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
    Show impact factor history
     
    Impact factor
  • 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
    0739-1102
  • OCLC
    9688706
  • Material type
    Periodical, Internet resource
  • Document type
    Journal / Magazine / Newspaper, Internet Resource

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Lipopolysaccharide and β-1,3 glucan-binding protein (LGBP) is a family of pattern-recognition transmembrane proteins (PRPs) which plays a vital role in the immune mechanism of crustaceans in adverse conditions. Fenneropenaeus indicus LGBP-deduced amino acid has conserved potential recognition motif for β-1,3 linkages of polysaccharides and putative RGD (Arg-Gly-Asp) cell adhesion sites for the activation of innate defense mechanism. In order to understand the stimulating activity of β-1,3 glucan (β-glucan) and its interaction with LGBP, a 3D model of LGBP is generated. Molecular docking is performed with this model, and the results indicate Arg71 with strong hydrogen bond from RGD domain of LGBP. Moreover, from the docking studies, we also suggest that Arg34, Lys68, Val135, and Ala146 in LGBP are important amino acid residues in binding as they have strong bonding interaction in the active site of LGBP. In our in vitro studies, yeast agglutination results suggest that shrimp F. indicus LGBP possesses sugar binding and recognition sites in its structure, which is responsible for agglutination reaction. Our results were synchronized with the already reported evidence both in vivo and in vitro experiments. This investigation may be valuable for further experimental investigation in the synthesis of novel immunomodulator.
    Journal of biomolecular structure & dynamics 08/2014;
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    ABSTRACT: Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-π and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to β-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.
    Journal of biomolecular structure & dynamics 08/2014;
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    ABSTRACT: Abstract Functionalized carbon nanotubes (CNTs) constitute a new class of nano-structured materials that have vast applications in CNT purification and separation, biosensing, drug delivery, etc. Hybrids formed from the functionalization of CNT with biological molecules have shown interesting properties and have attracted great attention in recent years. Of particular interest is the hybridization of single or double stranded nucleic acid (NA) with CNT. Nucleobases, as the building blocks of NA, interact with CNT and contribute strongly to the stability of the NA-CNT hybrids and their properties. In this work, we present a thorough review of previous studies on the binding of nucleobases with graphene and CNT, with a focus on the simulation works that attempted to evaluate the structure and strength of binding. Discrepancies among these works are identified, and factors that might contribute to such discrepancies are discussed.
    Journal of biomolecular structure & dynamics 08/2014;
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    ABSTRACT: ABRAXAS is an integral member of BRCA1-complex, which helps in its recruitment to the DNA damage site. It interacts with BRCA1 via its C-terminal phospho-peptide binding motif while the N-terminal associates with RAP80, and thereby recruits the BRCA1-complex at the site of DNA damage. Nonetheless, how ABRAXAS helps in the structural integrity of BRCA1-complex, and its DNA repair mechanism remains elusive. To elucidate the role of ABRAXAS in the DNA repair process, we characterized the ABRAXAS wild type and Arg361Gln mutant using in silico and in vitro approach. It has been observed that ABRAXAS Arg361Gln mutant is responsible for defective nuclear localization of BRCA1-complex, and hence important for DNA repair function. We found conformational changes in ABRAXAS mutant, which impaired binding to RAP80 and further disturb BRCA1-complex localization. The results presented in this paper will help to understand the cause of BRCA1 mislocalization, and various DNA repair defects that occur due to substitution. Comparative study of ABRAXAS wild type and mutant will provide helpful perspective for inhibitor designing that can potentially recompense the deleterious effect(s) of Arg361Gln mutation, and have therapeutic application.
    Journal of biomolecular structure & dynamics 08/2014;
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    ABSTRACT: Background: Type IV PHA synthase is a key enzyme responsible for catalyzing the formation of non-toxic, biocompatible, and biodegradable short-chain-length polyhydroxyalkanoates (scl-PHA) under the growth-limiting conditions in the members of the genus Bacillus. Results: The comparative in vitro and in silico analysis of the phaC subunit of type IV PHA synthases among Bacillus cereus FA11, B. cereus FC11, and B. cereus FS1 was done in our study to determine its structural and functional properties. Conserved domain analysis demonstrated that phaC subunit belongs to the alpha/beta (α/β) hydrolase fold. The catalytic triad comprising of cysteine (Cys), histidine (His), and aspartate (Asp) was found to be present at the active site. A shorter inter-atomic distance was found between the carboxyl (-COO) group of Asp and amino (NH2) group of His. Furthermore, slightly long inter-atomic distances between sulfhydryl (SH) group of Cys and NH2 group of His may be pointing toward the broader substrate specificity of type IV PHA synthases. However, a shorter distance between the SH group of Cys and NH2 group of His in case of B. cereus FC11 leads to a higher enzymatic activity and maximum PHA yield (49.26%). Conclusion: The in silico study verifies that the close proximity between SH group of Cys and NH2 group of His in phaC subunit of type IV PHA synthases can be crucial for synthesis of scl-PHA. However, the catalytic activity of type IV PHA synthases declines as the distance between the sulfur (S) atom of the SH group of Cys and the nitrogen (N) atom of NH2 group of His increases.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Little is known about the process of sex determination at the molecular level in species belonging to the subclass Acari, a taxon of arachnids that contains mites and ticks. The recent sequencing of the transcriptome and genome of the western orchard predatory mite Metaseiulus occidentalis allows investigation of molecular mechanisms underlying the biological processes of sex determination in this predator of phytophagous pest mites. We identified four doublesex-and-mab-3-related transcription factor (dmrt) genes, one transformer-2 gene, one intersex gene, and two fruitless-like genes in M. occidentalis. Phylogenetic analyses were conducted to infer the molecular relationships to sequences from species of arthropods, including insects, crustaceans, acarines, and a centipede, using available genomic data. Comparative analyses revealed high sequence identity within functional domains and confirmed that the architecture for certain sex-determination genes is conserved in arthropods. This study provides a framework for identifying potential target genes that could be implicated in the process of sex determination in M. occidentalis and provides insight into the conservation and change of the molecular components of sex determination in arthropods.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Liposomal cytarabine, DepoCyt, is a chemotherapy agent which is used in cancer treatment. This form of cytarabine has more efficacy and fewer side effects relative to the other forms. Since DepoCyt contains the cytarabine encapsulated within phosphatidylcholine and the sterol molecules, we modeled dioleoylphosphatidylcholine (DOPC)/cholesterol bilayer membrane as a carrier for cytarabine to study drug-bilayer interactions. For this purpose, we performed a series of united-atom molecular dynamics (MD) simulations for 25 ns to investigate the interactions between cytarabine and cholesterol-containing DOPC lipid bilayers. Only the uncharged form of cytarabine molecule was investigated. In this study, different levels of the cholesterol content (0, 20, and 40%) were used. MD simulations allowed us to determine dynamical and structural properties of the bilayer membrane and to estimate the preferred location and orientation of the cytarabine molecule inside the bilayer membrane. Properties such as membrane thickness, area per lipid, diffusion coefficient, mass density, bilayer packing, order parameters, and intermolecular interactions were examined. The results show that by increasing the cholesterol concentration in the lipid bilayers, the bilayer thickness increases and area per lipid decreases. Moreover, in accordance with the experiments, our calculations show that cholesterol molecules have ordering effect on the hydrocarbon acyl chains. Furthermore, the cytarabine molecule preferentially occupies the polar region of the lipid head groups to form specific interactions (hydrogen bonds). Our results fully support the experimental data. Our finding about drug-bilayer interaction is crucial for the liposomal drug design.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Prion is a misfolded protein found in mammals that causes infectious diseases of the nervous system in humans and animals. Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer, elk and humans etc. Recent studies have shown that rabbits have a low susceptibility to be infected by prion diseases with respect to other animals including humans. The present study employs molecular dynamics (MD) means to unravel the mechanism of rabbit prion proteins (RaPrPC) based on the recently available rabbit NMR structures (of the wild-type and its two mutants of two surface residues). The electrostatic charge distributions on the protein surface are the focus when analysing the MD trajectories. It is found that we can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrPC; this may be useful for the medicinal treatment of prion diseases.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Abstract Serpins like antithrombin, heparin cofactor II, plasminogen activator inhibitor, antitrypsin, antichymotrypsin and neuroserpin are involved in important biological processes by inhibiting specific serine proteases. Initially the protease recognizes the mobile reactive loop of the serpin eliciting conformational changes, where the cleaved loop together with the protease inserts into β-sheet A, translocating the protease to the opposite side of inhibitor leading to its inactivation. Serpin interaction with proteases is governed mainly by the reactive center loop residues (RCL). However, in some inhibitory serpins, exosite residues apart from reactive center loop have been shown to confer protease specificity. Further, this forms the basis of multi-specificity of some serpins but the residues and their dimension at interface in serpin-protease complexes remains elusive. Here we present a comprehensive structural analysis of the serpin-protease interfaces using bio Complexes COntact MAPS (COCOMAPS), PRotein Interface Conservation and Energetics (PRICE) and ProFace programs. We have carried out interface, burial and evolutionary analysis of different serpin-protease complexes. Among the studied complexes, non-inhibitory serpins exhibit larger interface region with greater number of residue involvement as compared to the inhibitory serpins. On comparing the multi specific serpins (antithrombin and antitrypsin) a difference in the interface area and residue number was observed suggestive of a differential mechanism of action of these serpins in regulating their different target proteases. Further, detailed study of these multi specific serpins listed few essential residues (common in all the complexes) and certain specificity (unique to each complex) determining residues at their interfaces. Structural mapping of interface residues suggested that individual patches with evolutionary conserved residues in specific serpins determine their specificity towards a particular protease.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Metropolis Monte Carlo (MMC) loop refinement has been performed on the three extracellular loops (ECLs) of rhodopsin and opsin-based homology models of the thyroid-stimulating hormone receptor transmembrane domain, a class A type G protein-coupled receptor. The Monte Carlo sampling technique, employing torsion angles of amino acid side chains and local moves for the six consecutive backbone torsion angles, has previously reproduced the conformation of several loops with known crystal structures with accuracy consistently less than 2 Å. A grid-based potential map, which includes van der Waals, electrostatics, hydrophobic as well as hydrogen-bond potentials for bulk protein environment and the solvation effect, has been used to significantly reduce the computational cost of energy evaluation. A modified sigmoidal distance-dependent dielectric function has been implemented in conjunction with the desolvation and hydrogen-bonding terms. A long high-temperature simulation with 2 kcal/mol repulsion potential resulted in extensive sampling of the conformational space. The slow annealing leading to the low-energy structures predicted secondary structure by the MMC technique. Molecular docking with the reported agonist reproduced the binding site within 1.5 Å. Virtual screening performed on the three lowest structures showed that the ligand-binding mode in the inter-helical region is dependent on the ECL conformations.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Cholera toxin (CT) is an AB5 protein complex secreted by the pathogen Vibrio cholera, which is responsible for cholera infection. N-acetylneuraminic acid (NeuNAc) is a derivative of neuraminic acid with nine-carbon backbone. NeuNAc is distributed on the cell surface mainly located in the terminal components of glycoconjugates, and also plays an important role in cell-cell interaction. In our current study, molecular docking and molecular dynamic (MD) simulations were implemented to identify the potent NeuNAc analogs with high-inhibitory activity against CT protein. Thirty-four NeuNAc analogs, modified in different positions C-1/C-2/C-4/C-5/C-7/C-8/C-9, were modeled and docked against the active site of CT protein. Among the 34 NeuNAc analogs, the analog Neu5Gc shows the least extra precision glide score of -9.52 and glide energy of -44.71 kcal/mol. NeuNAc analogs block the CT active site residues HIS:13, ASN:90, LYS:91, GLN:56, GLN:61, and TRP:88 through intermolecular hydrogen bonding. The MD simulation for CT-Neu5Gc docking complex was performed using Desmond. MD simulation of CT-Neu5Gc complex reveals the stable nature of docking interaction.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Abstract Organotin compounds, such as tri-n-butyltin(IV) chloride (TBT), are widespread toxicants which disrupt different functions in living organisms. TBT interacts with lipid membranes and membrane proteins. The inhibition of the calcium ATPase from sarcoplasmic reticulum membranes (SERCA1) by TBT was studied. It was found that the ATPase inhibition could not be reverted in a large time scale, moreover, an excess of TBT over enzyme did not fully inhibit the ATPase activity, therefore it was concluded that TBT irreversibly inhibits the enzyme, and this inhibition is accompanied by a decrease in the effective TBT concentration. The residual ATP hydrolysis activity was measured at different TBT concentrations with time, and the protective effect of different calcium concentrations on the TBT inhibition was also determined. The simplest kinetic mechanism to successfully explain all the observations and the kinetic behavior was found to be a single irreversible step of the inhibitor binding to the enzyme accompanied with a first-order inhibitor inactivation. A fluorescence study of fluorescein-5-isothiocyanate (FITC) labeled enzyme revealed that TBT binding to the enzyme entails a conformational change related to the high to low affinity calcium binding state transition (E1 to E2 transition), resembling the conformational change induced by vanadate linked to the formation of E2V complex from E1 state. A docking study allowed us to propose a binding pocket for TBT in the membrane region of E1 close to the high affinity calcium binding sites, as well as to define the interactions with amino acid residues interfering with calcium sites occupancy.
    Journal of biomolecular structure & dynamics 07/2014;
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    ABSTRACT: Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malaria epidemic. Here, a theoretical FP-2/hemoglobin complex has been proposed and the dynamical footprint and energetics of binding have been investigated using molecular and quantum mechanics approaches. The mapped interaction interface comprises residues 34-51 of hemoglobin and cysteine-42/histidine-174/glutamine-36/asparagine-173/204 and subsites S1, S1', and S3 of FP-2. In hemoglobin-bound FP-2, asparagine-173 preferentially partners histidine-174, while glutamine-36 is preferred in ligand-free state. Cysteine-42 exhibits dihedral switch from 110° to 30° in free and bound states, respectively, with exclusion of water from the binding core upon hemoglobin binding. Hemoglobin similarly exhibits high occupancy within .2 nm distance with charged amido acid-rich subsites S1 and S3 of FP-2 functioning in tandem to reduce conformational flexibility of hemoglobin and facilitate the formation of a stabilizing anti-parallel β-sheet between Leucine-172-valine-176 of FP-2 and phenylalanine-45-asparate-47 of hemoglobin and to overcome the + 1.13e + 5 eV activation energy required to optimize the FP-2/hemoglobin-β conformation that precedes hydrolysis.
    Journal of biomolecular structure & dynamics 06/2014;
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    ABSTRACT: Novel anti-Human immunodeficiency virus (HIV)-1 agents targeting the V3 loop of envelope protein gp120 were designed by computer modeling based on glycosphingolipid β-galactosylceramide (β-GalCer), which is an alternative receptor allowing HIV-1 entry into CD4-negative cells of neural and colonic origin. Models of these β-GalCer analogs bound to the V3 loops from five various HIV-1 variants were generated by molecular docking and their stability was estimated by molecular dynamics (MDs) and binding free energy simulations. Specific binding to the V3 loop was accomplished primarily by non-conventional XH…π interactions between CH/OH sugar groups of the glycolipids and the conserved V3 residues with π-conjugated side chains. The designed compounds were found to block the tip and/or the base of the V3 loop, which form invariant structural motifs that contain residues critical for cell tropism. With the MDs calculations, the docked models of the complexes of the β-GalCer analogs with V3 are energetically stable in all of the cases of interest and exhibit low values of free energy of their formation. Based on the data obtained, these compounds are considered as promising basic structures for the rational design of novel, potent, and broad-spectrum anti-HIV-1 therapeutics.
    Journal of biomolecular structure & dynamics 06/2014;
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    ABSTRACT: Abstract Guanine-rich sequences can form the G-quadruplex structure in the presence of specific metal ions. Here, Circular dichroism, UV-Vis absorption, fluorescence and molecular dynamics simulation studies revealed that insulin binding aptamer (IBA) could form an intramolecular G-quadruplex structure after binding K(+). CD spectra demonstrated that IBA could fold into a parallel G-quadruplex with a strong positive peak at 263 nm. Analysis of equilibrium titration data revealed that cation binding was cooperative with the Hill coefficient of 2.01 in K(+) and 1.90 in Na(+). Thermal denaturation assays indicated that K(+)-induced G-quadruplex is more stable than Na(+)-induced structure. Folding of IBA into G-quadruplex leading to the contact quenching occurs as a result of the formation of a nonfluorescent complex between donor and acceptor. Based on fluorescence quenching of IBA folding, a potassium sensing aptasensor in the range of 0-1.4 mM was proposed. Since the quenching process was predominantly static, the binding constant and the number of binding site were determined. In this research, based on the experimental data, the initial model of IBA G-quadruplex was constructed by molecular modeling method. The modeling structure of IBA is an intramolecular parallel-strand quadruplex conformation with two guanine tetrads. The extended molecular dynamics simulation for the model indicated that the G-quadruplex maintains its structure very well in aqueous solution in presence of K(+) in the central cavity. In contrast, it was demonstrated that the G-quadruplex structure of model in the water collapses in absence of this cation.
    Journal of biomolecular structure & dynamics 06/2014;

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