Journal of biomolecular Structure & Dynamics (J BIOMOL STRUCT DYN)

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: 2.92

Impact Factor Rankings

2016 Impact Factor Available summer 2017
2014 / 2015 Impact Factor 2.919
2013 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 2.42
Cited half-life 4.60
Immediacy index 0.94
Eigenfactor 0.00
Article influence 0.53
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

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: Mitochondrial carbonic anhydrase VA (CAVA) catalyzes the hydration of carbon dioxide to produce proton and bicarbonate which is primarily expressed in the mitochondrial matrix of liver, and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the effect of pH on the structure, function and stability of CAVA, we employed spectroscopic techniques such as circular dichroism, fluorescence and absorbance measurements in wide range of pH (from pH 2.0 to pH 11.5). CAVA showed an aggregation at acidic pH range from pH 2.0 to pH 5.0. However, it remains stable and maintains its secondary structure in the pH range, pH 7.0 - pH 11.5). Furthermore, this enzyme have an appreciable activity at more than pH 7.0 (7.0 < pH ≤ 11.5) with a maximum of activity at pH 9.0. The maximal values of kcat and kcat/Km at pH 9.0 are 3.7 x 10(6) s(-1) and 5.5 x10(7) M(-1)s(-1), respectively. However, this enzyme lose its activity in the acidic pH range. We further performed 20 ns molecular dynamics simulation of CAVA to see the dynamics at different pH values. An excellent agreement was observed between in silico and in vitro studies. This study provides an insight into the activity of CAVA in the pH range of subcellular environment.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Despite the recent resolutions of the crystal structure of the chemokine receptor CXCR4 in complex with small antagonists or viral chemokine, a description at the molecular level of the interactions between the full-length CXCR4 and its endogenous ligand, the chemokine CXCL12, in relationship with the receptor recognition and activation, is not yet completely elucidated. Moreover, since CXCR4 is able to form dimers, the question of whether the CXCR4-CXCL12 complex has a 1:1 or 2:1 preferential stoichiometry is still an open question. We present here results of coarse-grained protein-protein docking and molecular dynamics simulations of CXCL12 in association with CXCR4 in monomeric and dimeric states. Our proposed models for the 1:1 and 2:1 CXCR4-CXCL12 quaternary structures are consistent with recognition and activation motifs of both partners provided by the available site-directed mutagenesis data. Notably, we observed that in the 2:1 complex, the chemokine N-terminus makes more steady contacts with the receptor residues critical for binding and activation than in the 1:1 structure, suggesting that the 2:1 stoichiometry would favor the receptor signaling activity with respect to the 1:1 association.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: We report here two new small-size peptides acting as modulators of the BACE1 exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderated but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initio and DFT calculations, a simple and generally applicable procedure to evaluate the binding energies of small-size peptides interacting with the exosite of the BACE1 is reported here. The structural aspects obtained for the different complexes were analyzed providing a clear picture about the binding interactions of these peptides. These interactions have been investigated within the framework of the density functional theory and the quantum theory of atoms in molecules (QTAIM) using a reduced model. Although the approach used here was traditionally applied to the study of non covalent interactions in small molecules complexes in gas phase, we show through in this work that this methodology is also a very powerful tool for the study of biomolecular complexes, providing a very detailed description of the binding event of peptides modulators at the exosite of BACE1.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Tyrosine Kinase inhibitors (TKI) resistant mutations in epidermal growth factor receptor’s (EGFR) kinase domain is an important anomaly to look into. Studying the mutations at atomic level using molecular dynamics simulations gave us an insight into the architectural changes happening at the microscopic level. The knowledge was used to design new TKI whose function is devoid of the affect of the mutations in Kinase domain. Traditional Chinese medicinal library was used for structure based drug designing, where virtual screening was followed by ADME/Tox analysis and the shortlisted compounds were docked into the kinase domain of EGFR and simulated there using atomic level selection of the grid. The shortlisted compounds from molecular docking analysis were subjected to MM-PBSA calculations. The In-silico data generated is giving a strong lead compound for further In-vitro and In-vivo analysis.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Why the intrinsically disordered regions evolve within human proteome has became an interesting question for a decade. Till date it remains an unsolved yet an intriguing issue to investigate why some of the disordered regions evolve rapidly while the rest are highly conserved across mammalian species. Identifying the key biological factors, responsible for the variation in the conservation rate of different disordered regions within the human proteome, may revisit the above issue. We emphasized that among the other biological features (multifunctionality, gene essentiality, protein connectivity, number of unique domains, gene expression level and expression breadth) considered in our study, the number of unique protein domains acts as a strong determinant that negatively influences the conservation of disordered regions. In this context, we justified that proteins having a fewer types of domains preferably need to conserve their disordered regions to enhance their structural flexibility which in turn will facilitate their molecular interactions. In contrast, the selection pressure acting on the stretches of disordered regions is not so strong in the case of multi-domains proteins. Therefore, we reasoned that the presence of conserved disordered stretches may compensate the functions of multiple domains within a single domain protein. Interestingly, we noticed that the influence of the unique domain number and expression level acts differently on the evolution of disordered regions from that of well-structured ones.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Kallikrein, a physiologically vital serine protease was investigated for its functional and conformational transitions during chemical (organic solvents, Gdn-HCl), thermal, and pH induced denaturation using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach. The enzyme was exceptionally stable in isopropanol and ethanol showing 110% and 75% activity, respectively after 96h, showed moderate tolerance in acetonitrile (45% activity after 72 h) and much lower stability in methanol (40% activity after 24h) (all the solvents [90% v/v]). Far UV CD and fluorescence spectra indicated apparent reduction in compactness of KLKp structure in isopropanol system. MD simulation studies of the enzyme in isopropanol revealed 1) minimal deviation of the structure from native state 2) marginal increase in radius of gyration (Rg) and solvent accessible surface area (SASA) of the protein and the active site and 3) loss of density barrier at the active site possibly leading to increased accessibility of substrate to catalytic triad as compared to methanol and acetonitrile. Although kallikrein was structurally stable up to 90°C as indicated by secondary structure monitoring, it was functionally stable only up to 45°C, implicating thermolabile active site geometry. In GdnHCl [1.0 M], 75% of the activity of KLKp was retained after incubation for 4h, indicating its denaturant tolerance. A molten globule like structure of KLKp formed at pH 1.0 was more thermostable and exhibited interesting structural transitions in organic solvents. The above results provide deeper understanding of functional and structural stability of the serine proteases at molecular level.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Our earlier study on the nucleosomes containing TBP binding sites (TATA-boxes) indicated that, generally, the same sequence which harbors the TATA-box, encodes simultaneously an alternative rotational setting of the box, so that the TATA element is either exposed (position "minor groove out") or hidden in position "minor groove in". The sequence elements (dinucleotides) residing on the inner surface of DNA in contact with the histone octamers are identified by calculating the YR tracks in the promoter regions of the genes - periodically reappearing YR elements, at distances 10-11 bases from one another. The non-YR elements of the YR tracks are also verified by nucleosome mapping procedure based on alternation of runs of purines with runs of pyrimidines. The tracks observed in yeast promoter regions are found to split in two, passing further downstream either through TATA element or 4-6 bases toward the tail of the box. The points of the splitting which play role of the TATA-switches, are located in close vicinity or within transcription factor binding sites. This suggests the regulatory function of the transcription factors, changing the YR-tracks by over- or under-twisting DNA induced by their binding.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: The P.falciparum Serine Repeat Antigen (PfSERA5) is the most abundantly expressed protein in the parasitophorous vacuole (PV) during the asexual blood stage and serves as both drug and vaccine target. The processed central fragment (56KDa) of PfSERA5 is implicated to play an important role in parasite exit (egress) during schizont rupture from erythrocytes. Structural characterization of its enzymatic domain supports protease like function for this central domain. The understanding of exact functional role of PfSERA5 in parasite egress remains unconfirmed as recent studies also indicate an indispensable non-catalytic role for PfSERA5 putative enzyme domain in the blood stage. No structural insight into PfSERA5 prodomain is available. Structure prediction of PfSERA5 prodomain using insilico approach in our study, showed it to have structural similarity with calcium binding proteins. An earlier observation of steep rise in intracellular calcium concentration as an important factor in egress makes the prodomain calcium binding role significant. The implication of calcium on structure and activity of PfSERA5 putative enzyme domain is also unknown, and such information would aid to substantiating any calcium dependent effects on PfSERA5 To understand this, we performed Molecular Dynamic (MD) simulation both in the presence and absence of calcium. MD results show secondary structure conformational differences in local regions of protein structure. Our results support calcium to be an important parameter for stability and function of PfSERA5. This computational assessment suggest a need to design future experiments like calcium dependent inhibition studies to reveal exact functional role of PfSERA5 in parasite egress.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Protein prenylation is a post-translational modification critical for many cellular processes such as DNA replication, signaling and trafficking. It is mediated by protein farnesyltransferase (PFT) by recognizing 'CAAX' motif on protein substrate. Plasmodium falciparum also posses many such proteins with 'CAAX' motif, involved in various pathways of parasite. The interaction studies of PfPFT with its substrate were carried out using synthetic peptides but not with full protein. Therefore, in this study, we have modeled both PfPFT and its substrate protein tyrosine phosphatase (PfPRL-PTP) followed by interaction studies using protein-protein docking and molecular dynamics simulation. Our findings provided a clear picture of interactions at atomic level between prenyltransferase and its protein substrate. We are assured this piece of information can be extended to many other proteins of parasite containing 'CAAX' motif and it may also lead to development of anti-malarials based on inhibition of prenylation dependent pathways of parasite.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: In this paper, we describe the derivation and the validation of original RESP atomic partial charges for the N, N-dimethyl-dodecylamine oxide (LDAO) surfactant. These charges, designed to be fully compatible with all the AMBER force fields, are at first tested against molecular dynamics (MD) simulations of pure LDAO micelles and with a fragment of the lipid kinase PIK4A (DI) modeled with the QUARK molecular modeling server. To model the micelle, we used two distinct AMBER force fields (i.e. Amber99SB and Lipid14) and a variety of starting conditions. We find that the micelle structural properties (such as the shape, size, the LDAO headgroup hydration and alkyl chain conformation) slightly depend on the force field but not on the starting conditions and more importantly are in good agreement with experiments and previous simulations. We also show that the Lipid14 force field should be use instead of the Amber99SB one to better reproduce the C(sp3)C(sp3)C(sp3)C(sp3) conformation in the surfactant alkyl chain. Concerning the simulations with LDAO-DI protein, we carried out different runs at two NaCl concentrations (i.e. 0 and 300mM) to mimic, in the latter case, the experimental conditions. We notice a small dependence of the simulation results with the LDAO parameters and the salt concentration. However, we find that in the simulations 3 out of 4 tryptophans of the DI protein are not accessible to water in agreement with our fluorescence spectroscopy experiments reported in the paper.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Visceral leishmaniasis (VL) affects people from 70 countries worldwide, mostly from Indian, African and south American continent. The increasing resistance to antimonial, miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an antileishmanial drug with excellent efficacy and safety profile. In this study we have docked series of febrifugine analogues (n = 8,813) against trypanothione reductase in three sequential docking modes. Extra precision (XP) docking resulted into 108 ligands showing better docking score as compared to two reference ligand. Furthermore, 108 febrifugine analogues and reference inhibitor clomipramine were subjected to ADMET, QikProp and MM-GBSA study to ensure the toxicity caused by compounds and binding free energy respectively. Two best ligands (FFG7 and FFG2) qualifying above screening parameters were further subjected to molecular dynamics simulation. Conducting these studies, here we confirmed that 6-chloro-3-[3-(3-hydroxy-2-piperidyl)-2-oxo-propyl]-7-(4-pyridyl) quinazolin-4-one can be potential drug candidate to fight against Leishmania donovani parasites.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Familial inheritance of breast and ovarian cancer is attributed to mutations discovered in functional domains of BRCA1 gene. BRCA1 is a multifunctional protein responsible for maintaining the genomic integrity and has transcriptional regulatory function encoded in its C-terminal region. The different amino-terminal e extensions to BRCA1 BRCT domain are responsible for transcription activation. However, only BRCA1 BRCT (1649-1859) amino acids have been explored for its structural characteristics. Noting the importance of extended region to the N-terminus of BRCT different regions of BRCA1 which demonstrates maximum transactivation activity have been explored for their structure and functional activity. Secondary and tertiary structural analysis revealed a limited alpha-helical content with well folded tertiary structure. In silico tools were used to corroborate the in vitro results. Amino acids composition and sequence analysis display a propensity for intrinsic disorder and coiled-coil formation in BRCA1 (1396-1863) (BRCA1-TAD). The results presented in this paper suggest the extreme flexibility in coiled-coil motif might be an important requirement in the establishment of protein-protein interaction networks for BRCA1.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Two distinct crystal structures of prethrombin-2, the alternative and collapsed forms, are elucidated by X-ray crystallogrphy. We analyzed the conformational transition from the alternative to the collapsed form employing targeted molecular dynamics simulation. Despite small RMSD difference in the two X-ray crystal structures, some hydrophobic residues (W60d, W148, W215, and F227) show a significant difference between the two conformations. Targeted molecular dynamics (TMD) simulation shows that the four hydrophobic residues undergo concerted movement from dimer to trimer transition via tetramer state in the conformational change from the alternative to the collapsed form. We reveal that the concerted movement of the four hydrophobic residues is controlled by movement of specific loop regions behind. In this paper, we propose a sequential scenario for the conformational transition from the alternative form to the collapsed form, which is partially supported by the mutant W148A simulation.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: Brucella melitensisis is a pathogenic gram-negative bacterium which is known for causing zoonotic diseases (Brucellosis). The organism is highly contagious and has been reported to be used as bioterrorism agent against humans. Several antibiotics and vaccines have been developed but these antibiotics have exhibited the sign of antibiotic resistance or ineffective at lower concentrations, which imposes an urgent need to identify the novel drugs /drug targets against this organism. In this work, metabolic pathways analysis have been performed with different filters such as non-homology with humans, essentially of genes and choke point analysis, leading to identification of novel drug targets. A total of 18 potential drug target proteins were filtered out and used to develop the high confidence protein-protein interaction network The Phosphoribosyl-AMP cyclohydrolase (HisI) protein has been identified as potential drug target on the basis of topological parameters. Further, a homology model of (HisI) protein has been developed using Modeller with multiple template (1W6Q (48%), 1ZPS (55%) and 2ZKN (48%)) approach and validated using PROCHECK and Verify3D.The virtual high throughput screening (vHTS) using DockBlaster tool has been performed against 16,11,889 clean fragments from ZINC database. Top 500 molecules from DockBlaster were docked using Vina. The docking analysis resulted in ZINC04880153 showing the lowest binding energy (-9.1kcal/mol) with the drug target. The molecular dynamics study of the complex HisI-ZINC04880153 was conducted to analyze the stability and fluctuation of ligand within the binding pocket of HisI. The identified ligand could be analyzed in the wet-lab based experiments for future drug discovery.
    No preview · Article · Jan 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: The interaction between human hemoglobin (Hb) and oxali-palladium was studied using different spectroscopic methods of UV-Vis, fluorescence, circular dichroism (CD) and chemiluminescence at two temperatures of 25 and 37 °C. The experimental results showed that both dynamic and static quenching is occurred simultaneously when oxali-palladium quenches the fluorescence of Hb. According to the fluorescence quenching method, the binding site number, apparent binding constant and corresponding thermodynamic parameters were measured at two temperatures. The values of ΔH°, ΔS°, and ΔG° indicate that process of the formation of oxali-palladium-Hb complex is a spontaneous interaction procedure in which electrostatic interaction plays a major role. In addition, UV-vis and CD results showed that the addition of oxali-palladium changes the conformation of Hb. To evaluate the functional changes of Hb via destruction of the heme structure, fluorescence studies were performed. The results demonstrated that two fluorescent heme degradation products are found during the interaction of oxali-palladium with Hb. Also, the amount of hydrogen peroxide produced in the solution of hemoglobin due to the interaction of oxali-palladium with hemoglobin using chemiluminescence method indicated heme degradation in the protein is occurred. Structural and functional changes induced in hemoglobin via heme degradation are considered as side effects of this synthesized anti-cancer drug.
    No preview · Article · Dec 2015 · Journal of biomolecular Structure & Dynamics