Biophysical chemistry

Publisher: Elsevier


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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: We have measured the affinity of the CysF9[93]β sulfhydryl group of human deoxyhemoglobin and oxyhemoglobin for 5,5'-dithiobis(2-nitrobenzoate), DTNB, between pH ≈5.6 and 9 in order to understand the basis of the reported reduction of the Bohr effect induced by chemical modification of the sulfhydryl. We analyzed the results quantitatively on the basis of published data indicating that the sulfhydryl exists in two conformations that are coupled to the transition between two tertiary structures of hemoglobin in dynamic equilibrium. Our analyses show that the ionizable groups linked to the DTNB reaction have lower pKas of ionization in deoxyhemoglobin compared to oxyhemoglobin. So these ionizable groups should make negative contributions to the Bohr effect. We identify these groups as HisNA2[2]β, HisEF1[77]β and HisH21[143]β. We provide explanations for the finding that hemoglobin, chemically modified at CysF9[93]β, has a lower Bohr effect and a higher oxygen affinity than unmodified hemoglobin.
    Biophysical chemistry 04/2014; 190-191C:41-49.
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    ABSTRACT: The ion-binding between inorganic ions and charged functional groups of glycine zwitter-ion in NaCl(aq), KCl(aq), MgCl2(aq), and CaCl2(aq) has been investigated over a wide salt concentration range by using integral equation theory in the 3D-RISM approach. These systems mimic biological systems where binding of ions to charged residues at protein surfaces is relevant. It has been found that the stability of ion pairs formed by the carboxylate group and added inorganic cations decreases in the sequence Mg(2+)>Ca(2+)>Na(+)>K(+). However, all formed ion pairs are weak and decrease in stability with increasing salt concentration. On the other hand, at a given salt concentration the stability of (-NH3(+):Cl(-))aq ion pairs is similar in all studied systems. The features of ion-binding and the salt concentration effect on this process are discussed.
    Biophysical chemistry 04/2014; 190-191C:25-31.
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    ABSTRACT: Electron paramagnetic resonance (EPR) data reveal large differences between the ferric ((13)C-)cyanide complexes of wild-type human neuroglobin (NGB) and its H64Q and F28L point mutants and the cyanide complexes of mammalian myo- and haemoglobin. The point mutations, which involve residues comprising the distal haem pocket in NGB, induce smaller, but still significant changes, related to changes in the stabilization of the cyanide ligand. Furthermore, for the first time, the full (13)C hyperfine tensor of the cyanide carbon of cyanide-ligated horse heart myoglobin (hhMb) was determined using Davies ENDOR (electron nuclear double resonance). Disagreement of these experimental data with earlier predictions based on (13)C NMR data and a theoretical model reveal significant flaws in the model assumptions. The same ENDOR procedure allowed also partial determination of the corresponding (13)C hyperfine tensor of cyanide-ligated NGB and H64QNGB. These (13)C parameters differ significantly from those of cyanide-ligated hhMb and challenge our current theoretical understanding of how the haem environment influences the magnetic parameters obtained by EPR and NMR in cyanide-ligated haem proteins.
    Biophysical chemistry 04/2014; 190-191C:8-16.
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    ABSTRACT: The interactions between proteins and ligands often involve a conformational change in the protein. This conformational change can occur before (conformational selection) or after (induced fit) the association with ligand. It is often very difficult to distinguish induced fit from conformational selection when hyperbolic binding kinetics are observed. In light of a recent paper in this journal (Vogt et al., Biophys. Chem., 186, 2014, 13-21) and the current interest in binding mechanisms emerging from observed sampling of distinct conformations in protein domains, as well as from the field of intrinsically disordered proteins, we here describe a kinetic method that, at least in some cases, unequivocally distinguishes induced fit from conformational selection. The method relies on measuring the observed rate constant λ for binding and varying both the protein and the ligand in separate experiments. Whereas induced fit always yields a hyperbolic dependence of increasing λ values, the conformational selection mechanism gives rise to distinct kinetics when the ligand and protein (displaying the conformational change) concentration is varied in separate experiments. We provide examples from the literature and discuss the limitations of the approach.
    Biophysical chemistry 04/2014; 189C:33-39.
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    ABSTRACT: The effects of adding cis- and trans-unsaturated lipid to a fully interdigitated membrane were examined using differential scanning calorimetry (DSC) and X-ray diffraction. A monofluorinated analog of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was used as the interdigitated lipid. The single fluorine atom on the end of the sn-2 chain allows 1-palmitoyl-2-(16-fluoropalmitoyl)sn-glycero-3-phosphocholine (F-DPPC) to spontaneously form the interdigitated gel phase (LβI) below the main transition temperature (Tm). The cis 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and equivalent trans lipid 1,2-dielaidoyl-sn-glycero-3-phosphocholine (DEPC) are strongly disfavored to form the LβI phase. Wide-angle X-ray scattering (WAXS) data demonstrate that the unsaturated lipids progressively disrupt the intermolecular packing at higher concentrations. Small-angle X-ray scattering (SAXS) data show that as the ratio of unsaturated lipid increases, the amount of interdigitated lipid decreases. The cis isomer is more disruptive and inhibits interdigitation more effectively than the trans isomer.
    Biophysical chemistry 04/2014; 190-191C:1-7.
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    ABSTRACT: The effects of the central metal ion on complex formation between meso-tetrakis(N-methylpyridium-4-yl)porphyrin (TMPyP) and the thrombin-binding aptamer G-quadruplex, 5'G2T2G2TGTG2T2G2, were examined in this study. The central metal ions were vanadium and zinc. At a [porphyrin]/[G-quadruplex] ratio of less than one, the absorption and CD spectra were unaffected by the mixing ratio for all three porphyrins, suggesting that the binding mode is homogeneous. Relatively small changes in the absorption spectrum when forming the complexes with the G-quadruplex, the positive CD signal, and the large accessibility of the I(-) quencher, suggested that all these porphyrins are not intercalated between the G-quartet. Stabilization of the G-quadruplex by ZnTMPyP was most effective. The effect of VOTMPyP on G-quadruplex stabilization was moderate, whereas TMPyP slightly destabilized G-quadruplex. From this observation, the involvement of the ligation of one G-quartet component to the central metal ion in G-quadruplex stabilization by metallo-TMPyP is suggested.
    Biophysical chemistry 04/2014; 190-191C:17-24.
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    ABSTRACT: Transthyretin (TTR) dissociation and aggregation appear to cause several amyloid diseases. TTR dimer is an important intermediate that is hard to be observed from the biological experiments. To date, the molecular origin and the structural motifs for TTR dimer dissociation, as well as the unfolding process have not been rationalized at atomic resolution. To this end, we have investigated the effect of low pH and mutation L55P on stability as well as the unfolding pathway of TTR dimer using constant pH molecular dynamics simulations. The result shows that acidic environment results in loose TTR dimer structure. Mutation L55P causes the disruption of strand D and makes the CE-loop very flexible. In acidic conditions, dimeric L55P mutant exhibits notable conformation changes and an evident trend to separate. Our work shows that the movements of strand C and the loops nearby are the beginning of the unfolding process. In addition, hydrogen bond network at the interface of the two monomers plays a part in stabilizing TTR dimer. The dynamic investigation on TTR dimer provides important insights into the structure-function relationships of TTR, and rationalizes the structural origin for the tendency of unfolding and changes of structure that occur upon introduction of mutation and pH along the TTR dimer dissociation and unfolding process.
    Biophysical chemistry 03/2014; 189C:8-15.
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    ABSTRACT: We present a novel protein distance matrix based on the minimum line of arc between two points on the surface of a protein. Two methods for calculating this distance matrix are developed and contrasted. The first method, which we have called TOPOL, is an approximate rule based algorithm consisting of successive rounds of vector addition. The second method is adapted from the graph theoretic approach of Dijkstra. Both procedures are demonstrated using cytochrome c, a 12,500Da protein, as a test case. In respect to computational speed and accuracy the TOPOL procedure compares favorably against the more complex method based on shortest path enumeration over a surface manifold grid. Some potential uses of the algorithmic approaches and calculated surface protein distance measurement are discussed.
    Biophysical chemistry 02/2014;
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    ABSTRACT: In this work, molecular dynamics (MD) simulations were performed to investigate the effects of cholesterol on the interaction between the hydrophilic anticancer drug, 5-FU, and fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer. Several structural and dynamical parameters of DMPC bilayers with varying amounts of cholesterol (0, 25, and 50mol%) in the presence and absence of drug molecules were calculated. Moreover, the free energy barriers for translocation of one 5-FU molecule from water to the lipid bilayer were determined by using the potential of mean force (PMF). PMF studies indicated that the location of the maximum free energy barrier was in the hydrophobic middle region of bilayer, while the minimums of the barrier were located at the hydrophilic part of bilayer at the interface with water. The minimum and maximum of the free energy profiles were independent of cholesterol concentration and suggested that the drug molecules 5-FU were accumulated in the vicinity of the polar head group of lipid bilayers. Moreover, the results showed that with increasing cholesterol concentration in the bilayer, the free energy barrier for translocation of 5-FU across the bilayer also increases which can be attributed to the condensing effect of the cholesterol on the bilayer.
    Biophysical chemistry 02/2014; 187-188C:43-50.
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    ABSTRACT: Local DNA opening plays an important role in DNA metabolism as the double-helix must be melted before the information contained within may be accessed. Cells finely tune the torsional state of their genomes to strike a balance between stability and accessibility. For example, while mesophilic life forms maintain negatively superhelical genomes, thermophilic life forms use unique mechanisms to maintain relaxed or even positively supercoiled genomes. Here, we use a single-molecule magnetic tweezers approach to quantify the force-dependent equilibrium between DNA melting and supercoiling at high temperatures populated by Thermophiles. We show that negatively supercoiled DNA denatures at 0.5 pN lower tension at thermophilic vs. mesophilic temperatures. This work demonstrates the ability to monitor DNA supercoiling at high temperature and opens the possibility to perform magnetic tweezers assays on thermophilic systems. The data allow for an estimation of the relative energies of base-pairing and DNA bending as a function of temperature and support speculation as to different general mechanisms of DNA opening in different environments. Lastly, our results imply that average in vivo DNA tensions range between 0.3 and 1.1 pN.
    Biophysical chemistry 01/2014; 187-188C:23-28.
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    ABSTRACT: Self-assemblies formed by the new synthesized tricationic porphyrin derivative (TMPyP(3+)) on the polyanionic inorganic polyphosphate (PPS) in aqueous solution were studied using different spectroscopic techniques and DFT calculation method. From the fluorescence quenching of the bound TMPyP(3+) molecules and their Raman spectra we conclude that porphyrin chromophores form the stable π-π stacking-assemblies onto PPS polyanions. The transformation of the Soret band in absorption spectra at different PPS/TMPyP(3+)concentration ratios evidences that the assemblies are mixtures of J- and H-aggregates. Molecular modeling performed shows that the flexibility of PPS strand allows a realization of spiral or "face-to-face" one-dimensional structures formed by porphyrin molecules arranged in parallel and antiparallel modes. The peculiarity of PPS structure allows a formation of two porphyrin stacks on opposite sides of polymer strands that result in the appearance of higher-order aggregates. Their size was estimated from the light scattering data. Distinctions between TMPyP(3+) and TMPyP4 aggregation on PPS template are discussed.
    Biophysical chemistry 01/2014; 185:39-46.
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    ABSTRACT: The G-quadruplex DNA is a novel target for anticancer drug discovery and many scientific groups are investigating interaction of small molecules with G-quadruplex DNA to discover therapeutic agents for cancer. Here, interaction of a phthalocyanine (Cu(PcTs)) and two tetrapyridinoporphyrazines ([Cu(2,3-tmtppa)](4+) and [Cu(3,4-tmtppa)](4+)) with Na(+) and K(+) forms of human telomeric G-quadruplex DNA has been investigated by spectroscopic techniques. The results indicated that interaction of the cationic porphyrazines is remarkably stronger than the anionic phthalocyanine and they presumably bind to the G-quadruplex DNA through end-stacking. Fluorescent intercalator displacement assay implied the displacement ability of the complexes with thiazole orange. In addition, circular dichroism spectra of both quadruplex forms converge to the Na(+) isoform after binding to the porphyrazines. In conclusion, the porphyrazines as the complexes that bind to the G-quadruplex DNA, could be suitable candidates for further investigations about inhibition of telomerase enzyme.
    Biophysical chemistry 12/2013; 187-188C:7-13.
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    ABSTRACT: Simultaneous flipped-out conformation of two neighboring bases on opposite strands of DNAs has been observed in several X-ray structures. It has also been detected for two cytosines on opposite strands in different contexts of CpG sites. In this paper, we study by MD simulations the dual base flipping of the two cytosines in hemi-methylated CpG site. We calculate the potential of mean force of flipping-out the unmethylated cytosine in three model systems. The first is for DNA bound to the regulatory protein UHRF1. In this case, the methyl-cytosine on the complementary strand is flipped-out into the binding pocket of the SRA domain of the protein. The other two systems are for unbound DNAs in which the methyl-cytosine is either intra-helical or extra-helical. We find that when the methyl-cytosine is flipped-out it is easier to flip-out the other (unmethylated) cytosine on the opposite strand by about 14-16kJ/mol. This lower penalty for dual-base flipping is observed for both the bound and unbound states of the DNA. Analyses of the hydrogen bond network and stacking interactions within the CpG site indicate that the lower penalty is due to stabilization of the dual-base flipped-out conformation via interactions involving the orphan guanines. The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1.
    Biophysical chemistry 12/2013; 187-188C:14-22.
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    ABSTRACT: Despite their presence in many aspects of biology, the study of membrane proteins lags behind that of their soluble counterparts. Improving structural analysis of membrane proteins is essential. Deep-UV resonance Raman (DUVRR) spectroscopy is an emerging technique in this area and has demonstrated sensitivity to subtle structural transitions and changes in protein environment. The pH low insertion peptide (pHLIP) has three distinct structural states: disordered in an aqueous environment, partially folded and associated with a lipid membrane, and inserted into a lipid bilayer as a transmembrane helix. While the soluble and membrane-inserted forms are well characterized, the partially folded membrane-associated state has not yet been clearly described. The amide I mode, known to be sensitive to protein environment, is the same in spectra of membrane-associated and membrane-inserted pHLIP, indicating comparable levels of backbone dehydration. The amide S mode, sensitive to helical structure, indicates less helical character in the membrane-associated form compared to the membrane-inserted state, consistent with previous findings. However, the structurally sensitive amide III region is very similar in both membrane-associated and membrane-inserted pHLIP, suggesting that the membrane-associated form has a large amount of ordered structure. Where before the membrane-associated state was thought to contain mostly unordered structure and reside in a predominantly aqueous environment, we have shown that it contains a significant amount of ordered structure and rests deeper within the lipid membrane.
    Biophysical chemistry 12/2013; 187-188C:1-6.
  • Biophysical chemistry 12/2013;