low binding affinity of ISO. The binding constant Kb was 2.8 × 103 M-1 and binding stoichiometry (n) was approximately one and the Gibb's free energy change at 310 K was determined to be -8...
December 29, 2016: Journal of Biomolecular Structure & Dynamics
Dmitry A Altukhov, Anna A Talyzina, Yulia K Agapova, Anna V Vlaskina, Dmitry A Korzhenevskiy, Eduard V Bocharov, Tatiana V Rakitina, Vladimir I Timofeev, Vladimir O Popov
The histone-like (HU) protein is one of the major nucleoid-associated proteins involved in DNA supercoiling and compaction into bacterial nucleoid as well as in all DNA-dependent transactions. This small positively charged dimeric protein binds DNA in a non-sequence specific manner promoting DNA super-structures. The majority of HU proteins are highly conserved among bacteria; however, HU protein from Mycoplasma gallisepticum (HUMgal) has multiple amino acid substitutions in the most conserved regions, which are believed to contribute to its specificity to DNA targets unusual for canonical HU proteins...
December 29, 2016: Journal of Biomolecular Structure & Dynamics
Jianzhong Chen
Molecular dynamics (MD) simulations coupled with principal component (PC) analysis were carried out to study functional roles of Mg(2+) binding to extracellular signal-regulated kinase 2 (ERK2). The results suggest that Mg(2+) binding heavily decreases eigenvalue of the first principal component and totally inhibits motion strength of ERK2, which favors stabilization of ERK2 structure. Binding free energy predictions indicate that Mg(2+) binding produces an important effect on binding ability of ATP to ERK2 and strengthens the ATP binding...
December 28, 2016: Journal of Biomolecular Structure & Dynamics
Alison L E Pereira, Gabriela B Dos Santos, Márcia S F Franco, Leonardo B Federico, Carlos H T P da Silva, Cleydson B R Santos
Human Dipeptidyl Peptidase IV (hDDP-IV) has a considerable importance in inactivation of glucagon-like peptide-1 (GLP-1), which is related to type 2 diabetes. One approach for the treatment is the development of small hDDP-IV inhibitors. In order to design better inhibitors, we analyzed 5-(aminomethyl)-6-(2,4-dichlrophenyl)-2-(3,5-dimethoxyphenyl)pyrimidin-4-amine and a set of 24 molecules found in the BindingDB web database for model designing. The analysis of their molecular properties allowed the design of a Multiple Linear Regression Model for activity prediction...
December 28, 2016: Journal of Biomolecular Structure & Dynamics
Umar Ndagi, Ndumiso N Mhlongo, Mahmoud E Soliman
Recent studies have linked a deadly form of prostate cancer known as metastatic castration-resistant prostate cancer (mCRPC) to retinoic acid-related orphan-receptor gamma (ROR-γ). Most of these studies continued to place ROR-γ as orphan because of unidentifiable inhibitor. Recently identified inhibitors of ROR-γ and their therapeutic potential were evaluated, among which inhibitor XY018 was the potent. However, molecular understanding of the conformational features of XY018-ROR-γ complex is still elusive...
December 28, 2016: Journal of Biomolecular Structure & Dynamics
Hamid Dezhampanah, Roghaye Firouzi
Bis(indolyl)methane (BIM) as one of the main active components of anticancer and antibacterial drugs is applied in medicinal and extensive area of chemistry. In this research, interaction of human and bovine serum albumins as drug carriers with BIM was investigated using spectroscopy methods and molecular modeling study. The fluorescence quenching measurements at the range of 293-310 K revealed that the quenching mechanisms for human and bovine serum albumins are static and dynamic processes, respectively...
December 28, 2016: Journal of Biomolecular Structure & Dynamics
Sangeeta Kundu
The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution...
December 26, 2016: Journal of Biomolecular Structure & Dynamics
L A Uroshlev, I V Kulakovskiy, N G Esipova, V G Tumanyan, S V Rahmanov, V J Makeev
: Structures of many metal-binding proteins are often obtained without structural cations, in their apoprotein forms. Missing cation coordinates are usually updated from structural templates constructed from many holoprotein structures. Such templates usually do not include structural water, the important contributor to the ion binding energy. Structural templates are also inconvenient for taking into account structural modifications around the binding site at apo-/holo- transitions. An approach based upon statistical potentials readily takes into account structural modifications associated with binding as well as contribution of structural water molecules...
December 26, 2016: Journal of Biomolecular Structure & Dynamics
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