Journal of biomolecular structure & dynamics (J BIOMOL STRUCT DYN )

Description

The Journal of Biomolecular Structure and Dynamics cordially welcomes manuscripts from active investigators in biological structure, dynamics, interactions and expression. The Journal will cover both experimental and theoretical investigations in the area of nucleic acids, nucleotides, proteins, peptides, membranes, polysaccharides and all their components, metal complexes and model systems. The Journal publishes original articles, communications a la express and timely reviews.

  • Impact factor
    4.99
  • 5-year impact
    1.15
  • Cited half-life
    0.00
  • Immediacy index
    0.25
  • Eigenfactor
    0.00
  • Article influence
    0.32
  • Website
    Journal of Biomolecular Structure & Dynamics website
  • Other titles
    Journal of biomolecular structure & dynamics, Journal of biomolecular structure and dynamics
  • ISSN
    1538-0254
  • OCLC
    9688706
  • Material type
    Periodical, Internet resource
  • Document type
    Journal / Magazine / Newspaper, Internet Resource

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Abstract TSPY (Testis-specific protein, Y-encoded) binds to eukaryotic translation elongation factor 1 alpha (eEF1A) at its SET/NAP domain that is essential for the elongation during protein synthesis implicated with normal spermatogenesis. The eEF1A exists in two forms, eEF1A1 (alpha 1) and eEF1A2 (alpha 2), encoded by separate loci. Despite critical interplay of the TSPY and eEF1A proteins, literature remained silent on the residues playing significant roles during such interactions. We deduced 3D structures of TSPY and eEF1A variants by comparative modelling (Modeller 9.13) and assessed protein-protein interactions employing HADDOCK docking. Pairwise alignment using EMBOSS Needle for eEF1A1 and eEF1A2 proteins revealed high degree (~92%) of homology. Efficient binding of TSPY with eEF1A2 as compared to eEF1A1 was observed, in spite of the occurrence of significant structural similarities between the two variants. We also detected strong interactions of domain III followed by domains II and I of both eEF1A variants with TSPY. In the process, seven interacting residues of TSPY's NAP domain namely, Asp 175, Glu 176, Asp 179, Tyr 183, Asp 240, Glu 244 and Tyr 246 common to both eEF1A variants were detected. Additionally, six lysine residues observed in eEF1A2 suggest their possible role in TSPY-eEF1A2 complex formation essential for germ cell development and spermatogenesis. Thus, more efficient binding of TSPY with eEF1A2 as compared to that of eEF1A1 established autonomous functioning of these two variants. Studies on mutated protein following similar approach would uncover the causative obstruction, between the interacting partners leading to deeper understanding on the structure-function relationship.
    Journal of biomolecular structure & dynamics 08/2014;
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    ABSTRACT: Post-translational modifications on the tails of core and linker histones dictate transcription and have vital roles in disease and development. Acetylation and deacetylation events enabled by histone acetyl transferases and histone deacetylases (HDACs) on the chromatin milieu are intricately involved in gene regulation. Inhibition of HDACs is emerging as a powerful strategy in regenerative therapy, transplantation, development and in nuclear reprogramming events. Valproic acid (VPA), belonging to the short-chain fatty acid group of HDAC inhibitors, modulates the epigenome altering gene expression profiles across cell lines. This work attempts to explore the methylation profiles triggered by VPA treatment on human embryonic kidney cells (HEK 293) through a biochemical and computational approach. VPA treatment (for 48 h) has been observed to hypermethylate lysine 4 on the core histone H3 and confers a hypomethylation status of H3 lysine 27 in HEK 293 cells leaving the nuclear area and nuclear contour unaltered. Our structural docking and Binding Free Energy (BFE) calculations establish an active role for VPA in inhibiting the demethylase JARID1A (Jumonji, AT Rich Interactive Domain 1A) and the methyl-transferase EZH2 (Enhancer of Zeste Homologue 2). This work has also proven that VPA can inhibit the activity of proteins like GSK3β and PKCβII involved in developmental disorders. This work establishes a dynamic correlation between histone methylation events and HDAC inhibition and may define newer epigenetic strategies for treating neurodevelopmental and oncological disorders.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new anti-malarial compounds or inhibitors. Here a systematic in silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three-dimensional (3D) structure of Plasmodium LytB taking Escherichia coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand data-set containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, five were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB-inhibitory mechanism which can provide valuable support for the anti-malarial-inhibitor design in future.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Because intrinsically disordered proteins are incapable of forming unique tertiary structures in isolation, their interaction with partner structures enables them to play important roles in many different biological functions. Therefore, such proteins are usually multifunctional, and their ability to perform their major function, as well as accessory functions, depends on the characteristics of a given interaction. The present paper demonstrates, using predictions from two programs, that the transmembrane proteoglycans syndecans are natively disordered because of their diverse functions and large number of interaction partners. Syndecans perform multiple functions during development, damage repair, tumor growth, angiogenesis, and neurogenesis. By mediating the binding of a large number of extracellular ligands to their receptors, these proteoglycans trigger a cascade of reactions that subsequently regulate various cell processes: cytoskeleton formation, proliferation, differentiation, adhesion, and migration. The occurrences of 20 amino acids in syndecans 1-4 from 25 animals were compared with those in 17 animal proteomes. Gly + Ala, Thr, Glu, and Pro were observed to predominate in the syndecans, contributing to the lack of an ordered structure. In contrast, there were many fewer amino acids in syndecans that promote an ordered structure, such as Cys, Trp, Asn, and His. In addition, a region rich in Asp has been identified between two heparan sulfate-binding sites in the ectodomains, and a region rich in Lys has been identified in the conserved C1 site of the cytoplasmic domain. These particular regions play an essential role in the various functions of syndecans due to their lack of structure.
    Journal of biomolecular structure & dynamics 06/2014;
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    ABSTRACT: Abstract There is a need for continued development of acetylcholinesterase (AChE) inhibitors that could prolong the life of acetylcholine in the synaptic cleft and also prevent the aggregation of amyloid peptides associated with Alzheimer's disease. The lack of a 3D-QSAR model which specifically deconvulates the type of interactions and quantifies them in terms of energies has motivated us to report a CoRIA model vis-à-vis the standard 3D-QSAR methods CoMFA and CoMSIA. The CoRIA model was found to be statistically superior to the CoMFA and CoMSIA models and it could efficiently extract key residues involved in ligand recognition and binding to AChE. These interactions were quantified to gauge the magnitude of their contribution to the biological activity. In order to validate the CoRIA model, a pharmacophore map was first constructed and then used to virtually screen public databases, from which novel scaffolds were cherry picked that were not present in the training set. The biological activities of these novel molecules were then predicted by the CoRIA, CoMFA and CoMSIA models. The hits identified were purchased and their biological activities measured by the Ellman's method for AChE inhibition. The predicted activities are in unison with the experimentally measured biological activities.
    Journal of biomolecular structure & dynamics 06/2014;
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    ABSTRACT: Aspartate β-semialdehyde dehydrogenase (ASADH) is a key enzyme for the biosynthesis of essential amino acids and several important metabolites in microbes. Inhibition of ASADH enzyme is a promising drug target strategy against Mycobacterium tuberculosis (Mtb). In this work, in silico approach was used to identify potent inhibitors of Mtb-ASADH. Aspartyl β-difluorophosphonate (β-AFP), a known lead compound, was used to understand the molecular recognition interactions (using molecular docking and molecular dynamics analysis). This analysis helped in validating the computational protocol and established the participation of Arg99, Glu224, Cys130, Arg249 and His256 amino acids as the key amino acids in stabilizing ligand-enzyme interactions for effective binding, an essential feature is H-bonding interactions with the two arginyl residues at the two ends of the ligand. Best binding conformation of β-AFP was selected as a template for shape-based virtual screening (ZINC and NCI databases) to identify compounds that competitively inhibit the Mtb-ASADH. The top rank hits were further subjected to ADME and toxicity filters. Final filter was based on molecular docking analysis. Each screened molecule carry the characteristics highly electronegative groups on both sides separated by an average distance of 6 Å. Finally, best predicted 20 compounds exhibited minimum three H-bonding interactions with Arg99 and Arg249. These identified hits can be further used for designing the more potent inhibitors against ASADH family. MD simulations were also performed on two selected compounds (NSC4862 and ZINC02534243) for further validation. During the MD simulations, both compounds showed same H-bonding interactions and remains bound to key active residues of Mtb-ASADH.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: Abstract Mcl-1 has emerged as a potential therapeutic target in the treatment of several malignancies. Peptides representing BH3 region of pro-apoptotic proteins have been shown to bind the hydrophobic cleft of anti-apoptotic Mcl-1 and this segment is responsible for modulating the apoptotic pathways in living cells. Understanding the molecular basis of protein-peptide interaction is required to develop potent inhibitors specific for Mcl-1. Molecular dynamics (MD) simulations were performed for Mcl-1 in complex with three different BH3 peptides derived from Mcl-1, Bax, and Bim. Accordingly, the calculated binding free energies by using MM-PBSA method are obtained and comparison with the experimental determined binding free energies is made. The interactions involving two conserved charged residues (Aspi, and Arg/Lysi-4) and three upstream conserved hydrophobic residues (Leui-5, Ile/Vali-2, and Glyi-1, respectively) of BH3 peptides play the important roles in the structural stability of the complexes. The calculated results exhibit that the interactions of Bim BH3 peptides to Mcl-1 is stronger than the complex with Bax 19BH3 peptides. The hydrophobic residues (position i-9, i-8 and i+2) of BH3 peptides can be involved in their inhibitory specificity. The calculated results can be used for designing more effective MCL-1 inhibitors.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: A series of surfactant-copper(II) Schiff base complexes (1-6) of the general formula, [Cu(sal-R2)2] and [Cu(5-OMe-sal-R2)2], {where, sal = salicylaldehyde, 5-OMe-sal = 5-methoxy- salicylaldehyde, and R2 = dodecylamine (DA), tetradecylamine (TA), or cetylamine (CA)} have been synthesized and characterized by spectroscopic, ESI-MS, and elemental analysis methods. For a special reason, the structure of one of the complexes (2) was resolved by single crystal X-ray diffraction analysis and it indicates the presence of a distorted square-planar geometry in the complex. Analysis of the binding of these complexes with DNA has been carried out adapting UV-visible-, fluorescence-, as well as circular dichroism spectroscopic methods and viscosity experiments. The results indicate that the complexes bind via minor groove mode involving the hydrophobic surfactant chain. Increase in the length of the aliphatic chain of the ligands facilitates the binding. Further, molecular docking calculations have been performed to understand the nature as well as order of binding of these complexes with DNA. This docking analysis also suggested that the complexes interact with DNA through the alkyl chain present in the Schiff base ligands via the minor groove. In addition, the cytotoxic property of the surfactant-copper(II) Schiff base complexes have been studied against a breast cancer cell line. All six complexes reduced the visibility of the cells but complexes 2, 3, 5, and 6 brought about this effect at fairly low concentrations. Analyzed further, but a small percentage of cells succumbed to necrosis. Of these complexes (6) proved to be the most efficient aptotoxic agent.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: Abstract Resistance to antibiotics in bacteria, is one of the major problems of mankind. Each year, a large number of patients due to infection, lose their lives. One of the main mechanisms of antibiotic resistance, is beta-lactamase secretion. This enzyme, hydrolyzes the amide bond of a lactam ring in beta-lactam antibiotics. Bacillus licheniformis is a mesophilic gram-positive bacterium, Which has a high potential to produce beta-lactamase class A. in this study, the inhibitory effects of some malate analogous were studies by in vitro and in vivo studies. In addition, The effects of inhibitor binding on beta-lactamase were studied using MD simulations. Our results showed that diethyl malate and 1-methyl malate can decrease the MIC value of benzyl penicillin by 16 and 8 fold, respectively. Data derived from in vitro studies revealed that decreasing in MIC values is correlated with bata-lactamase inhibition. Molecular docking studies predicted the binding mode of inhibitors with the beta-lactamase active site. The structural analysis from MD simulations exhibits that binding of citrate and diethyl malate cause earlier equilibrium of beta-lactamase. After binding, the fluctuation of Ser 70 is also decreased. Based on our data, diethyl malate can be used to design the potent inhibitor against beta-lactamase class A.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: Abstract Adverse side effects of drugs are often caused by the interaction of drug molecules to targets other than the intended ones. In this study, we investigated the off-target interactions of some commercially available drugs with human α-thrombin. The drugs used in the study were selected from Super Drug Database based on the structural similarity to a known thrombin inhibitor argatroban. Interactions of these drugs with thrombin were initially checked by in-silico docking studies and then confirmed by thrombin inhibition assay using a fluorescence microplate based method. Results show that the three commonly used drugs piperacillin (anti-bacterial), azlocillin (anti-bacterial) and metolazone (anti-hypertensive and diuretic) have thrombin inhibitory activity almost similar to that of argatroban. The Ki values of piperacillin, azlocillin and metolazone with thrombin are 0.55 nM, 0.95 nM and 0.62 nM respectively. The IC50 values of piperacillin, azlocillin and metolazone with thrombin are 1.7 nM, 2.9 nM and 1.92 nM respectively. This thrombin inhibitory activity might be a reason for the observed side effects of these drugs related to blood coagulation and other thrombin activities. Furthermore, these compounds (drugs) may be used as anti-coagulants as such or with structural modifications.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: Abstract Neuropathological cascades leading to reduced cholinergic transmission in Alzheimer's disease led to development of AChE inhibitors. Although lethal dose of some inhibitors cause interruption with AChE mediated mechanism but reversible AChE inhibitors can assist in protection from inhibition of AChE and hence in an aim to probe potential molecules as anticholinesterase and as reactivators, computationally structure-based approach has been exploited in this work for designing new 2-amino-3-pyridoixime-dipeptides conjugates. We have combined MD simulations with flexible ligand docking approach to determine binding specificity of 2-amino-3-pyridoixime dipeptides towards AChE (PDB 2WHP). PAS residues are found to be responsible for oxime dipeptides binding along with π-π interactions with Trp86 and Tyr286, hydrogen bonding with side chains of Asp74 and Tyr341 (Gscore -10.801 and MM-GBSA free energy -34.89 kcal/mol). The docking results depicted complementary multivalent interactions along with good binding affinity as predicted from MM-GBSA analysis. The 2-amino-3-pyridoxime-(Arg-Asn) AChE systems subjected to MD simulations under explicit solvent systems with NPT and NVT ensemble. MD simulations uncovered dynamic behavior of 2-amino-3-pyridoxime-(Arg-Asn) and exposed its mobile nature and competence to form strong long range order contacts towards active site residues to approach inhibited serine residue and facilitated via large contribution from hydrogen bonding and water bridges along with slow and large movements of adjacent important residues. In an effort to evaluate the complete potential surface profile, 2-amino-3-pyridoxime induced reactivation pathway of sarin-serine adduct has been investigated by the DFT approach at the vacuum MO6/6-311G (d, p) level along with the Poisson-Boltzmann solvation model and found to be of relatively low energy barrier. The pKa evaluation has revealed the major deprotonated 2-amino-3-pyridoixime species having pKa of 6.47 and hence making 2-amino-3-pyridoxime-(Arg-Asn) potential anticholinesterase and reactivator for AChE under the physiological pH.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: Abstract Hen egg white lysozyme (HEWL) adopts a molten globule like state at high pH (~12.75) and is found to form amyloid fibrils at alkaline pH. Here, we report that Cu(II) inhibits self-association of hen egg white lysozyme (HEWL) at pH 12.75 both at 37 °C and 65 °C. A significant reduction in Thioflavin T (ThT) fluorescence intensity, attenuation in β-sheet content, reduction in hydrophobic exposure were observed with increasing Cu(II) stoichiometry. Electron paramagnetic resonance (EPR) spectroscopy suggests a 4N type of coordination pattern around Cu(II) during fibrillation. Cu(II) is also capable of altering the cytotoxicity of the proteinaceous aggregates. Fibrillar species of diverse morphology were found in the absence of Cu(II) with the generation of amorphous aggregates in the presence of Cu(II), that are more toxic compared to the fibrils alone.
    Journal of biomolecular structure & dynamics 05/2014;
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    ABSTRACT: Molecular dynamics simulations were employed to analyze the conformational preferences and binding modes of epothilones A and B as a source of structural information regarding the antitumor properties of these species. Our results suggest that the conformation of free and tubulin-bound epothilones is strongly influenced by the presence of a methyl group at C12 and that epothilones A and B exploit the binding cavity in a unique and different way. The binding sites of epothilones A and B share a common region of association (Leu215, Leu217, His227, Leu228, Ala231, Phe270, Gly360, and Leu361), but lead to different ligand-residue interactions. Average interaction energies predict a larger stabilization for the epothilone B-tubulin complex, which is mainly driven by the enhancement of the electrostatic component of ligand-residue interactions compared to the epothilone A-tubulin complex. These structural and energetic results can be useful to account for the activity difference between epothilones A and B, and to design more active and potent analogs that resemble the mechanism of action of epothilones against cancer cells.
    Journal of biomolecular structure & dynamics 04/2014;
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    ABSTRACT: Protein thiol/sulfenic acid oxidation potentials provide a tool to select specific oxidation agents, but are experimentally difficult to obtain. Here, insights into the thiol sulfenylation thermodynamics are obtained from model calculations on small systems and from a quantum mechanics/molecular mechanics (QM/MM) analysis on human 2-Cys peroxiredoxin thioredoxin peroxidase B (Tpx-B). To study thiol sulfenylation in Tpx-B, our recently developed computational method to determine reduction potentials relatively compared to a reference system and based on reaction energies reduction potential from electronic energies is updated. Tpx-B forms a sulfenic acid (R-SO(-)) on one of its active site cysteines during reactive oxygen scavenging. The observed effect of the conserved active site residues is consistent with the observed hydrogen bond interactions in the QM/MM optimized Tpx-B structures and with free energy calculations on small model systems. The ligand effect could be linked to the complexation energies of ligand L with CH3S(-) and CH3SO(-). Compared to QM only calculations on Tpx-B's active site, the QM/MM calculations give an improved understanding of sulfenylation thermodynamics by showing that other residues from the protein environment other than the active site residues can play an important role.
    Journal of biomolecular structure & dynamics 04/2014;
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    ABSTRACT: Abstract In different types of chromosome pairing (meiotic, somatic, sister chromatids pairing) initiation stages are less elucidated. In somatic homolog pairing initiation the long intron RNA products interference may play the essential role .The strongest somatic pairing in Drosophila melanogaser 28B1-B2 locus and its enrichment by long bi-directional transcripts prone us to analyze the pre-mRNA secondary structures. The comparison of sense (pre-mRNA) and antisense (lncRNA) portions corresponding to the lengthy introns for some others genes loci reveals the significant correlation of stretched folding form lengths with the homologue pairing percentage. Also for 28B1-B2 locus the most significant homologue pairing is justified by the plurality of sense and antisense RNA variants for lengthy introns. The stretched forms of long intron products with multiple stem-loops clusters widely presented for sense and antisense strands may interact by multiple loops during transcription being connected to different chromosomes and hypothetically may serve for the pairing initiation. Stretched rod-like or V-shape -like are dominating forms for the whole intron RNA products or their central portions while predominantly star-like for others intron fragments.
    Journal of biomolecular structure & dynamics 04/2014;
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    ABSTRACT: A conceptually new idea in quantitative structure-activity relationships (QSAR) which makes use of ensembles from molecular dynamics (MD) trajectories and information retrieved from enzyme-inhibitor binding thermodynamics is presented in this study. This new methodology, termed ensemble comparative residue interaction analysis (eCoRIA), attempts to overcome the current one chemical-one structure-one parameter value dogma in computational chemistry by modeling the biological activity as a function of molecular descriptors derived from an ensemble of conformers of enzyme-inhibitor complexes. The approach is distinctly different from the standard QSAR methodology which uses a single low-energy conformation or the properties averaged over a set of conformers to correlate with the activity. Each conformational ensemble derived from MD simulations is analyzed for the distribution of the non-bonded interaction energies (steric, electrostatic, and hydrophobic) along with solvation, strain, and entropic energy of the inhibitors with the individual amino acid residues in the receptor and these are correlated to the activity through a QSAR model. The scope of the new method is demonstrated with three diverse enzyme-inhibitor data-sets - glycogen phosphorylase b, human immunodeficiency virus-1 protease and cyclin-dependent kinase 2. The QSAR equations derived from the methodology have revealed all the structure activity relationships previously reported for these classes of molecules as well as uncovered some features that were hitherto unknown and may have a hidden role in driving the ligand-receptor-binding process. Impressive improvements in the predictions of affinity have been achieved compared to other QSAR formalisms namely CoMFA, CoMSIA (receptor-independent QSAR techniques), and CoRIA (a receptor-dependent QSAR technique). eCoRIA could provide an understanding of the thermodynamic properties influencing the ligand-receptor binding over a time scale as sampled by the MD simulation. The advantage of analyzing enzyme-inhibitor interaction energies in a statistical domain is that the noise due to inaccuracies in the potential energy functions can be reduced and mechanistically important interaction terms related to protein-ligand binding specificity can be identified which can assist the medicinal chemists in designing new molecules and biologists in studying the influence of position-specific mutations in the receptor on ligand binding.
    Journal of biomolecular structure & dynamics 04/2014;
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    ABSTRACT: Abstract Urease (EC 3.5.1.5., urea amidohydrolase) catalyzes the hydrolysis of urea to ammonia and carbon dioxide. Urease is present to a greater abundance in plants and plays significant role related to nitrogen recycling from urea. But little is known about the structure and function of the urease derived from the Arabidopsis thaliana, the model system of choice for research in plant biology. In this study, a three-dimensional structural model of Arabidopsis thaliana urease was constructed using computer-aided molecular modeling technique. The characteristic structural features of the modelled structure were then studied using atomistic molecular dynamics simulation. It was observed that the modelled structure was stable and regions between residues index (50-80, 500-700) to be significantly flexible. From the docking studies, we detected the possible binding interactions of modeled urease with urea. Ala399, Ile675, Thr398 and Thr679 residues of Arabidopsis thaliana urease were observed to be significantly involved in binding with the substrate urea. We also compared the docking studies of ureases from other sources such as Canavalia ensiformis, Helicobacter pylori and Bacillus pasteurii. In addition, we carried out mutation analysis to find the highly mutable amino acid residues of modelled Arabidopsis thaliana urease. In this particular study, we observed Met485, Tyr510, Ser786, Val426 and Lys765 to be highly mutable amino acids. These results are significant for the mutagenesis analysis. As a whole this study expounds the salient structural features as well the binding interactions of the modelled structure of arabidopsis thaliana urease.
    Journal of biomolecular structure & dynamics 04/2014;

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