Journal of biomolecular Structure & Dynamics Impact Factor & Information

Publisher: Taylor & Francis

Journal 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.

Current impact factor: 2.98

Impact Factor Rankings

2015 Impact Factor Available summer 2015
2013 / 2014 Impact Factor 2.983
2010 Impact Factor 4.986
2009 Impact Factor 1.124
2008 Impact Factor 1.289
2007 Impact Factor 1.413
2006 Impact Factor 1.299
2005 Impact Factor 1.43
2004 Impact Factor 1.113
2003 Impact Factor 1.131
2002 Impact Factor 1.009
2001 Impact Factor 1.243
2000 Impact Factor 1.826
1999 Impact Factor 1.407
1998 Impact Factor 1.643
1997 Impact Factor 1.283

Impact factor over time

Impact factor
Year

Additional details

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

Publisher details

Taylor & Francis

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Some individual journals may have policies prohibiting pre-print archiving
    • On author's personal website or departmental website immediately
    • On institutional repository or subject-based repository after either 12 months embargo
    • Publisher's version/PDF cannot be used
    • On a non-profit server
    • Published source must be acknowledged
    • Must link to publisher version
    • Set statements to accompany deposits (see policy)
    • The publisher will deposit in on behalf of authors to a designated institutional repository including PubMed Central, where a deposit agreement exists with the repository
    • STM: Science, Technology and Medicine
    • Publisher last contacted on 25/03/2014
    • This policy is an exception to the default policies of 'Taylor & Francis'
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Visceral leishmaniasis (VL) affects Indian subcontinent, African and South American continent and it covers 70 countries worldwide. Visceral form of leishmaniasis is caused by Leishmania donovani in Indian subcontinent which is lethal if left untreated. Extensive resistance to antileishmanial drugs such as sodium stibogluconate, pentamidine and miltefosine and their decreased efficacy have been reported in the endemic region. Amphotericin B drug has shown good antileishmanial activity with significant toxicity, but its cost of treatment has limited the outreach of this treatment to affected people living in endemic zone. So there is an urgent need to identify new antileishmanial drugs with excellent activity and minimal toxicity issues. Trypanothione reductase, a component of antioxidant system is necessary for parasite growth and survival to raise infection. To develop potential inhibitor, we docked nine hundred eighty four 5-Nitroimidazole analogues along with clomipramine which is a well-known inhibitor for trypanothione reductase. Total one hundred forty seven 5-Nitoimidazole analogues with better docking score than clomipramine were chosen for ADMET and QikProp studies. Among these imidazole analogues, total twenty four imidazole analogues and clomipramine were chosen on the basis of their ADMET, QikProp and prime MM-GBSA study. Later on, two analogues with best MM-GBSA dG bind were undergone molecular dynamic simulation to ensure protein ligand interactions. Using above approach we confirm that ethyl 2-acetyl-5-[4-butyl-2-(3-hydroxypentyl)-5-nitro-1H-imidazol-1-yl]pent-2-enoate can be a drug candidate against L. donovani for the treatment of VL in the Indian subcontinent.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1085904
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    ABSTRACT: There is a huge variety of RNA- and DNA-containing entities that multiply within and propagate between cells across all kingdoms of life, having no cells of their own. Apart from cellular organisms these entities (viroids, plasmids, mobile elements and viruses among others) are the only ones with distinct genetic identities but which are not included in any traditional tree of life. We suggest to introduce or, rather, revive the distinct category of acellular organisms, Acytota, as an additional, undeservedly ignored full-fledged kingdom of life. Acytota are indispensable players in cellular life and its evolution. The six traditional kingdoms (Cytota) and Acytota together complete the classification of the biological world (Biota), leaving nothing beyond.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1086959
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    ABSTRACT: Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the drug development. However, structural details on the binding between PKC and its modulators, especially bryostatin-the highly potent and non-tumor promoting activator for PKCs, are still lacking. Here we report the first comparative molecular dynamics (MD) study aimed at gaining structural insight into the mechanisms by which the PKC delta cys2 activator domain is used in its binding to phorbol ester and bryostatin-1. As anticipated in the phorbol ester binding, hydrogen bonds are formed through the backbone atoms of Thr242, Leu251 and Gly253 of PKC. However, the opposition of H-bond formation between Thr242 and Gly253 may cause the phorbol ester complex to become less stable when compared with the bryostatin binding. For the PKC delta-bryostatin complex, hydrogen bonds are formed between the Gly253 backbone carbonyl and the C30 carbomethoxy substituent of the ligand. Additionally, the indole Nε1 of the highly homologous Trp252 also forms an H-bond to the C20 ester group on bryostatin. Backbone fluctuations also suggest that this latter H-bond formation may abrogate the transient interaction between Trp252 and His269, thus dampening the fluctuations observed on the nearby Zn(2+)-coordinating residues. This new dynamic fluctuation dampening model can potentially benefit future design of new PKC modulators.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1084479
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    ABSTRACT: Protease activated receptor 2 (PAR2) has emerged as one of the promising therapeutic targets to inhibit rapidly metastasizing breast cancer cells. However, its elusive molecular mechanism of activation and signaling has made it a difficult target for drug development. In this study, in silico methods were used to unfold PAR2 molecular mechanism of signaling based on the concept of GPCR receptor plasticity. Although, there are no conclusive evidences of the presence of specific endogenous ligands for PAR2, the efficacy of synthetic agonist and antagonist in PAR2 signaling has opened up the possibilities of ligand mediated signaling. Furthermore, it has been proved that ligands specific for one GPCR can induce signaling in receptors belonging to other subfamilies. Therefore, the aim of the present study was to identify potential agonists and antagonists from the GPCR ligand database (GLL), which may induce biased signaling in PAR2 using the concept of existence of multiple ligand stabilized receptor conformations. The results of our in silico study suggest that PAR2 may show biased signaling with agonists of serotonin type1, β adrenergic type 1 and antagonists of substance K (NK1), serotonin type 2, dopamine type 4 and thromboxane receptors. Further, this study could also throw light on the putative ligand specific conformations of PAR2. Thus, the results of this study provide structural insights to putative conformations of PAR2 and also gives initial clues to medicinal chemists for rational drug design targeting this challenging receptor.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1079556
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    ABSTRACT: The sterile alpha motif (SAM) domain of the protein ANKS6, a protein-protein interaction domain, is responsible for autosomal dominant polycystic kidney disease (ADPKD). Although the disease is the result of the R823W point mutation in the SAM domain of the protein ANKS6, the molecular details is still unclear. We applied molecular dynamics (MD) simulations, principal component analysis (PCA) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculation to explore the structural and dynamic effects of the R823W point mutation on the complex ANKS6-ANKS3 (PDB ID: 4NL9) in comparison to the wild proteins. The energetic analysis presents that the wide type has a more stable structure than the mutant. The R823W point mutation not only disrupts the structure of the ANKS6 SAM domain but also negatively affects the interaction of the ANKS6-ANKS3. These results further clarify the previous experiments to understand the ANKS6-ANKS3 interaction comprehensively. In summary, this study would provide useful suggestions to understand the interaction of these proteins and their fatal action on mediating kidney function.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1071281
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    ABSTRACT: The ribose binding protein (RBP), a sugar-binding periplasmic protein, is involved in the transport and signaling processes in both prokaryotes and eukaryotes. Although several cellular and structural studies have been reported, a description of the thermostability of RBP at the molecular level remains elusive. Focused on the hyperthermophilic Thermoytoga maritima RBP (tmRBP) and mesophilic Escherichia coli homolog (ecRBP), we applied molecular dynamics simulations at four different temperatures (300, 380, 450, and 500 K) to obtain a deeper insight into the structural features responsible for the reduced thermostability of the ecRBP. The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two homologues and the ecRBP unfolds faster than the hyperthermophilic homologues at certain temperatures in accordance with the lower thermal stability found experimentally. Essential dynamics analysis uncovers that the essential subspaces of ecRBP and tmRBP are non-overlapping and these two proteins show different direction of motion within the simulations trajectories. Such an understanding is required for designing efficient proteins with characteristics for a particular application.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1084480
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    ABSTRACT: In recent years, using heavy metal compounds such as platinum as anticancer agent is one of the common ways in chemical therapy. In this study, a new anticancer compound of glycine derivatives of Pt(II) complex (amyl-glycine1, 10-phenanthroline Platinum nitrate) was designed, and the biological effects of this novel compound on the alterations in the function and structure of human hemoglobin (Hb) at different temperatures of 25 and 37°C were assessed by applying various spectroscopic (fluorescence and circular dichroism (CD)) and theoretical methods. Fluorescence data indicated the strong ability of Pt(II) complex to quench the intrinsic fluorescence of Hb. The binding constant, number of binding sites, and thermodynamic parameters at two temperatures were calculated, and the results indicated the major possibility of occurring van der Waals force or hydrogen bond interactions in the Pt(II) complex-Hb interaction. For evaluating the alteration of secondary structure of Hb upon interaction with various concentrations of complex, far-UV CD spectra were used and it was observed that in high dose of complex, significant changes were occurred which is indicative of some side effects in overdosing of this complex. On the other hand, the molecular docking results illustrate that are well in agreement in obtaining data with spectroscopy. Above results suggested that using Pt(II) complex as an anticancer agent, model drug in high-dose usage might cause some disordering in structure and function of Hb as well as improve understanding of the side effects of newly designed metal anticancer drugs undergoing.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1071280
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    ABSTRACT: Cyclosporine (CsA) is widely used in organ-transplant patients to help prevent the patient's body from rejecting the organ. CsA has been shown to be a safe and highly effective immunosuppressive drug that binds with the protein Cyclophilin A (CypA) at active sites. However, the exact mechanism of this binding at the molecular level remains unknown. In this project, we elucidate the binding of CsA to CypA at the molecular level by computing their electron structures and revealing their interactions. We employ a novel technique called eCADD (electron Computer-Aided Drug Design) on the protein's full electron structure along with its hydrophobic pocket and the perturbation theory of the interaction between two wave functions. We have identified the wave function of CypA, the biological active residues and active atoms of CypA and CsA, the interaction site between CypA and CsA, and the hydrogen bonds in the ligand CsA binding site. All these calculated active residues, active atoms and hydrogen bonds are in good agreement with recorded lab experiments and provide guidelines for designing new ligands of CypA. We believe that our eCADD framework can provide researchers with a cost-efficient new method of drug design based on the full electron structure of proteins.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1057527
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    ABSTRACT: The emerging field of synthetic biology has led to the design of tailor-made synthetic circuits for several therapeutic applications. Biological networks can be re-programmed by designing synthetic circuits that modulate the expression of target proteins. IPCS (Inositol phosphorylceramide synthase) has been an attractive target in the sphingolipid metabolism of the parasite 'Leishmania'. In the present study, we have constructed a tristable circuit for the IPCS protein. The circuit has been validated and its long term behaviour has been assessed. The robustness and evolvability of the circuit has been estimated by using evolutionary algorithms. The tristable synthetic circuit has been specifically designed to improve the rate of production of Phosphatidylcholine: ceramide cholinephosphotransferase 4 (SLS4 protein). Site specific delivery of the circuit into the parasite infected macrophages could serve as a possible therapeutic intervention of the infectious disease 'Leishmaniasis'.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1082150
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    ABSTRACT: Precise functioning and fine-tuning of Toll-like receptor 4 (TLR4) signaling is a critical requirement for the smooth functioning of the innate immune system, since aberrant TLR4 activation causes excessive production of pro-inflammatory cytokines and interferons. This can result in life threatening conditions such as septic shock and other inflammatory disorders. The TRIF-related adaptor molecule (TRAM) adaptor protein is unique to the TLR4 signaling pathway and abrogation of TRAM-mediated TLR4 signaling is a promising strategy for developing therapeutics aimed at disrupting TRAM interactions with other components of the TLR4 signaling complex. The VIPER motif from the vaccinia virus-producing protein, A46 has been reported to disrupt TRAM-TLR4 interactions. We have exploited this information, in combination with homology modelling and docking approaches, to identify a potential binding site on TRAM lined by the BB loop and αC helix. Virtual screening of commercially available small molecules targeting the binding site enabled to short-list 12 small molecules to abrogate TRAM-mediated TLR4 signaling. Molecular dynamics and molecular mechanics calculations have been performed for the analysis of these receptor-ligand interactions.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1079243
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    ABSTRACT: Dengue is a major public health concern in tropical and subtropical countries of the world. There are no specific drugs available to treat dengue. Even though several candidates targeted both viral and host proteins to overcome dengue infection, they have not yet entered into the later stages of clinical trails. In order to design a drug for dengue fever, newly emerged fragment based drug designing technique was applied. RNA dependent RNA polymerase, which is essential for dengue viral replication is chosen as a drug target for dengue drug discovery. A cascade of methods, fragment screening, fragment growing and fragment linking revealed the compound [2-(4-carbamoylpiperidin-1-yl)-2-oxoethyl]8-(1,3-benzothiazol-2-yl)naphthalene-1-carboxylate, as a potent dengue viral polymerase inhibitor. Both strain energy and binding free energy calculations predicted that this could be a better inhibitor than the existing ones. Molecular dynamics simulation studies showed that the dengue polymerase-lead complex is stable and their interactions are consistent throughout the simulation. The hydrogen bonded interactions formed by the residues Arg792, Thr794, Ser796 and Asn405 are the primary contributors for the stability and the rigidity of the polymerase-lead complex. This might keep the polymerase in closed conformation and thus inhibit viral replication. Hence, this might be a promising lead molecule for dengue drug designing. Further optimization of this lead molecule would result in a potent drug for dengue.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1081620
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    ABSTRACT: Effects of sodium (octyl, dodecyl, hexadecyl) sulfate and their cationic analogous on the structure of adenosine deaminase (ADA) were investigated by fluorescence and circular dichroism (CD) spectroscopy as well as molecular dynamics (MDs) simulation and docking calculation. Root-mean-square derivations (RMSD), radius of gyration (Rgyr), solvent accessible surface area (SASA) and radial distribution function (RDF) were obtained. The results showed that anionic and cationic surfactants reduce protein stability. Cationic surfactants have more effect on the ADA structure in comparison with anionic surfactants. More concentration and longer surfactants are parallel to higher denaturation. Furthermore, aggregation in the presence of anionic surfactants is more than cationic surfactants. Docking data showed that, longer surfactants have more interaction energy and smaller ones bound to the active site.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1081571
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    ABSTRACT: Paenibacillus polymxca β-glucosidase B (BglB), belongs to a GH family 1 (GH1), is a monomeric enzyme that acts as an exo-β-glucosidase hydrolyzing cellobiose and cellodextrins of higher degree of polymerization using retaining mechanism. A molecular dynamics (MD) simulation was performed at 300 K under periodic boundary condition for 5 ns using the complexes structure obtained from previous docking study namely BglB-Beta-D-glucose (BglB-BGC) and BglB-Cellobiose (BglB-CBI). From the Root Mean Squared Deviation (RMSD) analysis, both enzyme complexes were reported to deviate from the initial structure in the early part of the simulation but it was stable afterwards. The Root Mean Squared Fluctuation (RMSF) analysis revealed that the most flexible regions comprised of the residues from 26-29, 43-53, 272-276, 306-325, and 364-367. The Radius of Gyration (RG) analysis had shown the structure of BglB without substrate became more compact towards the end of the simulation compare to other two complexes. The residues His122 and Trp410 were observed to form stable hydrogen bond with occupancy higher than 10%. In conclusion, the behaviour of BglB enzyme towards the substrate binding was successfully explored via MD simulation approaches.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1081570
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    ABSTRACT: Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation) and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB to double-stranded DNA (ds-DNA) has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction.
    Journal of biomolecular Structure & Dynamics 08/2015; DOI:10.1080/07391102.2015.1079557