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Journal of Biomolecular Structure & Dynamics

Yamuna Kalyani Mathiharan, M R N Murthy
Stationary phase survival protein SurE from Salmonella typhimurium is a dimeric protein formed by the swapping of a tetramerization loop involved in the formation of a loose tetramer and a C-terminal helix. It functions as a phosphatase. The two-fold symmetry of the dimeric protein was lost in the mutants H234A and D230A/H234A in which a crucial hydrogen bond in the hinge involved in C-terminal helix swapping was eliminated. The catalytic activity of both mutants was drastically reduced. In contrast to the native protein, H234A exhibited positive cooperativity in its catalytic activity...
July 17, 2017: Journal of Biomolecular Structure & Dynamics
Sefa Celik, Serda Kecel-Gunduz, Sevim Akyuz, Aysen E Ozel
The theoretically possible stable conformer of the cyclic heptapeptide, that has significant anti-metastatic activity, was examined by conformational analysis followed by DFT calculations. Experimental infrared and Raman spectroscopy, together with theoretical DFT (6-31G (d,p) basis set)-based quantum chemical calculations, have been used to understand the structural and spectral characteristics of cyclo(Gly-Arg-Gly-Asp-Ser-Pro-Ala) {cyclo(GRGDSPA)}. A complete analysis of the vibrational spectrum has been reported on the basis of potential energy distribution (PED %) data of the vibrational modes...
July 17, 2017: Journal of Biomolecular Structure & Dynamics
Eshel Faraggi, Keith Dunker, Joel Sussman, Andrzej Kloczkowski
Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure...
July 17, 2017: Journal of Biomolecular Structure & Dynamics
Ji-Xia Ren, Cheng-Ping Li, Xiu-Ling Zhou, Xue-Song Cao, Yong Xie
Myeloid cell leukemia-1 (Mcl-1) has been a validated and attractive target for cancer therapy. Over-expression of Mcl-1 in many cancers allows cancer cells to evade apoptosis and contributes to the resistance to current chemotherapeutics. Here, we identified new Mcl-1 inhibitors using a multi-step virtual screening approach. First, based on two different ligand-receptor complexes, 20 pharmacophore models were established by simultaneously using "Receptor-Ligand Pharmacophore Generation" method and manual build feature method, and then carefully validated by a test database...
July 17, 2017: Journal of Biomolecular Structure & Dynamics
Namrata Singh, Darshana Pagariya, Surbhi Jain, Sunil Naik, Nand Kishore
Serum albumins being the most abundant proteins in the blood and cerebrospinal fluid are significant carriers of essential transition metal ions in the human body. Studies of copper (II) complexes have gained attention because of their potential applications in synthetic, biological and industrial processes. Study of binding interactions of such bioinorganic complexes with serum albumins improves our understanding of biomolecular recognition process essential for rational drug desig. In the present investigation, we have applied quantitative approach to explore interactions of novel synthesized copper (II) complexes viz...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
Sarfaraz Alam, Feroz Khan
To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure-activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity-descriptors relationship accuracy of 94% referred by regression coefficient (r(2)= 0.94) and a high activity prediction accuracy of 91%. The QSAR study indicates that chemical descriptors, chiV5, T_T_Cl_7, T_2_T_4, SsCH3count, and Epsilon3 are significantly correlated with anticancer activity...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
Dhivya Shanmugarajan, C Suresh Kumar, Vijayakumar Bommuraj, Rethavathi Janarthanam, Meena Chandran, Usha Talambedu, Sushilkumar Middha
The G-coupled receptors seen on the cell surface are composites with a lipid bilayer. The chemokines are kind of G-coupled receptor which majorly involved in the activation and downstream signalling of the cell. In general, many G-coupled receptors are lack of its 3D structure that become a hurdle in the drug designing process. In this study, comparative modelling of the CXCR3 receptor was carried out, structure evaluation was done using various tools and software's. Additionally, molecular dynamics and docking were performed to prove the structural quality and architecture...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
Amresh Prakash, Gunjan Dixit, Naveen Kumar Meena, Ruhar Singh, Poonam Vishwakarma, Smriti Mishra, Andrew M Lynn
Human carbonic anhydrase IX (CAIX) has evolved as a promising biomarker for cancer prognosis, due to its overexpression in various cancer and restricted expression in normal tissue. However, limited information is available on its biophysical behavior. The unfolding of CAIX in aqueous urea solution was studied using all-atom molecular dynamics simulation approach. The results of this study revealed a stable intermediate state along the unfolding pathway of CAIX. At intermediate concentrations of urea (2.0-4...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
Shruti Mathur, Prashant Deshmukh, Shailesh Tripathi, Palaniappan Marimuthu, Balasundaram Padmanbhan
BET (Bromodomain and Extra-terminal) family proteins recognize the acetylated histone code on chromatin and participate in downstream processes like DNA replication, modification, and repair. As part of epigenetic approaches, BRD2 and BRD4 were identified as putative targets, for the management of chronic diseases. We have recently reported the discovery of a new scaffold of the phenanthridinone based inhibitor (L10) of the second bromodomain of BRD2 (BRD2-BD2). Here, we present the crystal structure of the BRD2-BD2, refined to 1...
July 11, 2017: Journal of Biomolecular Structure & Dynamics
Xiaofeng Ji, Yi Xiao, Shiyong Liu
The pore domain of human voltage-dependent cardiac sodium channel Nav1.5 (hNav1.5) is the crucial binding targets for antiarrhythmic drugs and some local anesthetic drugs but its three-dimensional structure is still lacking. This has affected the detailed studies of the binding features and mechanism of these drugs. In this paper, we present a structural model for open-state pore domain of hNav1.5 built by using single template ROSETTA-membrane homology modeling with the crystal structure of NavMs. The assembled structural models are evaluated by rosettaMP energy and locations of binding sites...
July 6, 2017: Journal of Biomolecular Structure & Dynamics
Reza Hosseinzadeh, Khatereh Khorsandi, Ghader Hosseinzadeh
The interaction of methylene blue (MB) as a photosensitizer with graphene oxide nano-sheets (GO) was examined in aqueous solution using UV-vis spectrophotometric techniques. MB-GO composites were prepared by mixing the solutions of GO nano-sheets and methylene blue due to interacting of the cationic methylene blue photosensitizer via electrostatic and π-π stacking or hydrophobic cooperative interactions. The cell killing potential of nanocomposite was examined on the MDA-MB-231 breast cancer cells in the absence and presence of red LED irradiation...
July 6, 2017: Journal of Biomolecular Structure & Dynamics
Aravind Kumar Konda, Rohit Farmer, Khela Ram Soren, P S Shanmugavadivel, Aravind Setti
Chickpea is a premier food legume crop with high nutritional quality and attains prime importance in the current era of 795 million people being undernourished worldwide. Chickpea production encounters setbacks due to various stresses and understanding the role of key transcription factors involved in multiple stresses becomes inevitable. We have recently identified a multi-stress responsive WRKY transcription factor (TF) in chickpea. The present study was conducted to predict the structure of WRKY TF to identify the DNA interacting residues and decipher DNA-protein interactions...
July 5, 2017: Journal of Biomolecular Structure & Dynamics
Jin Ha Park, Hyun Suk Lee, Myung Duk Jang, Sung Wook Han, Seog K Kim, Young-Ae Lee
The interaction of Δ- and Λ-[Ru(phen)2DPPZ](2+) (DPPZ = dipyrido[3,2-a:2', 3'-c]phenazine, phen = phenanthroline) with a G-quadruplex formed from 5'-G2T2G2TGTG2T2G2-3'(15-mer) was investigated. The well-known enhancement of luminescence intensity (the 'light-switch' effect) was observed for the [Ru(phen)2DPPZ](2+) complexes upon formation of an adduct with the G-quadruplex. The emission intensity of the G-quadruplex-bound Λ-isomer was 3-fold larger than that of the Δ-isomer when bound to the G-quadruplex, which is opposite of the result observed in the case of double stranded DNA (dsDNA); the light switch effect is larger for the dsDNA-bound Δ-isomer...
July 4, 2017: Journal of Biomolecular Structure & Dynamics
Sedighehsadat Hojati, Arezou Ghahghaei, Milad Lagzian
Aβ1-40 and Aβ1-42 have been shown to be the main components of the amyloid plaques found in the extracellular environment of neurons in Alzheimer's disease. β-Casein, a milk protein, has been shown to display a remarkable chaperone ability in preventing the aggregation of proteins. In this study, the ability of β-casein to suppress the amyloid fibril formation of Aβ1-42 has been examined through in vitro studies and molecular docking simulation. The results demonstrate the inhibitory effect of β-casein on fibril formation in Aβ1-42, in a concentration dependent manner, suggesting that the chaperone binds to the Aβ1-42 and prevents amyloid fibril formation...
July 4, 2017: Journal of Biomolecular Structure & Dynamics
Anupriya Sadhasivam, Umashankar Vetrivel
Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC...
July 4, 2017: Journal of Biomolecular Structure & Dynamics
Rohit Shukla, Harish Shukla, Parismita Kalita, Amit Sonkar, Tripti Pandey, Dev Bukhsh Singh, Awanish Kumar, Timir Tripathi
Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score...
July 4, 2017: Journal of Biomolecular Structure & Dynamics
Priya Yadav, Ganesh Shahane, Sushama Gaikwad
Polyproline II (PPII) fold, a peculiar structural element was detected in the Amaranthus caudatus seed lectin (ACL) based on far UV circular dichroism spectrum, conformational transitions of the lectin and a distinct isodichroic point in thermal denaturation. It was confirmed by using PolyprOnline database to estimate the percentage of amino acids contributing to PPII fold and showed the values as 13.5% and 13.9% for PROSS and XTLSSTR, respectively. Investigations of the functional and conformational transitions of ACL during thermal, pH and guanidine hydrochloride (GdnHCl) induced denaturation were carried out using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach...
July 3, 2017: Journal of Biomolecular Structure & Dynamics
Valeriya M Trusova, Galyna P Gorbenko
Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40 and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase of the gyration radius and the decrease in RMSD of polypeptide chain...
June 30, 2017: Journal of Biomolecular Structure & Dynamics
Sankari Mohan, Hridya Hemachandran, P Sneha, C George Priya Doss, J Godwin Christopher, Gurunathan Jayaraman, Siva Ramamoorthy
Bixin and crocin are natural apocarotenoids utilized as food colorants and additives in food industries worldwide. For safety assessment, it is necessary to understand the biological interaction of food colorants. In our present study, we report the interaction of two apocarotenoids with bovine serum albumin (BSA) at physiological pH using spectroscopic techniques and in silico tools. The binding constant and the mode of binding sites have been studied. The enthalpic and entropic contribution to the intermolecular binding event was analyzed and it was found that the contribution of hydrogen bonding and hydrophobic interactions was dominant...
June 30, 2017: Journal of Biomolecular Structure & Dynamics
Elmira I Yakupova, Ivan M Vikhlyantsev, Liya G Bobyleva, Nikita V Penkov, Alexander A Timchenko, Maria A Timchenko, Gennady A Enin, Sergei S Khutzian, Olga M Selivanova, Alexander G Bobylev
A comparative study of amyloid properties of the aggregates of smooth muscle titin (SMT) from chicken gizzard was carried out. These aggregates were formed in two solutions: 0.15 M glycine-KOH, pH 7.2-7.4 (SMT(Gly)) and 0.2 M KCl, 10 mM imidazole, pH 7.0 (SMT(KCl)). Electron microscopy data showed that SMT aggregates has an amorphous structure in both cases. The results of atomic-force microscopy demonstrated slight differences in morphology in two types of aggregates. The SMT(Gly) aggregates were represented as branching chains, composed of spherical aggregates approximately 300-500 nm in diameter and up to 35 nm in height...
June 29, 2017: Journal of Biomolecular Structure & Dynamics
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