Biophysical chemistry Journal Impact Factor & Information

Publisher: Elsevier

Current impact factor: 1.99

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 Impact Factor 1.986
2013 Impact Factor 2.319
2012 Impact Factor 2.283
2011 Impact Factor 2.203
2010 Impact Factor 2.108
2009 Impact Factor 2.276
2008 Impact Factor 2.362
2007 Impact Factor 1.913
2006 Impact Factor 1.784
2005 Impact Factor 1.925
2004 Impact Factor 2.102
2003 Impact Factor 1.728
2002 Impact Factor 1.494
2001 Impact Factor 1.918
2000 Impact Factor 1.578
1999 Impact Factor 1.498
1998 Impact Factor 1.522
1997 Impact Factor 1.596
1996 Impact Factor 2.294
1995 Impact Factor 1.696
1994 Impact Factor 1.157
1993 Impact Factor 1.059
1992 Impact Factor 1.314

Impact factor over time

Impact factor

Additional details

5-year impact 2.00
Cited half-life >10.0
Immediacy index 0.87
Eigenfactor 0.01
Article influence 0.64
ISSN 1873-4200

Publisher details


  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Authors pre-print on any website, including arXiv and RePEC
    • Author's post-print on author's personal website immediately
    • Author's post-print on open access repository after an embargo period of between 12 months and 48 months
    • Permitted deposit due to Funding Body, Institutional and Governmental policy or mandate, may be required to comply with embargo periods of 12 months to 48 months
    • Author's post-print may be used to update arXiv and RepEC
    • Publisher's version/PDF cannot be used
    • Must link to publisher version with DOI
    • Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License
    • Publisher last reviewed on 03/06/2015
  • Classification

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Identifying protein-DNA interactions is essential to understand the regulatory networks of cells and their influence on gene expression. In this study, we use native electrospray mass spectrometry (ESI-MS) to investigate how the heterodimerization of retinoic acid receptor-retinoid X receptor (RAR-RXR) is mediated by DNA sequence. In presence of various RAR response elements (RAREs), three oligomeric states of RAR-RXR DNA binding domains (DBDs) bound to RAREs (monomer, homo- or heterodimers) were detected and individually monitored to follow subunit assembly and disassembly upon RAREs' abundancy or sequence. In particular, a cooperative heterodimerization was shown with RARb2 DR5 (5 base pair spaced direct repeat) while a high heterogeneity reflecting random complex formation could be observed with the DR0 response elements, in agreement with native gel electrophoresis data or molecular modeling. Such MS information will help to identify the composition of species formed in solution and to define which DR sequence is specific for RAR-RXR heterodimerization.
    Biophysical chemistry 11/2015; DOI:10.1016/j.bpc.2015.10.006
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    ABSTRACT: Water-miscible cosolvents may stabilize or destabilize proteins, nucleic acids, and their complexes or may exert no influence. The mode of action of a specific cosolvent is determined by the interplay between the excluded volume effect and direct solute-cosolvent interactions. Excluded volume refers to the steric exclusion of water and cosolvent molecules from the space occupied by solute, an event accompanied by a decrease in translational entropy. In thermodynamic terms, the excluded volume effect is modeled by creating a cavity which is sufficiently large to accommodate the solute and which is inaccessible to surrounding molecules of water and cosolvent(s). An understanding of the relationship between the energetic contributions of cavity formation and direct solute-cosolvent interactions is required for elucidating the molecular origins of the stabilizing or destabilizing influence of specific cosolvents. In this work, we employed the concepts of scaled particle theory to compute changes in free energy of cavity formation, ∆∆GC, accompanying the ligand-protein binding, protein dimerization, protein folding, and DNA duplex formation events. The computations were performed as a function of the concentration of methanol, urea, ethanol, ethylene glycol, and glycine betaine. Resulting data were used in conjunction with a previously developed statistical thermodynamic algorithm to estimate the excluded volume contribution to changes in preferential hydration, ∆Γ21, and interaction, ∆Γ23, parameters and m-values associated with the reactions under study. The excluded volume contributions to ∆Γ21, ∆Γ23, and m-values are very significant ranging from 30 to 70% correlating with the size of the cosolvent molecule. Our results suggest that a pair of "fully excluded cosolvents" with negligible solute-solvent interactions may differ significantly with respect to their excluded volume contributions to ∆Γ21, ∆Γ23, and m-values thereby differently influencing the equilibrium of the reaction being sampled. This notion has implications for understanding the long-standing observation that, in osmotic stress studies, various osmolytes may produce significantly distinct estimates of hydration/dehydration for the same reaction.
    Biophysical chemistry 11/2015; 209. DOI:10.1016/j.bpc.2015.11.001
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    ABSTRACT: Tau has long been associated with Alzheimer's disease, where it forms neurofibrillary tangles. Here we show for the first time by electron microscopy that MAP2c prevents arachidonic acid-induced in vitro aggregation of tau. However, phosphorylated MAP2c failed to prevent the same. Previously we reported that MAP2c possesses chaperone-like activity while tau does not (Sarkar et al., 2004, Eur J Biochem., 271(8), 1488-96). Here we demonstrate that phosphorylation severely impaired the chaperone activity of MAP2c, implying a crucial role of chaperone in preventing tau fibrillation. Additionally, the ability of MAP2c to induce microtubule polymerization was abolished completely upon phosphorylation. As tau and MAP2c possess highly homologous C-termini, we speculated that the N-terminus of MAP2c might account for its chaperone activity. Nevertheless, experiments showed that N-terminus of MAP2c alone is inactive as a chaperone. Our preliminary findings suggest that MAP2c/MAP2 could be one of the regulators maintaining tau homeostasis in the cell. Copyright © 2015. Published by Elsevier B.V.
    Biophysical chemistry 10/2015; 205. DOI:10.1016/j.bpc.2015.06.003
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    ABSTRACT: Cytochrome c (Cyt c) is an essential component of the inner mitochondrial respiratory chain because of its function of transferring electrons. The feature is closely related to the interaction between Cyt c and membrane lipids. We used Langmuir-Blodgett monolayer technique combined with AFM to study the interaction of Cyt c with lipid monolayers at air-buffer interface. In our work, by comparing the mixed Cyt c-anionic (DPPS) and Cyt c-zwitterionic (DPPC/DPPE) monolayers, the adsorption capacity of Cyt c on lipid monolayers is DPPS>DPPE>DPPC, which is attributed to their different headgroup structures. π-A isothermal data show that Cyt c (v=2.5μL) molecules are at maximum adsorption quantity on lipid monolayer. Moreover, Cyt c molecules would form aggregations and drag some lipids with them into subphase if the protein exceeds the maximum adsorption quantity. π-T curve indicates that it takes more time for Cyt c molecular conformation to rearrange on DPPE monolayer than on DPPC. The compressibility study reveals that the adsorption or intermolecular aggregation of Cyt c molecules on lipid monolayer will change the membrane fluidization. In order to quantitatively estimate Cyt c molecular adsorption properties on lipid monolayers, we fit the experimental isotherm with a simple surface state equation. A theoretical model is also introduced to analyze the liquid expanded (LE) to liquid condensed (LC) phase transition of DPPC monolayer. The results of theoretical analysis are in good agreement with the experiment. Copyright © 2015 Elsevier B.V. All rights reserved.
    Biophysical chemistry 10/2015; 205. DOI:10.1016/j.bpc.2015.05.008
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    ABSTRACT: In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney.
    Biophysical chemistry 10/2015; 207:107-113. DOI:10.1016/j.bpc.2015.10.002
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    ABSTRACT: According to the cancer stem cell theory malignant glioma is incurable because of the presence of the cancer stem cells - a subpopulation of cells that are resistant to therapy and cause the recurrence of a tumor after surgical resection. Several protein markers of cancer stem cell were reported but none of those is fully reliable to grade the content of stem cells in a tumor. Hereby we propose Fourier transform infrared (FTIR) microspectroscopy as an alternative, labelfree, non-damaging and fast method to identify glioma stem cells based on their own spectral characteristics. The analysis of FTIR data revealed that in NCH421k cells, a model of glioma stem cells, the relative content of lipids is higher than in their all-trans retinoic acid-differentiated counterparts. Moreover, it has been assessed that stem cells have more rigid cellular membranes and more phosphorylated proteins, whereas after differentiation glycogen level increases. The ability of FTIR to estimate the content of stem cells in a heterogeneous sample, on the base of the identified spectral markers, and to classify stem and non-stem cells into two separate populations was probed. Although it was not possible to calculate the exact percentage of each subpopulation, we could clearly see that with the increasing amount of differentiated cells in a sample, more hits occupy the PC space previously identified as a space of differentiated cells. The present study is therefore an initial step towards the development of a FTIR based protocol in clinical practice to estimate the content of stem cells in a tumor sample.
    Biophysical chemistry 10/2015; 207:90-96. DOI:10.1016/j.bpc.2015.09.005
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    ABSTRACT: Cell-penetrating compounds (CPCs) are often conjugated to drugs and genes to facilitate cellular uptake. We hypothesize that the electrostatic interaction between the positively charged amines of the cell-penetrating compounds and the negatively charged glycosaminoglycans (GAGs) extending from cell surfaces is the initiating step in the internalization process. The interactions of generation 5 PAMAM dendrimer, Tat peptide and 25kDa linear PEI with four different GAGs have been studied using isothermal titration calorimetry to elucidate structure-function relationships that could lead to improved drug and gene delivery methods to a wide variety of cell types. Detailed thermodynamic analysis has determined that CPC-GAG binding constants range from 8.7×10(3) to 2.4×10(6)M(-1) and that affinity is dependent upon GAG charge density and stereochemistry and CPC molecular weight. The effect of GAG composition on affinity is likely due to hydrogen bonding between CPC amines and amides and GAG hydroxyl and amine groups. These results were compared to the association of CPCs with lipid vesicles of varying composition as model plasma membranes to finally clarify the relative importance of each cell surface component in initial cell recognition. CPC-lipid affinity increases with anionic lipid content, but GAG affinity is higher for all cell-penetrating compounds, confirming the role these heterogeneous polysaccharides play in cellular association and clustering.
    Biophysical chemistry 09/2015; 207:40-50. DOI:10.1016/j.bpc.2015.08.003
  • [Show abstract] [Hide abstract]
    ABSTRACT: Carbonmonoxycytochrome c refolds to a native-like compact state (NCO-state), where the non-native Fe(2+)-CO interaction persists. Structural and molecular properties extracted from CD, fluorescence and NMR experiments reveal that the NCO-state shows the generic properties of molten globules. Slow thermal-dissociation of CO transforms the NCO-state to native-state (N-state), where the native Fe(2+)-M80 bond recovers. To determine the role of crowding agents and salt ions on the structural-fluctuation of NCO, the kinetic and thermodynamic parameters for CO-dissociation from NCO (NCO→N+CO) were measured at varying concentrations of crowding agents (dextran 70, dextran 40, ficoll 70) and salt ions (anion: ClO4(-), I(-), Br(-), NO3(-), Cl(-); cation: NH4(+), K(+), Na(+)). As [crowding agent] or [ion] is increased, the rate coefficient of CO-dissociation (kdiss) decreases exponentially. Furthermore, the extent of decrease in kdiss is found to be dependent on (i) size, charge density and charge dispersion of the ion, and (ii) size, shape, and viscosity of the crowding agent.
    Biophysical chemistry 09/2015; 207. DOI:10.1016/j.bpc.2015.09.001

  • Biophysical chemistry 09/2015; DOI:10.1016/j.bpc.2015.09.001.

  • Biophysical chemistry 09/2015; DOI:10.1016/j.bpc.2015.09.006
  • [Show abstract] [Hide abstract]
    ABSTRACT: Prokaryotic metal-ion receptor proteins, or solute-binding proteins, facilitate the acquisition of metal ions from the extracellular environment. Pneumococcal surface antigen A (PsaA) is the primary Mn2+-recruiting protein of the human pathogen Streptococcus pneumoniae and is essential for its in vivo colonization and virulence. The recently reported high-resolution structures of metal-free and metal-bound PsaA have provided the first insights into the mechanism of PsaA-facilitated metal binding. However, the conformational dynamics of metal-free PsaA in solution remain unknown. Here, we use continuous wave electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations to study the relative flexibility of the structural domains in metal-free PsaA and its distribution of conformations in solution. The results show that the crystal structure of metal-free PsaA is a good representation of the dominant conformation in solution, but the protein also samples structurally distinct conformations that are not captured by the crystal structure. Further, these results suggest that the metal binding site is both larger and more solvent exposed than indicated by the metal-free crystal structure. Collectively, this study provides atomic-resolution insight into the conformational dynamics of PsaA prior to metal binding and lays the groundwork for future EPR and MD based studies of PsaA in solution.
    Biophysical chemistry 09/2015; 207:51-60. DOI:10.1016/j.bpc.2015.08.004
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    ABSTRACT: The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up to ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development of this method. Next, we discuss its validation against the results of plain MD protein folding simulations performed by the DE-Shaw group using the Anton supercomputer. Finally, we review a few representative applications of the DRP approach to study reactions which are far too complex and rare to be investigated by plain MD, even on the Anton machine. Copyright © 2015 Elsevier B.V. All rights reserved.
    Biophysical chemistry 08/2015; DOI:10.1016/j.bpc.2015.06.014