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Journal of Biomolecular Structure & Dynamics

Girish G Ariga, Praveen N Naik, Sharanappa T Nandibewoor, Shivamurti A Chimatadar
The goal of this study was to investigate the interactions between meclizine (MEC) and human serum albumin (HSA) under physiological conditions by different spectroscopies and molecular modeling technique. The drug, MEC quenched the intrinsic fluorescence of HSA and the analysis of the results revealed that static quenching mechanism. The binding of MEC quenches the HSA fluorescence; stoichiometry was 1:1 interaction. Thermodynamic quantities were calculated at different temperatures suggested that hydrophobic and van der Waals interaction with HSA-MEC...
October 21, 2016: Journal of Biomolecular Structure & Dynamics
Somaye Shahraki, Maryam Saeidifar, Fereshteh Shiri, Ameneh Heidari
In this study, a cytotoxic Pt(IV) complex [Pt(5,5'-dmbpy)Cl4 (5,5'-dmbpy is 5,5'-dimethyl-2,2'-bipyridine) was selected to investigate its affinity to human serum albumin (HSA) by spectroscopy and molecular docking methods. This complex has a bidentate nitrogen donor ligand with four chloride anions attached to a Pt(IV) metal in a distorted octahedral environment. The fluorescence data showed this complex quench the intrinsic fluorescence of HSA through a static quenching mechanism. The binding constant (Kb) and the number of binding sites (n) were obtained based on the results of fluorescence measurements...
October 21, 2016: Journal of Biomolecular Structure & Dynamics
Elham Sadat Mostafavi, Mohammad Ali Nasiri Khalili, Sirus Khodadadi, Gholam Hossein Riazi
No abstract text is available yet for this article.
October 18, 2016: Journal of Biomolecular Structure & Dynamics
Farha Naz, Neha Sami, Abu Turab Naqvi, Asimul Islam, Faizan Ahmad, Md Imtaiyaz Hassan
Human microtubule affinity-regulating kinase 4 (MARK4) is considered as an encouraging drug target for the design and development of inhibitors to cure several life threatening diseases such as Alzheimer disease, cancer, obesity and type-II diabetes. Recently, we have reported four ligands namely, BX-912, BX-795, PKR-inhibitor and OTSSP167 (hydrochloride) which bind preferentially to the two different constructs of human MARK4 containing kinase domain. To ensure the role of ubiquitin associated (UBA) domain in the ligand binding, we made a newer construct of MARK4 which contain both kinase and UBA domains, named as MARK4-F3...
October 16, 2016: Journal of Biomolecular Structure & Dynamics
Ting Ren, Lijiao Zhang, Jinqian Wang, Chuanjun Song, Ruiyong Wang, Junbiao Chang
In this work, an attempt has been made to study the interaction of four taiwaniaquinoids with fat mass and obesity associated protein (FTO) by UV-Vis absorption, fluorescence spectroscopy and molecular docking techniques. The results indicated that taiwaniaquinoids effectively quenched the intrinsic fluorescence of FTO via static quenching. According to the binding constants and thermodynamic parameters at three different temperatures, the hydrophobic force and electrostatic interactions appeared be the predominant intermolecular forces in stabilizing the complex...
October 16, 2016: Journal of Biomolecular Structure & Dynamics
Carlos Henrique Tomich de Paula da Silva, Carlton Anthony Taft
The knowledge of the bioactive conformation for an active hit is relevant because of the easier interpretation and the general quality of the recognition models of protein and ligand. With the aim of investigating potential bioactive conformations without previous structural knowledge of the molecular target, we present herewith a 'protocol' that could be used which includes generation of low-energy conformations, calculations of tridimensional descriptors and investigation of structural similarity via principal component analysis...
October 14, 2016: Journal of Biomolecular Structure & Dynamics
Recep Vatansever, Mehmet Emin Uras, Ugur Sen, Ibrahim Ilker Ozyigit, Ertugrul Filiz
A transcription factor DREB1A (dehydration-responsive element-binding 1A) gene was amplified and sequenced from the common bean (Phaseolus vulgaris). PvDREB1A had a 777 base pairs (bp) open reading frame encoding a protein of 225 residues. The protein sequence contained a conserved DNA-binding AP2 domain of about 60 residues and a nuclear localization signal (NLS) at N-terminus site. PvDREB1A demonstrated high homology with other DREB1 members only in AP2 domain and NLS site. The phylogenetic distribution of different DREB members showed three main groups as DREB1-3 and PvDREB1A was a member of DREB1 group...
October 14, 2016: Journal of Biomolecular Structure & Dynamics
Felipe Rodrigues de Souza, Ana Paula Guimarães, Teobaldo Cuya, Matheus Puggina de Freitas, Arlan da Silva Gonçalves, Pat Forgione, Tanos Celmar Costa França
Coxiella burnetii is a gram-negative bacterium able to infect several eukaryotic cells, mainly monocytes and macrophages. It is found widely in nature with ticks, birds, and mammals as major hosts. C. burnetii is also the biological warfare agent that causes Q fever, a disease that has no vaccine or proven chemotherapy available. Considering the current geopolitical context, this fact reinforces the need for discovering new treatments and molecular targets for drug design against C. burnetii. Among the main molecular targets against bacterial diseases reported, the enzyme dihydrofolate reductase (DHFR) has been investigated for several infectious diseases...
October 11, 2016: Journal of Biomolecular Structure & Dynamics
Bahareh Koohshekan, Adeleh Divsalar
No abstract text is available yet for this article.
October 11, 2016: Journal of Biomolecular Structure & Dynamics
Sanga Mitra, Arpa Samadder, Pijush Das, Smarajit Das, Medhanjali Dasgupta, Jayprokas Chakrabarti
Screening large-scale ENCODE data of 625 cytoplasmic transfer RNA (tRNAs) and 37 aminoacyl tRNA synthetase (AARSs) human genes, we deconstruct the array of relations between 10 histone marks affecting 15 chromatin states; their tissue specificity and variations and interchange amongst normal, cancerous and stem cells. The histone marks of RNA Pol II transcribed AARS genes share, but also contrast with that on RNA Pol III transcribed tRNA genes. tRNAs with identical/similar sequences may be in significantly varying states even within the same cell line; the chromatin scaffold, where the tRNA gene resides, is the key determinant...
October 6, 2016: Journal of Biomolecular Structure & Dynamics
Gülru Kayık, Nurcan Ş Tüzün, Serdar Durdagi
Cyclic nucleotide phosphodiesterase enzymes (PDEs) have functions in regulating the levels of intracellular second messengers, 3', 5'-cyclic adenosine monophosphate (cAMP) and 3', 5'-cyclic guanosine monophosphate (cGMP), via hydrolysis and decomposing mechanisms in cells. They take essential roles in modulating various cellular activities such as memory and smooth muscle functions. PDE type 5 (PDE5) inhibitors enhance the vasodilatory effects of cGMP in the corpus cavernosum and they are used to treat erectile dysfunction...
October 6, 2016: Journal of Biomolecular Structure & Dynamics
Magdalena A Mozolewska, Adam K Sieradzan, Andrei Niadzvedstki, Cezary Czaplewski, Adam Liwo, Paweł Krupa
Thurincin H is a small protein produced by Bacillus thuringiensis SF361 with gram-positive antimicrobial properties. The toxins produced by B. thuringiensis are widely used in the agriculture as, e.g. natural preservatives in dairy products. The structure of thurincin H possesses four covalent sulfur to [Formula: see text]-carbon bonds that involve the cysteine side-chains; these bonds are probably responsible for the shape and stability of the protein and, thereby, for its antimicrobial properties. To examine the influence of the formation of the sulfur-carbon bonds on the folding pathways and stability of the protein, a series of canonical and multiplexed replica-exchange simulations with the coarse-grained UNRES force field was carried out without and with distance restraints imposed on selected S-C[Formula: see text] atom pairs...
October 5, 2016: Journal of Biomolecular Structure & Dynamics
Martiniano Bello, Mixtli J Torres, Alfonso Méndez-Tenorio, José Correa-Basurto
Peripheral myelin protein 22 (PMP22) resides in the plasma membrane and is required for myelin formation in the peripheral nervous system. Excess PMP22 mutants accumulate in the endoplasmic reticulum (ER) resulting in the inherited neuropathies of Charcot-Marie-Tooth disease. However, there was no evidence of the structure of PMP22 or how mutations affect its folding. Therefore, in this study, we combined bioinformatics and homology modeling approaches to obtain three-dimensional native and mutated PMP22 models and its anchoring to a POPC membrane, submitted to ...
October 5, 2016: Journal of Biomolecular Structure & Dynamics
Thirupathi Dasari, Bhargavi Kondagari, Ramasree Dulapalli, Aboubakr Haredi Abdelmonsef, Thirupathi Mukkera, Lavanya Souda Padmarao, Vasavi Malkhed, Uma Vuruputuri
Cancer is a class of diseases characterized by uncontrolled cell growth. Every year More than 2 million people are affected by the disease. Rho family proteins are actively involved in cytoskeleton regulation. Over-expression of Rho family proteins show oncogenic activity and promote cancer progression. In the present work RhoG protein is considered as novel target of cancer. It is a member of Rho family and Rac subfamily protein, which plays pivotal role in regulation of microtubule formation, cell migration and contributes in cancer progression...
October 3, 2016: Journal of Biomolecular Structure & Dynamics
Jingxuan Zhu, Xin Li, Siqi Zhang, Hen Ye, Hui Zhao, Hanyong Jin, Weiwei Han
Wild-type phosphotriesterase (PTE) prefers the SP-enantiomers over the corresponding RP-enantiomers by factors ranging from 10 to 90. To satisfy the binding modes of the PTE of SP- and RP-enantiomers, all-atom molecular dynamics simulations were carried out on two paraoxon SP and RP derivatives, namely, Sp-1 and Rp-1. Molecular mechanics Poisson-Boltzmann surface area and molecular mechanics generalized Born surface area (MM-PBSA and MM-GBSA) calculations indicated that His230 in Sp-1-PTE had a closer interaction with the substrate than that in Rp-1-PTE and that such interaction increased the catalytic efficiency of PTE for Sp-1...
October 3, 2016: Journal of Biomolecular Structure & Dynamics
Indrani Kar, Rajagopal Chattopadhyaya
The influence of substoichiometric amounts of seven plant extracts in the Fenton reaction-mediated damage to deoxynucleosides, deoxynucleoside monophosphates, deoxynucleoside triphosphates and supercoiled plasmid DNA were studied to rationalize anticancer properties reported in some of these extracts. Extracts from Acacia catechu, Emblica officinalis, Spondias dulcis, Terminalia belerica, Terminalia chebula, as well as gallic acid, epicatechin, chebulagic acid and chebulinic acid enhance the extent of damage in Fenton reactions with all monomeric substrates but protect supercoiled plasmid DNA, compared to standard Fenton reactions...
October 3, 2016: Journal of Biomolecular Structure & Dynamics
Alireza Farasat, Fatemeh Rahbarizadeh, Ghader Hosseinzadeh, Sharareh Sajjadi, Mehdi Kamali, Amir Homayoun Keihan
Epidermal growth factor receptor (EGFR), a transmembrane glycoprotein, is overexpressed in many cancers such as head-neck, breast, prostate, and skin cancers for this reason it is a good target in cancer therapy and diagnosis. In nanobody-based cancer diagnosis and treatment, nanobodies with high affinity toward receptor (e.g. EGFR) results in effective treatment or diagnosis of cancer. In this regard, the main aim of this study is to develop a method based on molecular dynamic (MD) simulations for designing of 7D12 based nanobody with high affinity compared with wild-type nanobody...
October 3, 2016: Journal of Biomolecular Structure & Dynamics
Perumal Manivel, Manickam Paulpandi, Kadarkarai Murugan, Giovanni Benelli, Malaichamy Ilanchelian
The studies on protein-dye interactions are important in biological process and it is regarded as vital step in rational drug design. The interaction of thionine (TH) with human serum albumin (HSA) was analyzed using isothermal titration calorimetry (ITC), spectroscopic and molecular docking technique. The emission spectral titration of HSA with TH revealed the formation of HSA-TH complex via static quenching process. The results obtained from absorption, synchronous emission, circular dichroism (CD) and three dimensional (3D) emission spectral studies demonstrated that TH induces changes in the microenvironment and secondary structure of HSA...
October 3, 2016: Journal of Biomolecular Structure & Dynamics
Mohd Quadir Siddiqui, Rajan Kumar Choudhary, Pankaj Thapa, Neha Kulkarni, Yogendra S Rajpurohit, Hari S Misra, Nikhil Gadewal, Satish Kumar, Syed K Hasan, Ashok K Varma
Fanconi anemia complementation groups - I (FANCI) protein facilitates DNA ICL (Inter-Cross-link) repair and plays a crucial role in genomic integrity. FANCI is a 1328 amino acids protein which contains armadillo (ARM) repeats and EDGE motif at the C-terminus. ARM repeats are functionally diverse and evolutionarily conserved domain that plays a pivotal role in protein-protein and protein-DNA interactions. Considering the importance of ARM repeats, we have explored comprehensive in-silico and in-vitro approach to examine folding pattern...
September 30, 2016: Journal of Biomolecular Structure & Dynamics
Mohd Ashraf Rather, Irfan Ahmad Bhat, Pravesh Kumar Rathor, P Gireesh-Babu, Aparna Chaudhari, Sundaray Jeetendra Kumar, Rupam Sharma
We report the characterization of kisspeptin gene which is considered to be essential for successful animal reproduction. The full-length cDNA sequence of kiss2 was 583 bp, consisted of 11 bp 5'-UTR (untranslated region) and 194 bp 3'-UTR, respectively. Open reading frame of 378 bp encoding a putative protein of 125 amino acids. The Catla catla kiss2 protein was having a molecular weight of 14.51 kDa and isoelectric point (pI) of 8.46. There were four serine (Ser), four threonine (Thr) and two tyrosine (Tyr) phosphorylation sites and no N-glycosylation sites on the predicted protein...
September 29, 2016: Journal of Biomolecular Structure & Dynamics
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