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Journal of Biomolecular Structure & Dynamics

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August 20, 2017: Journal of Biomolecular Structure & Dynamics
Justin P Peters, Ewa A Kowal, Pradeep S Pallan, Martin Egli, L James Maher
Leveraging structural biology tools, we report the results of experimentsseeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry...
August 18, 2017: Journal of Biomolecular Structure & Dynamics
Farzin Sohraby, Milad Bagheri, Mostafa Javaheri Moghadam, Hassan Aryapour
No abstract text is available yet for this article.
August 18, 2017: Journal of Biomolecular Structure & Dynamics
Ryan C Godwin, William H Gmeiner, Freddie R Salsbury
An important regulatory domain of NEMO is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To discern structural and dynamical differences between these disease states, we present results of 48-$\mu s$ of molecular dynamics simulations for three zinc finger systems each in two states, with and without zinc-bound and correspondingly appropriate cysteine thiol/thiolate configurations...
August 17, 2017: Journal of Biomolecular Structure & Dynamics
Varsha Bhavnani, Kaviraj Swarnendu, Priyabrata Panigrahi, C G Suresh, SuneelShekar Yapara, Jayanta Pal
The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understanding its mechanism of functionality. In the present study, we report the thermostability achieved by the catalytic kinase domain of HRI (HRI.CKD) upon ligand (heme) binding. Our CD data demonstrates that the HRI...
August 17, 2017: Journal of Biomolecular Structure & Dynamics
Somaye Shahraki, Ali Heydari
Ligand binding studies on carrier proteins are crucial in determining the pharmacological properties of drug candidates. Here, a new palladium(II) complex was synthesized and characterized. The in vitro binding studies of this complexwith two carrier proteins, human serum albumin (HSA) and β-lactoglobulin (βLG) was investigated by employing biophysical techniques as well as computational modeling. The experimental results showed thatthe Pd(II) complex interacted with two carrier proteins with moderate binding affinity (Kb ~̴ 0...
August 16, 2017: Journal of Biomolecular Structure & Dynamics
Anton M Kargatov, Eugenia A Boshkova, Yuri N Chirgadze
Glyoxalase is one of two enzymes of the glyoxalase detoxification system against methylglyoxal and other aldehydes, the metabolites derived from glycolysis. The glyoxalase system is found almost in all living organisms: bacteria, protozoa, plants and animals, including humans, and is related to the class of "life essential proteins". The enzyme belongs to the expanded Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily. At present the GenBank contains about seven hundreds of amino acid sequences of this enzyme type, and the Protein Data Bank includes dozens of spatial structures...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
Ramin Ekhteiari Salmas, Yusuf Serhat Is, Serdar Durdagi, Matthias Stein, Mine Yurtsever
The dopamine D2 Receptor (D2R) is a member of the G-Protein Coupled Receptor (GPCR) family and plays a critical role in neurotransmission activities in the human brain. Dysfunction in dopamine receptor signaling may lead to mental health illnesses such as schizophrenia and Parkinson's disease. D2R is the target protein of the commonly used anti-psychotic drugs such as risperidone, clozapine, aripiprazole, olanzapine, ziprasidone and quetiapine. Due to their significant side effects and nonselective profiles, the discovery of novel drugs has become a challenge for researchers working in this field...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
V M Vidhya, Vikash Kumar Dubey, Karthe Ponnuraj
Visceral leishmaniasis caused by the protozoan Leishmania donovani is the most severe form of leishmaniasis and it is potentially lethal if untreated. Despite the availability of drugs for treating the disease, the current drug regime suffers from drawbacks like antibiotic resistance and toxicity. New drugs have to be discovered in order to overcome these limitations. Our aim is to identify natural compounds from plant sources as putative inhibitors considering the occurrence of structural diversity in plant sources...
August 10, 2017: Journal of Biomolecular Structure & Dynamics
Parthiban Marimuthu, Pavithra K Balasubramanian, Kalaimathy Singaravelu
The Bcl-2 family proteins are the central regulators of apoptosis. Due to its predominant role in cancer progression, the Bcl-2 family proteins act as attractive therapeutic targets. Recently,molecular series of BenzothiazoleHydrazone(BH) inhibitorsthat exhibits drug-likenesscharacteristics,whichselectivelytargets Bcl-xLhave been reported.In the present study,dockingwas used toexplore the plausible binding mode of the highly active BH inhibitorwith Bcl-xL;and Molecular Dynamics(MD) simulation wasapplied toinvestigate the stability of predicted conformationover time...
August 10, 2017: Journal of Biomolecular Structure & Dynamics
Sidra Islam, Moinuddin, Abdul Rouf Mir, Alok Raghav, Safia Habib, Khursheed Alam, Asif Ali
Glycation and oxidation induce structural alterations in the proteins in an inter-dependent manner with consequent pathological implications. The published literature presents wide range of modifications in conformational characteristics of proteins by glycation and oxidation; however, there is little data that could elaborate the cumulative effect of both the processes. This study has analysed the modifications in IgG by methylglyoxal (MG) (glycative stress), hydroxyl radical (OH(•)) (oxidative stress) and by their combined action i...
August 9, 2017: Journal of Biomolecular Structure & Dynamics
Dhani Ram Mahato, Wolfgang B Fischer
Interaction of E5 of papillomavirus-16 based on its three transmembrane domains (TMDs) with a peptide mimicking the fourth TMD of the 16 kDac subunit of the human vacuolar H(+)-ATPase, ATP6V0C, and one of its mutant is investigated. Docking reveals binding of the peptide between the second and third TMD of E5. A series of hydrophobic residues are responsible for the contact. Estimated weak binding energies based on potential of mean force calculations reveal marginal differences of the estimated binding energies between wild type (WT) and mutant peptide...
August 8, 2017: Journal of Biomolecular Structure & Dynamics
Asma Yasmeen Khan, Gopinatha Suresh Kumar
This manuscript describes the interaction of the topoisomerase I inhibitor anticancer drug topotecan with human serum albumin using microcalorimetry, circular dichroism, and atomic force microscopy imaging techniques. Conformational change in albumin was ascertained from circular dichroism and synchronous fluorescence study that revealed a small but definitive partial unfolding of the protein structure upon drug binding. Isothermal titration calorimetry study indicated a favorable exothermic interaction with a binding affinity of the order of ~10(5) M(-1) at 293...
August 7, 2017: Journal of Biomolecular Structure & Dynamics
Jie-Hua Shi, Yan-Yue Lou, Kai-Li Zhou, Dong-Qi Pan
No abstract text is available yet for this article.
August 6, 2017: Journal of Biomolecular Structure & Dynamics
Amresh Prakash, Vijay Kumar, Preeti Pandey, Deepak R Bharti, Poonam Vishwakarma, Ruhar Singh, Md Imtaiyaz Hassan, Andrew M Lynn
Misfolding and aggregation of Cu, Zn Superoxide Dismutase (SOD1) is often found in amyotrophic lateral sclerosis (ALS) patients. The central apo SOD1 barrel was involved in protein maturation and pathological aggregation in ALS. In this work, we employed atomistic molecular dynamics (MD) simulations to study the conformational dynamics of SOD1(barrel) monomer in different concentrations of trifluoroethanol (TFE). We find concentration dependence unusual structural and dynamical features, characterized by the local unfolding of SOD1(barrel)...
August 6, 2017: Journal of Biomolecular Structure & Dynamics
Wei Yang, Blake T Riley, Xiangyun Lei, Benjamin T Porebski, Itamar Kass, Ashley M Buckle, Sheena McGowan
The M1 and M17 aminopeptidases are metallo-exopeptidases that rely on the presence of divalent cations, usually zinc, in their active site for proteolytic activity. They are from separate protease superfamilies, however, members often have overlapping substrate specificity. Inhibitors of one or both enzymes can be used to modulate hypertension, reduce proliferation of certain types of cancers and control malaria parasites. Current inhibitors act to chelate the zinc ions in the active site, locking the enzymes in an inactive transition state...
August 6, 2017: Journal of Biomolecular Structure & Dynamics
Zhiwei Yang, Yang Cao, Dongxiao Hao, Xiaohui Yuan, Lei Zhang, Shengli Zhang
Although the pharmacological inhibition of cholesterol ester transport protein (CETP) has been proposed as a method of preventing and treating cardiovascular disease (CVD), the adverse effects of currentinhibitors have cast doubton theinteraction mechanisms of inhibitors and CETP.In response,a molecular dynamicssimulation was used to investigate their interaction and shed light onthe lipid exchange mechanism of CETP.Results showed that torcetrapib, anacetrapib, and evacetrapib can induce the incremental rigidityof CETP, yet decrease the stability of Helix X and the hydrophobic tunnel of CETP, withpassable binding abilities (ΔGbind, -61...
August 4, 2017: Journal of Biomolecular Structure & Dynamics
Hassan Mansouri-Torshizi, Fatemeh Khosravi, Arezou Ghahghaei, Somaye Shahraki, Sareh Zareian-Jahromi
Two Zn(II) complexes of formula [Zn(bpy)(Gly)]NO3 (I) and [Zn(phen)(Gly)]NO3 (II) (where bpy=2,2'-bipyridine, phen=1,10-phenanthroline and Gly=glycine) were synthesized and characterized by elemental analysis, molar conductance measurements, UV-Vis, FT-IR and (1)H NMR spectra. The interaction ability of these complexes with calf thymus DNA was monitored using spectroscopic methods, including UV-Vis absorption spectroscopy, ethidium bromide displacement, Fourier transform infrared and electrophoretic mobility assay...
August 3, 2017: Journal of Biomolecular Structure & Dynamics
Hui Yu, Lianjuan Yang, Lu Liu, Xi Zhao, Xuri Huang
Acid-sensing ion channel 1a (ASIC1a) is a cation channel activated by protons and causes neuronal death through central nervous system. Psalmotoxin1 (PcTx1) is a gating modifier for ASIC1a. The process of PcTx1 regulating the channel gating from the extracellular domain to the transmembrane domain is unclear. Here we used molecular dynamics (MD) simulations method to investigate how PcTx1 regulates the gating of the ASIC1a. Our results indicated that PcTx1can mainly regulate ASIC1a gating process through hydrogen bonds, which can affect their relative positions of several key domains in ASIC1a, further, a long-range conformational changes path was determined, which is composed of β1, β2, β10, α6, α7, β11 and β12 in ASIC1a...
August 3, 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...
August 3, 2017: Journal of Biomolecular Structure & Dynamics
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