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Biophysical Chemistry

Current research reports and chronological list of recent articles..




The scientific journal Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal.

The publisher is Elsevier. The copyright and publishing rights of specialized products listed below are in this publishing house. This is also responsible for the content shown.

To search this web page for specific words type "Ctrl" + "F" on your keyboard (Command + "F" on a Mac). Then: type the word you are searching for in the window that pops up!

Additional research articles see Current Chemistry Research Articles. Magazines with similar content (biophysical chemistry):

 - Biomacromolecules.

 - Faraday Discussions.

 - Journal of Physical Chemistry B.

 - Physical Chemistry Chemical Physics PCCP.



Biophysical Chemistry - Abstracts



Sequence length dependence in arginine/phenylalanine oligopeptides: Implications for self-assembly and cytotoxicity

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): Emerson R. Silva, Eduardo Listik, Sang W. Han, Wendel A. Alves, Bruna M. Soares, Mehedi Reza, Janne Ruokolainen, Ian W. Hamley

We present a detailed study on the self-assembly and cytotoxicity of arginine-rich fragments with general form [RF]n (n=1–5). These highly simplified sequences, containing only two l-amino acids, provide suitable models for exploring both structure and cytotoxicity features of arginine-based oligopeptides. The organization of the sequences is revealed over a range of length scales, from the nanometer range down to the level of molecular packing, and their cytotoxicity toward C6 rat glioma and RAW264.7 macrophage cell lines is investigated. We found that the polymorphism is dependent on peptide length, with a progressive increase in crystalline ordering upon increasing the number of [RF] pairs along the backbone. A dependence on length was also found for other observables, including critical aggregation concentrations, formation of chiral assemblies and half maximum inhibitory concentrations (IC50). Whereas shorter peptides self-assemble into fractal-like aggregates, clear fibrillogenic capabilities are identified for longer sequences with octameric and decameric chains exhibiting crystalline phases organized into cross-β structures. Cell viability assays revealed dose-dependent cytotoxicity profiles with very similar behavior for both glioma and macrophage cell lines, which has been interpreted as evidence for a nonspecific mechanism involved in toxicity. We propose that structural organization of [RF]n peptides plays a paramount role regarding toxicity due to strong increase of local charge density induced by self-assemblies rich in cationic groups when interacting with cell membranes.

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Datum: 20.02.2018


Full title pg and editorial board

Publication date: January 2018
Source:Biophysical Chemistry, Volume 232










Datum: 20.02.2018


Osmolyte depletion viewed in terms of the dividing membrane and its work of expansion against osmotic pressure

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Seishi Shimizu, Nobuyuki Matubayasi

How osmolytes enhance the folding, binding, and self-assembly of biological macromolecules at a microscopic scale has long been a matter of debate. Ambiguities persist on the key interpretive concepts, such as the “effective membrane” (which marks the boundary of the volume from which osmolytes are excluded) and the “free energy of exclusion” of osmolytes from biomolecular surfaces. In this paper, we formulate these elusive concepts based upon chemical thermodynamics and rigorous statistical thermodynamics (the Kirkwood-Buff theory). Positioning of the membrane at the osmotic dividing surface is crucial in order not to affect the thermodynamics of solvation. The notion of the free energy (work) of excluding osmolytes is refined to the expansion work against the osmotic pressure, which indeed describes the change of solvation free energy at dilute osmolyte concentrations.

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Datum: 20.02.2018


Photosystem I, when excited in the chlorophyll Qy absorption band, feeds on negative entropy

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): Robert C. Jennings, Erica Belgio, Giuseppe Zucchelli

It is often suggested that Life may lay outside the normal laws of Physics and particularly of Thermodynamics, though this point of view is refuted by many. As the Living State may be thought of as an open system, often far from equilibrium, most attempts at placing Life under the umbrella of the laws of Physics have been based, particularly in recent years, on non-equilibrium Thermodynamics and particularly the Maximum Entropy Production Principle. In this view it is the dissipation of entropy (heat) which permits the ever increasing complexity of Living Systems in biological evolution and the maintenance of this complexity. However, these studies usually consider such biological entities as whole cells, organs, whole organisms and even Life itself at the entire terrestrial level. This requires making assumptions concerning the Living State, which are often not soundly based on observation and lack a defined model structure. The present study is based on an entirely different approach, in which a classical thermodynamic analysis of a well-defined biological nanoparticle, plant Photosystem I, is performed. This photosynthetic structure, which absorbs light and performs primary and secondary charge separation, operates with a quantum efficiency close to one. It is demonstrated that when monochromatic light is absorbed by the lowest lying electronic transition, the chlorophyll Qy transition, entropy production in the system bath plus entropy changes internal to the system are numerically less than the entropy decrease of the light field. A Second Law violation is therefore suggested for these experimental conditions. This conclusion, while at first sight is supportive of the famous and much discussed statement of Schroedinger, that “Life feeds on negentropy”, is analysed and the conditions in which this statement may be considered valid for a Plant Photosystem are defined and delimited. The remarkably high quantum efficiency, leading to minimal entropy production (energy wastage), seems to suggest that evolution of Photosystem I has gone down the road of maximal energy efficiency as distinct from maximal entropy production. Photosystem I cannot be considered a maximum entropy dissipation structure.

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Datum: 20.02.2018


Location of fluorescent probes (2′-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation

Publication date: April 2018
Source:Biophysical Chemistry, Volume 235

Author(s): Yevgen Posokhov, Alexander Kyrychenko

2′-Hydroxy derivatives of 2,5-diaryl-1,3-oxazole are known as environment-sensitive ratiometric excited-state intramolecular proton transfer (ESIPT) fluorescent probes, which are used to monitor physicochemical properties of lipid membranes. However, because of their heterogeneous membrane distribution, accurate experimental determination of the probe position is difficult. To estimate the location of the ESIPT probes in lipid membranes we have performed fluorescence measurements and molecular dynamics (MD) simulations. In the series composed of 2-(2′-hydroxy-phenyl)-5-phenyl-1,3-oxazole (1), 2-(2′-hydroxy-phenyl)-5-(4′-biphenyl)-1,3-oxazole (2), and 2-(2′-hydroxy-phenyl)-phenanthro[9,10-d]-1,3-oxazole (3), the structure of the ESIPT-moiety of 2-(2′-hydroxy-phenyl)-oxazole was varied by either aromatic ring substitution or annealing, leading to the systematical increase in the hydrophobic character of the probes. The comparison of the fluorescence behavior of probes 13 in a wide variety of solvents with those in phospholipid vesicles revealed that all three probes prefer to reside inside a membrane. Our MD results demonstrate that the probes locate from the glycerol residues and the polar carbonyl groups of phospholipids up to hydrophobic acyl chain units. It has been found that the probe location correlates well with the size of the aromatic moiety, being gradually shifted from 11.1 Å to 7.6 Å from the bilayer center for probes 1 to 3, respectively. Our results may be useful for the design of novel fluorescent probes for fluorescence sensing of specific regions within a lipid membrane.

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Datum: 20.02.2018


The importance of pKa in an analysis of the interaction of compounds with DNA

Publication date: Available online 6 February 2018
Source:Biophysical Chemistry

Author(s): Mouli Saha, Promita Nandy, Mousumi Chakraborty, Piyal Das, Saurabh Das

pKa of a compound is crucial for determining the contributions of different forms of it towards overall binding with DNA. Hence it is important to use correct pKa values in DNA interaction studies. This study takes a look at the importance of pKa values to realize binding of compounds with DNA. Since pKa of a compound determined in the presence of DNA is quite different from that determined in its absence hence, presence of different forms of a compound during interaction with DNA is different from that realized if the determination of pKa is done in normal aqueous solution in absence of DNA. Hence, calculations determining contributions of different forms of a compound interacting with DNA are affected accordingly. Two simple analogues of anthracyclines, alizarin and purpurin, were used to investigate the influence DNA has on pKa values. Indeed, they were different in presence of DNA than when determined in normal aqueous solution. pKa1 for alizarin and purpurin determined in the absence and presence of calf thymus DNA were used in equations that determine contributions of two forms (neutral and anionic) towards overall binding with DNA. The study concludes that correct pKa values, determined correctly i.e. under appropriate conditions, must be used for DNA binding experiments to evaluate contributions of individual forms.

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Datum: 20.02.2018


Pressure response of 31P chemical shifts of adenine nucleotides

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Matthias Karl, Michael Spoerner, Thuy-Vy Pham, Sunilkumar Puthenpurackal Narayanan, Werner Kremer, Hans Robert Kalbitzer

High pressure NMR spectroscopy is a powerful method for identifying rare conformational states of proteins from the pressure response of their chemical shifts. Many proteins have bound adenine nucleotides at their active centers, in most cases in a complex with Mg2+-ions. The 31P NMR signals of phosphate groups of the nucleotides can be used as probes for conformational transitions in the proteins themselves. For distinguishing protein specific pressure effects from trivial pressure responses not due to the protein interaction, data of the pressure response of the free nucleotides must be available. Therefore, the pressure response of 31P chemical shifts of the adenine nucleotides AMP, ADP, and ATP and their Mg2+-complexes has been determined at pH values several units distant from the respective pK-values. It is clearly non-linear for most of the resonances. A negative first order pressure coefficient B 1 was determined for all 31P resonances except Mg2+·AMP indicating an upfield shift of the resonances with pressure. The smallest and largest negative values are obtained for the α-phosphate group of ADP and β-phosphate group of Mg2+·ATP with −0.32 and −4.59ppm/GPa, respectively. With exception of the α-phosphate group of Mg2+·AMP the second order pressure coefficients are positive leading to a saturation like behaviour. The pressure response of the adenine nucleotides is similar but not identical to that observed earlier for guanine nucleotides. The obtained data show that the chemical shift pressure response of the different phosphate groups is rather different dependent on the position of phosphate group in the nucleotide and the nucleotide used.

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Datum: 20.02.2018


Cooperative protein unfolding. A statistical-mechanical model for the action of denaturants

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): J. Seelig

Knowledge of protein stability is of utmost importance in various fields of biotechnology. Protein stability can be assessed in solution by increasing the concentration of denaturant and recording the structural changes with spectroscopic or thermodynamic methods. The standard interpretation of the experimental data is to assume a 2-state equilibrium between completely folded and completely unfolded protein molecules. Here we propose a cooperative model based on the statistical-mechanical Zimm-Bragg theory. In this model protein unfolding is driven by the weak binding of a rather small number of denaturant molecules, inducing the cooperative unfolding with multiple dynamic intermediates. The modified Zimm-Bragg theory is applied to published thermodynamic and spectroscopic data leading to the following conclusions. (i) The binding constant KD is correlated with the midpoint concentration, c0, of the unfolding reaction according to c0 1/KD. The better the binding of denaturant the lower is the concentration to achieve unfolding. (ii) The binding constant KD agrees with direct thermodynamic measurements. A rather small number of bound denaturants suffices to induce the cooperative unfolding of the whole protein. (iii) Chemical unfolding occurs in the concentration range Δc D = c end c ini . The theory predicts the unfolding energy per amino acid residue as g nu = RTK D (c end c ini ). The Gibbs free energy of an osmotic gradient of the same size is ΔG Diff = RT ln(c end /c ini ). In all examples investigated ΔGDiff exactly balances the unfolding energy gnu. The total unfolding energy is thus close to zero. (iv) Protein cooperativity in chemical unfolding is rather low with cooperativity parameters σ 3x103. As a consequence, the theory predicts a dynamic mixture of conformations during the unfolding reaction. The probabilities of individual conformations are easily accessible via the partition function Z(cD,σ).

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Datum: 20.02.2018


Non-canonical DNA structures: Comparative quantum mechanical study

Publication date: April 2018
Source:Biophysical Chemistry, Volume 235

Author(s): Stanislav S. Bachurin, Mikhail E. Kletskii, Oleg N. Burov, Sergey V. Kurbatov

A study of relative thermodynamic stability of non-canonical DNA structures (triplexes, G-quadruplexes, i-motifs) for the first time was conducted on the basis of quantum chemical DFT/B3LYP/6-31++G (d) calculations. Results of the calculations completely reproduce the experimental data on stability of G-quadruplexes comparatively Watson-Crick B-DNA. It was discovered that combinations of non-canonical DNA structures were energetically more favorable than separated nitrogenous bases. Supramolecular complexes of the non-canonical DNA structures (NSs) can be considered as a biological drug targets in gene regulation (for example in tumor therapy), in contrast to previous works, where NSs were studied independently.

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Datum: 20.02.2018


Protective effect of quercetin and rutin encapsulated liposomes on induced oxidative stress

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): Claudia Bonechi, Alessandro Donati, Gabriella Tamasi, Gemma Leone, Marco Consumi, Claudio Rossi, Stefania Lamponi, Agnese Magnani

Natural antioxidants show many pharmacological properties, but poor solubility and inability to cross cell membrane. Liposomes are biocompatible and phospholipid vesicles able to carry hydrophilic, hydrophobic, and amphiphilic molecules. This paper focus on the synthesis of anionic, cationic and zwitterionic liposomes, loaded with quercetin or rutin, and on the evaluation of their cytotoxicity and protective effects against oxidative stress. Chemical characterization was obtained by dynamic light scattering and z-potential experiments. In vitro cell behavior was evaluated by Neutral Red Uptake test. All liposomes, empty and loaded with antioxidants, are stable. The cytotoxicity of both quercetin and rutin encapsulated in zwitterionic and anionic liposomes is higher than that of their solutions. Quercetin and rutin loaded in cationic liposomes are able to inhibit the toxic effect of empty liposomes. The encapsulation of rutin at 5.0×105 and 5.0×104 M, in zwitterionic and anionic liposomes, protects fibroblasts by H2O2 treatment, while the loading with quercetin does not have effect on improving cell viability. All data suggest that the tested liposomes are stable and able to include quercetin and rutin. The liposomes encapsulation of antioxidants makes easier their internalization by cells. Moreover, zwitterionic and anionic liposomes loaded with rutin protect cells by oxidative stress. Liposomes stability together with their good in vitro cytocompatibility, both empty and loaded with antioxidant molecules, makes these systems suitable candidates as drug delivery systems. Moreover, the encapsulation of rutin, is able to protect cells by oxidative stress.

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Datum: 20.02.2018


Conformational dynamics and free energy of BHRF1 binding to Bim BH3

Publication date: January 2018
Source:Biophysical Chemistry, Volume 232

Author(s): Mauro Lapelosa

The interaction between the Bim BH3 peptide and the viral protein BHRF1 is pivotal to understanding the fundamental molecular details of the mechanism used by the Epstein-Barr virus to trick the mammalian immune system. Here, we study the mechanism of binding/unbinding and compute the free energy for the association of the Bim peptide to the BHRF1 protein. Key elements of the binding mechanism are the conformational rearrangement together with a main free energy barrier of 11.5kcal/mol. The simulations show complete unbinding and rebinding of the Bim peptide to BHRF1. The peptide slowly dissociates, disrupting the hydrophobic contacts, then tilting to one side. The peptide then completely disrupts all the remaining interactions and moves into the bulk solvent. The rebinding of the peptide from the solvent to the receptor binding site occurs slowly. This is because the helix partially unfolds in the unbound state. Rebinding involves an intermediate state, in which the peptide interacts with the hydrophobic binding pocket, which mainly involves Leu 62, Arg 63, Ile 65, and Phe 69. This novel intermediate structure forms 65 contacts with the receptor before the peptide again reaches the bound state. The standard binding free energy value is close to the experimental Kd in the nanomolar range. Finally, we observe how the breathing motions of α3-α4 are coupled with the binding/unbinding of the Bim BH3 peptide. The structure of the intermediate can be used for designing novel peptide inhibitors of the BHRF1 protein.

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Datum: 20.02.2018


Impact of high hydrostatic pressure on bacterial proteostasis

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Elisa Gayán, Sander K. Govers, Abram Aertsen

High hydrostatic pressure (HHP) is an important factor that limits microbial growth in deep-sea ecosystems to specifically adapted piezophiles. Furthermore, HHP treatment is used as a novel food preservation technique because of its ability to inactivate pathogenic and spoilage bacteria while minimizing the loss of food quality. Disruption of protein homeostasis (i.e. proteostasis) as a result of HHP-induced conformational changes in ribosomes and proteins has been considered as one of the limiting factors for both microbial growth and survival under HHP conditions. This work therefore reviews the effects of sublethal (≤100MPa) and lethal (>100MPa) pressures on protein synthesis, structure, and functionality in bacteria. Furthermore, current understanding on the mechanisms adopted by piezophiles to maintain proteostasis in HHP environments and responses developed by atmospheric-adapted bacteria to protect or restore proteostasis after HHP exposure are discussed.






Datum: 20.02.2018


Thermodynamic analysis of Kex2 activity: The acylation and deacylation steps are potassium- and substrate-dependent

Publication date: April 2018
Source:Biophysical Chemistry, Volume 235

Author(s): Alyne Alexandrino Antunes, Larissa de Oliveira Passos Jesus, Marcella Araújo Manfredi, Aline Aparecida de Souza, Maurício Ferreira Marcondes Machado, Pamela Moraes e Silva, Marcelo Yudi Icimoto, Maria Aparecida Juliano, Luiz Juliano, Wagner Alves de Souza Judice

Kex2 is the prototype of a large family of eukaryotic subtilisin-related proprotein-processing proteases that cleave at sites containing pairs of basic residues. Here, we studied the effects of KCl on the individual rate constants of association, dissociation, acylation and deacylation and determined the thermodynamic parameters at each step of the Kex2 reaction. Potassium bound Kex2 with K D =20.3mM. The order in which potassium entered the reaction system modified the effect of activation or inhibition, which depended on the size of the substrate. A possible allosteric potassium binding site at the S6 subsite was involved in activation, and a distant site located between the catalytic domain and the P-domain was involved in inhibition. Potassium decreased the energetic barriers of almost all steps of catalysis. The acylation of Ac-PMYKR-AMC in the absence of potassium was the rate-limiting step. Therefore, for substrates containing a P1-Arg, the deacylation step is not necessarily the rate-limiting event, and other residues at the P′ positions may participate in controlling the acylation and deacylation steps. Thus, it is reasonable to conclude that potassium is involved in the processing of the α-mating factor that promotes Ca2+ mobilization by activating a high-affinity Ca2+-influx system to increase the cytosolic [Ca2+], resulting in the activation of channels that are essential for the survival of Saccharomyces cerevisiae cells.

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Datum: 20.02.2018


Editorial Board

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233










Datum: 20.02.2018


Hydrogen bonds in the vicinity of the special pair of the bacterial reaction center probed by hydrostatic high-pressure absorption spectroscopy

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Liina Kangur, Michael R. Jones, Arvi Freiberg

Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13–14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds.

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Datum: 20.02.2018


Dynamic content exchange between liprotides

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): Henriette S. Frislev, Stine C.L. Jakobsen, Signe A. Frank, Daniel E. Otzen

Liprotides are complexes composed of partially denatured proteins and fatty acids in which the fatty acids form a micelle-like core surrounded by a shell of proteins. Liprotides, composed of α-lactalbumin (aLA) and oleic acid (OA), are similar in components and cytotoxicity to the original HAMLET protein-fatty acid complex. Liprotides composed of aLA and OA kill tumor cells by transferring the OA component to, and thus destabilizing, the cell membrane. Here we investigate liprotides' dynamics of transfer of contents between themselves and membranes using the hydrophobic fluorescent probe pyrene. We find that pyrene incorporated into liprotides is exchanged between liprotides within the dead time of a stopped-flow instrument, while the transfer to membranes occurs within 20s. Transfer kinetics was not affected by the presence of the membrane stabilizing lipid cholesterol. Thus, transfer is a remarkably rapid process which illustrates liprotides' efficacy as transporters of hydrophobic compounds.

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Datum: 20.02.2018


Ac-LVFFARK-NH2 conjugation to β-cyclodextrin exhibits significantly enhanced performance on inhibiting amyloid β-protein fibrillogenesis and cytotoxicity

Publication date: April 2018
Source:Biophysical Chemistry, Volume 235

Author(s): Huan Zhang, Xiaoyan Dong, Fufeng Liu, Jie Zheng, Yan Sun

Inhibition of amyloid β-protein (Aβ) aggregation is of significance for the potential treatment of Alzheimer's disease. We have herein conjugated heptapeptide Ac-LVFFARK-NH2 (LK7) to β-cyclodextrin (βCyD) and studied the inhibitory effect of the LK7-βCyD conjugate on Aβ aggregation. The conjugation significantly improved the peptide solubility and suppressed the self-assembly propensity. This led to 30% increase of the binding affinity of LK7 for Aβ in the conjugate due to increased hydrophobic interactions. Thus, LK7-βCyD suppressed the conformational transition of Aβ and showed stronger inhibitory effect on Aβ fibrillation than LK7. Thus, LK7-βCyD exhibited protective effect on Aβ40-induced cytotoxicity, and the cells completely survived at 10 molar excess of LK7-βCyD (from 67% to 100%). By contrast, LK7 showed only a moderate inhibition on Aβ fibrillation, and could not inhibit the amyloid cytotoxicity. The research proved that conjugation of hydrophobic peptide to βCyD was promising to increase its inhibition potency against Aβ aggregation.

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Datum: 20.02.2018


Electronic properties of DNA: Description of weak interactions in TATA-box-like chains

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): Jorge Gutiérrez-Flores, Estrella Ramos, Carlos I. Mendoza, Enrique Hernández-Lemus

DNA is one of the most important biomolecules since it contains all the genetic information about an organism. The tridimensional structure of DNA is a determinant factor that influences the physiological and biochemical mechanisms by which this molecule carries out its biological functions. It is believed that hydrogen bonds and π-π stacking are the most relevant non-covalent interactions regarding DNA stability. Due to its importance, several theoretical works have been made to describe these interactions, however, most of them often consider only the presence of two nitrogenous bases, having a limited overview of the participation of these in B-DNA stabilization. Furthermore, due to the complexity of the system, there are discrepancies between which involved interaction is more important in duplex stability. Therefore, in this project we describe these interactions considering the effect of chain length on the energy related to both hydrogen bonds and π-π stacking, using as model TATA-box-like chains with n base pairs (n =1 to 14) and taking into consideration two different models: ideal and optimized B-DNA. We have found that there is a cooperative effect on hydrogen bond and π-π stacking mean energies when the presence of other base pairs is considered. In addition, it was found that hydrogen bonds contribute more importantly than π-π stacking to B-DNA stability; nevertheless, the participation of π-π stacking is not negligible: when B-DNA looks for a conformation of lower energy, π-π stacking interaction are the first to be optimized. All work was realized under the framework of DFT using the DMol3 code (M06-L/DNP).

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Datum: 20.02.2018


Petit-High Pressure Carbon Dioxide stress increases synthesis of S-Adenosylmethionine and phosphatidylcholine in yeast Saccharomyces cerevisiae

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Liyuan Niu, Kazuki Nomura, Hitoshi Iwahashi, Hiroyuki Matsuoka, Satoshi Kawachi, Yoshihisa Suzuki, Katsuhiro Tamura

Petit-High Pressure Carbon Dioxide (p-HPCD) is a promising nonthermal technology for foods pasteurization. Cluster analysis of gene expression profiles of Saccharomyces cerevisiae exposed to various stresses exhibited that gene expression profile for p-HPCD stress (0.5MPa, 25°C) was grouped into a cluster including profiles for Sodium Dodecyl Sulfate and Roundup herbicide. Both are detergents that can disorder membrane structurally and functionally, which suggests that cell membrane may be a target of p-HPCD stress to cause cell growth inhibition. Through metabolomic analysis, amount of S-Adenosylmethionine (AdoMet) that is used as methyl donor to participate in phosphatidylcholine synthesis via phosphatidylethanolamine (PE) methylation pathway, was increased after p-HPCD treatment for 2h. The key gene OPI3 encoding phospholipid methyltransferase that catalyzes the last two steps in PE methylation pathway was confirmed significantly induced by RT-PCR. Transcriptional expression of genes (MET13, MET16, MET10, MET17, MET6 and SAM2) related to AdoMet biosynthesis was also significantly induced. Choline as the PC precursor and ethanolamine as PE precursor in Kennedy pathway were also found increased under p-HPCD condition. We also found that amounts of most of amino acids involving protein synthesis were found decreased after p-HPCD treatment for 2h. Moreover, morphological changes on cell surface were observed by scanning electron microscope. In conclusion, the effects of p-HPCD stress on cell membrane appear to be a very likely cause of yeast growth inhibition and the enhancement of PC synthesis could contribute to maintain optimum structure and functions of cell membrane and improve cell resistance to inactivation.

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Datum: 20.02.2018


Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study

Publication date: February 2018
Source:Biophysical Chemistry, Volume 233

Author(s): Esmaeil Behmard, Parviz Abdolmaleki, Majid Taghdir

P7 is the only viral channel encoded by the Hepatitis C Virus (HCV) genome. It is a small, highly hydrophobic protein containing 63 amino acids. Structural studies have shown that p7 has two transmembrane (TM) α helices linked by a short dibasic cytoplasmic loop. P7, mostly placed in the endoplasmic reticulum (ER), is a membrane-associated protein. The results obtained from different studies revealed that p7 is a polytopic membrane protein that could oligomerize in membrane bilayer to create ion channels with cation selectivity. In addition, p7 is highly conserved and plays an important role in the assembly and release of mature viral particles. Thus, it can be considered as a potential target for anti-HCV drugs. It has been found that several compounds (amantadine, rimantadine, hexamethylene amiloride (HMA) and long-alkyl-chain iminosugar (IS) derivatives) inhibit p7 channel ability. Another new inhibitor identified as BIT225, a derivative of amiloride, also inhibits the viroporin function of HIV-1 Vpu and HCV p7. In the present study, molecular dynamics simulations were applied to get insights into molecular details of a BIT225 binding site. In addition, the g_mmpbsa approach was employed to calculate the binding free energy and free energy decomposition per residue. MD simulation results in the p7–BIT225 complex revealed that drug binding to hydrophobic pocket can allosterically inhibit ion conduction via the funnel tip by restricting significant intrinsic channel breath at the tip of the funnel. Based on the molecular dynamics simulation (MD) analysis and the energy profiles, the hydrophobic interactions were the main driving force for BIT225 binding.






Datum: 20.02.2018


Editorial Board

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234










Datum: 20.02.2018


Inside front cover: editorial board

Publication date: January 2018
Source:Biophysical Chemistry, Volume 232










Datum: 20.02.2018


Development of CDK-targeted scoring functions for prediction of binding affinity

Publication date: April 2018
Source:Biophysical Chemistry, Volume 235

Author(s): Nayara Maria Bernhardt Levin, Val Oliveira Pintro, Gabriela Bitencourt-Ferreira, Bruna Boldrini de Mattos, Ariadne de Castro Silvério, Walter Filgueira de Azevedo

Cyclin-dependent kinase (CDK) is an interesting biological macromolecule due to its role in cell cycle progression, transcription control, and neuronal development, to mention the most studied biological activities. Furthermore, the availability of hundreds of structural studies focused on the intermolecular interactions of CDK with competitive inhibitors makes possible to develop computational models to predict binding affinity, where the atomic coordinates of binary complexes involving CDK and ligands can be used to train a machine learning model. The present work is focused on the development of new machine learning models to predict binding affinity for CDK. The CDK-targeted machine learning models were compared with classical scoring functions such as MolDock, AutoDock 4, and Vina Scores. The overall performance of our CDK-targeted scoring function was higher than the previously mentioned scoring functions, which opens the possibility of increasing the reliability of virtual screening studies focused on CDK.






Datum: 20.02.2018


Capping effects on polymorphic Aβ16–21 amyloids depend on their size: A molecular dynamics simulation study

Publication date: January 2018
Source:Biophysical Chemistry, Volume 232

Author(s): Myeongsang Lee, Hyun Joon Chang, Hyunsung Choi, Sungsoo Na

Understanding Aβ amyloid oligomers associated with neuro-degenerative diseases is needed due to their toxic characteristics and mediation of amyloid fibril growth. Depending on various physiological circumstances such as ionic strength, metal ion, and point-residue mutation, oligomeric amyloids exhibit polymorphic behavior and structural stabilities, i.e. showing different conformation and stabilities. Specifically, experimental and computational researchers have found that the capping modulates the physical and chemical properties of amyloids by preserving electrostatic energy interactions, which is one of the dominant factors for amyloid stability. Still, there is no detailed knowledge for the polymorphic amyloids with reflecting the terminal capping effects. In the present study, we investigated the role of terminal capping (i.e. N-terminal acetylation and C-terminal amidation) on polymorphic Aβ16–21 amyloid oligomer and protofibrils via molecular dynamics (MD) simulations. We found that the capping effects have differently altered the conformation of polymorphic antiparallel-homo and –hetero Aβ16–21 amyloid oligomer, but not Aβ16–21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aβ16–21 amyloid oligomers, but does not show any distinct affect on Aβ16–21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aβ16–21 amyloids. We hope that our computation study about the role of the capping effects on the polymorphic amyloids will facilitate additional efforts to enhance degradation of amyloids and to design a selective drug in the future.

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Datum: 20.02.2018


WPBMB Entrez: An interface to NCBI Entrez for Wordpress

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234

Author(s): David W. Gohara

Research-oriented websites are an important means for the timely communication of information. These websites fall under a number of categories including: research laboratories, training grant and program projects, and online service portals. Invariably there is content on a site, such as publication listings, that require frequent updating. A number of content management systems exist to aid in the task of developing and managing a website, each with their strengths and weaknesses. One popular choice is Wordpress, a free, open source and actively developed application for the creation of web content. During a recent site redesign for our department, the need arose to ensure publications were up to date for each of the research labs and department as a whole. Several plugins for Wordpress offer this type of functionality, but in many cases the plugins are either no longer maintained, are missing features that would require the use of several, possibly incompatible, plugins or lack features for layout on a webpage. WPBMB Entrez was developed to address these needs. WPBMB Entrez utilizes a subset of NCBI Entrez and RCSB databases to maintain up to date records of publications, and publication related information on Wordpress-based websites. The core functionality uses the same search query syntax as on the NCBI Entrez site, including advanced query syntaxes. The plugin is extensible allowing for rapid development and addition of new data sources as the need arises. WPBMB Entrez was designed to be easy to use, yet flexible enough to address more complex usage scenarios. Features of the plugin include: an easy to use interface, design customization, multiple templates for displaying publication results, a caching mechanism to reduce page load times, supports multiple distinct queries and retrieval modes, and the ability to aggregate multiple queries into unified lists. Additionally, developer documentation is provided to aid in customization of the plugin. WPBMB Entrez is available at no cost, is open source and works with all recent versions of Wordpress.

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Datum: 20.02.2018


Mechanism of aggregation of UV-irradiated glycogen phosphorylase b at a low temperature in the presence of crowders and trimethylamine N-oxide

Publication date: January 2018
Source:Biophysical Chemistry, Volume 232

Author(s): Tatiana B. Eronina, Valeriya V. Mikhaylova, Natalia A. Chebotareva, Vera A. Borzova, Igor K. Yudin, Boris I. Kurganov

To characterize the initial stages of protein aggregation, the kinetics of aggregation of UV-irradiated glycogen phosphorylase b (UV-Phb) was studied under conditions when the aggregation proceeded at a low rate (10°C, 0.03M Hepes buffer, pH6.8, containing 0.1M NaCl). Aggregation of UV-Phb was induced by polyethylene glycol and Ficoll-70, acting as crowders, or a natural osmolyte trimethylamine N-oxide (TMAO). It has been shown that the initial rate of the stage of aggregate growth is proportional to the protein concentration squared, suggesting that the order of aggregation with respect to the protein is equal to two. It has been concluded that the aggregation mechanism of UV-Phb at 10°C in the presence of crowders includes the nucleation stage and stages of protein aggregate growth (the basic aggregation pathway). The aggregation mechanism is complicated in the presence of TMAO, and the stage of aggregate-aggregate assembly induced by TMAO should be added to the basic aggregation pathway. It has been shown that the ability of TMAO at a low concentration (0.05M) to induce aggregation of UV-Phb is due to the decrease in the absolute value of zeta potential of the protein in the presence of TMAO.

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Datum: 20.02.2018


Full title pg and editorial board

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231










Datum: 20.02.2018


Inside front cover: editorial board

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231










Datum: 20.02.2018


Influence of the surrounding environment in re-naturalized β-barrel membrane proteins

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234

Author(s): Maximilien Lopes-Rodrigues, Jordi Triguero, Juan Torras, Eric A. Perpète, Catherine Michaux, David Zanuy, Carlos Alemán

Outer-membrane porins are currently being used to prepare bioinspired nanomembranes for selective ion transport by immobilizing them into polymeric matrices. However, the fabrication of these protein-integrated devices has been found to be strongly influenced by the instability of the β-barrel porin structure, which depends on surrounding environment. In this work, molecular dynamics simulations have been used to investigate the structural stability of a representative porin, OmpF, in three different environments: (i) aqueous solution at pH=7; (ii) a solution of neutral detergent in a concentration similar to the critical micelle concentration; and (iii) the protein embedded into a neutral detergent bilayer. The results indicate that the surrounding environment not only alters the stability of the β-barrel but affects the internal loop responsible of the ions transport, as well as the tendency of the porin proteins to aggregate into trimers. The detergent bilayer preserves the structure of OmpF protein as is found bacteria membranes, while pure aqueous solution induces a strong destabilization of the protein. An intermediate situation occurs for detergent solution. Our results have been rationalized in terms of proteinwater and proteindetergent interactions, which makes them extremely useful for the future design of new generation of bioinspired protein-integrated devices.

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Datum: 20.02.2018


Editorial: High Pressure Bioscience and Biotechnology

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231










Datum: 20.02.2018


Effect of urea on protein-ligand association

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Lora Stepanian, Ikbae Son, Tigran V. Chalikian

We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc)3] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc)3 for the protein steadily decreases as the concentration of urea increases. We analyze the urea dependence of the binding free energy within the framework of a simplified statistical thermodynamics-based model that accounts for the excluded volume effect and direct solute-solvent interactions. The analysis reveals that the detrimental action of urea on the inhibitor-lysozyme binding originates from competition between the free energy contributions of the excluded volume effect and direct solute-solvent interactions. The free energy contribution of direct urea-solute interactions narrowly overcomes the excluded volume contribution thereby resulting in urea weakening the protein-ligand association. More broadly, the successful application of the simple model employed in this work points to the possibility of its use in quantifying the stabilizing/destabilizing action of individual cosolvents on biochemical folding and binding reactions.

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Datum: 20.02.2018


Direct high-pressure NMR observation of dipicolinic acid leaking from bacterial spore: A crucial step for thermal inactivation

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Kazuyuki Akasaka, Akihiro Maeno, Akira Yamazaki

A bacterial spore protects itself with an unusually high concentration (~10% in dry weight of spore) of dipicolinic acid (DPA), the release of which is considered the crucial step for inactivating it under mild pressure and temperature conditions. However, the process of how the spore releases DPA in response to pressure remains obscure. Here we apply 1H high-resolution high-pressure NMR spectroscopy, for the first time, to the spore suspension of Bacillus subtilis natto and monitor directly and in real-time the leaking process of DPA in response to pressure of 200MPa at 20°C. We find that about one third of the total DPA leaks immediately upon applying pressure, but that the rest leaks slowly in hrs upon decreasing the pressure. Once DPA is fully released from the spore, the proteins of the spore become easily denatured at a mild temperature, e.g., 80°C, much below the temperature commonly used to inactivate spores (121°C). The success of the present experiment opens a new avenue for studying bacterial spores and cells at the molecular level in response to pressure, temperature and other perturbations.

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Datum: 20.02.2018


The amyloidogenicity of the influenza virus PB1-derived peptide sheds light on its antiviral activity

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234

Author(s): Yana A. Zabrodskaya, Dmitry V. Lebedev, Marja A. Egorova, Aram A. Shaldzhyan, Alexey V. Shvetsov, Alexander I. Kuklin, Daria S. Vinogradova, Nikolay V. Klopov, Oleg V. Matusevich, Taisiia A. Cheremnykh, Rajeev Dattani, Vladimir V. Egorov

The influenza virus polymerase complex is a promising target for new antiviral drug development. It is known that, within the influenza virus polymerase complex, the PB1 subunit region from the 1st to the 25th amino acid residues has to be is in an alpha-helical conformation for proper interaction with the PA subunit. We have previously shown that PB1(6–13) peptide at low concentrations is able to interact with the PB1 subunit N-terminal region in a peptide model which shows aggregate formation and antiviral activity in cell cultures. In this paper, it was shown that PB1(6–13) peptide is prone to form the amyloid-like fibrillar aggregates. The peptide homo-oligomerization kinetics were examined, and the affinity and characteristic interaction time of PB1(6–13) peptide monomers and the influenza virus polymerase complex PB1 subunit N-terminal region were evaluated by the SPR and TR-SAXS methods. Based on the data obtained, a hypothesis about the PB1(6–13) peptide mechanism of action was proposed: the peptide in its monomeric form is capable of altering the conformation of the PB1 subunit N-terminal region, causing a change from an alpha helix to a beta structure. This conformational change disrupts PB1 and PA subunit interaction and, by that mechanism, the peptide displays antiviral activity.

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Datum: 20.02.2018


The push-and-pull hypothesis in protein unfolding, misfolding and aggregation

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Guilherme A.P. de Oliveira, Jerson L. Silva

The combination of biophysical and structural techniques has allowed the visualization of species classified as dry molten-globule states. Further destabilization causes these structures to follow through a wet-globule stage to reach an unfolded chain. We have recently combined small angle X-ray scattering and nuclear magnetic resonance to observe these species, and we introduce a push-and-pull hypothesis to explain the dissimilar actions of urea and high pressure on proteins. The implications of these molten-globule states are further discussed in light of their potential physiological and pathological roles, especially in protein misfolding diseases.

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Datum: 20.02.2018


Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Brian Fuglestad, Matthew A. Stetz, Zachary Belnavis, A. Joshua Wand

Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately −115mlmol1 and an average pressure dependent change in compressibility of approximately 30mlmol1 kbar1. In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state.

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Datum: 20.02.2018


Hydrostatic pressure effect on PNIPAM cononsolvency in water-methanol solutions

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Andrea Pica, Giuseppe Graziano

When methanol is added to water at room temperature and 1atm, poly (N-isopropylacrylamide), PNIPAM, undergoes a coil-to-globule collapse transition. This intriguing phenomenon is called cononsolvency. Spectroscopic measurements have shown that application of high hydrostatic pressure destroys PNIPAM cononsolvency in water-methanol solutions. We have developed a theoretical approach that identifies the decrease in solvent-excluded volume effect as the driving force of PNIPAM collapse on increasing the temperature. The same approach indicates that cononsolvency, at room temperature and P=1atm, is caused by the inability of PNIPAM to make all the attractive energetic interactions that it could be engaged in, due to competition between water and methanol molecules. The present analysis suggests that high hydrostatic pressure destroys cononsolvency because the coil state becomes more compact, and the quantity measuring PNIPAM-solvent attractions increases in magnitude due to the solution density increase, and the ability of small water molecules to substitute methanol molecules on PNIPAM surface.

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Datum: 20.02.2018


A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234

Author(s): Victor M. Golyshev, Tatyana V. Abramova, Dmitrii V. Pyshnyi, Alexander A. Lomzov

The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.

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Datum: 20.02.2018


Antibodies under pressure: A Small-Angle X-ray Scattering study of Immunoglobulin G under high hydrostatic pressure

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Nico König, Michael Paulus, Karin Julius, Julian Schulze, Matthias Voetz, Metin Tolan

In the present work two subclasses of the human antibody Immunoglobulin G (IgG) have been investigated by Small-Angle X-ray Scattering under high hydrostatic pressures up to 5kbar. It is shown that IgG adopts a symmetric T-shape in solution which differs significantly from available crystal structures. Moreover, high-pressure experiments verify the high stability of the IgG molecule. It is not unfolded by hydrostatic pressures of up to 5kbar but a slight increase of the radius of gyration was observed at elevated pressures.

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Datum: 20.02.2018


Effect of pressure on bilayer phase behavior of N-methylated di-O-hexadecylphosphatidylethanolamines: relevance of head-group modification on the bilayer interdigitation

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Masaki Goto, Yuya Aoki, Nobutake Tamai, Hitoshi Matsuki

The phase transitions of N-methylated di-O-hexadecylphosphatidylethanolamines (DHPE, DH-N-methyl-PE (DHMePE) and DH-N,N-dimethyl-PE (DHMe2PE)) were observed by differential scanning calorimetry (DSC) and fluorometry under atmospheric pressure and by light-transmittance measurements under high pressure. The DSC thermograms showed that the N-methylated DHPE bilayers underwent the phase transition from the gel phase to the liquid crystalline (Lα) phase under atmospheric pressure. The gel phase was identified by fluorometry as the lamellar gel (Lβ) phase, and not interdigitated gel (LβI) phase. The gel/Lα transition temperature increased with pressure while decreased stepwise with increasing polar head-group size. This stepwise depression of the transition temperature may be caused by the inverse-proportional hydrogen-bonding capabilities of the head-group to the head-group size. The thermodynamic quantities of the gel/Lα transition were comparable for the N-methylated DHPE bilayers. The pressure-induced LβI phase was not found in these bilayers although the bilayer of di-O-hexadecylphosphatidylcholine (DHPC), which is a kind of N-methylated DHPEs, forms the LβI phase only by hydration under atmospheric pressure. Taking into account that the bilayers of diacyl-homologs of N-methylated DHPEs, N-methylated dipalmitoyl-PEs except for dipalmitoylphosphatidylcholine (DPPC), do not form the LβI phase in the whole pressure range investigated but the DPPC bilayer forms the LβI phase under high pressure, we can say that the interdigitation requires weaker interaction between large-sized head groups like the bulky choline group.

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Datum: 20.02.2018


The role of loops and cation on the volume of unfolding of G-quadruplexes related to HTel

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Yang Yun Li, David N. Dubins, Dianna My Nhi Thi Le, Karen Leung, Robert B. Macgregor

In aqueous solutions containing sodium or potassium cations, oligodeoxyribonucleotides (ODNs) rich in guanine form four-stranded DNA structures called G-quadruplexes (G4s). These structures are destabilized by elevated hydrostatic pressure. Here, we use pressure to investigate the volumetric changes arising from the formation of G4 structures. G4s display a great deal of structural heterogeneity that depends on the stabilizing cation as well as the oligonucleotide sequence. Using UV thermal unfolding at different pressures, we have investigated the volume change of the helix-coil equilibrium of a series of ODNs whose sequences are related to the G-rich ODN HTel (d[A(GGGTTA)3GGG]), which contains four repeats of the human telomeric sequence. The experiments are conducted in aqueous buffers containing either 100mM NaCl or KCl at pH7.4. The G4s stabilized by Na+ are less sensitive to pressure perturbation than those stabilized by K+. The overall molar volume changes (ΔV tot ) of the unfolding transition for all of the G4s are large and negative. A large fraction of the measured ΔV tot value arises from the re-hydration of the cations released from the interior of the folded structure. However, the differences in the measured ΔV tot values demonstrate that variations in the structure of G4s formed by each ODN, arising from differences in the sequence of the loops, contribute significantly to ΔV tot and presumably the hydration of the folded structures. Depending on the sequence of the loops, the magnitude of the measured ΔV tot can be larger or smaller than that of HTel in solutions containing sodium. However, the magnitude of ΔV tot is smaller than HTel for the unfolding of all G4s that are stabilized by potassium ions.

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Datum: 20.02.2018


Biophysical evidence for differential gallated green tea catechins binding to membrane type-1 matrix metalloproteinase and its interactors

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234

Author(s): Djahida Djerir, Mustapha Iddir, Steve Bourgault, Sylvie Lamy, Borhane Annabi

Membrane type-1 matrix metalloproteinase (MT1-MMP) is a transmembrane MMP which triggers intracellular signaling and regulates extracellular matrix proteolysis, two functions that are critical for tumor-associated angiogenesis and inflammation. While green tea catechins, particularly epigallocatechin gallate (EGCG), are considered very effective in preventing MT1-MMP-mediated functions, lack of structure-function studies and evidence regarding their direct interaction with MT1-MMP-mediated biological activities remain. Here, we assessed the impact in both cellular and biophysical assays of four ungallated catechins along with their gallated counterparts on MT1-MMP-mediated functions and molecular binding partners. Concanavalin-A (ConA) was used to trigger MT1-MMP-mediated proMMP-2 activation, expression of MT1-MMP and of endoplasmic reticulum stress biomarker GRP78 in U87 glioblastoma cells. We found that ConA-mediated MT1-MMP induction was inhibited by EGCG and catechin gallate (CG), that GRP78 induction was inhibited by EGCG, CG, and gallocatechin gallate (GCG), whereas proMMP-2 activation was inhibited by EGCG and GCG. Surface plasmon resonance was used to assess direct interaction between catechins and MT1-MMP interactors. We found that gallated catechins interacted better than their ungallated analogs with MT1-MMP as well as with MT1-MMP binding partners MMP-2, TIMP-2, MTCBP-1 and LRP1-clusterIV. Overall, current structure-function evidence supports a role for the galloyl moiety in both direct and indirect interactions of green tea catechins with MT1-MMP-mediated oncogenic processes.

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Datum: 20.02.2018


High-pressure microscopy for tracking dynamic properties of molecular machines

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Masayoshi Nishiyama

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli.

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Datum: 20.02.2018


Investigation of the electrostatic and hydration properties of DNA minor groove-binding by a heterocyclic diamidine by osmotic pressure

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Noa Erlitzki, Kenneth Huang, Suela Xhani, Abdelbasset A. Farahat, Arvind Kumar, David W. Boykin, Gregory M.K. Poon

Previous investigations of sequence-specific DNA binding by model minor groove-binding compounds showed that the ligand/DNA complex was destabilized in the presence of compatible co-solutes. Inhibition was interpreted in terms of osmotic stress theory as the uptake of significant numbers of excess water molecules from bulk solvent upon complex formation. Here, we interrogated the AT-specific DNA complex formed with the symmetric heterocyclic diamidine DB1976 as a model for minor groove DNA recognition using both ionic (NaCl) and non-ionic cosolutes (ethylene glycol, glycine betaine, maltose, nicotinamide, urea). While the non-ionic cosolutes all destabilized the ligand/DNA complex, their quantitative effects were heterogeneous in a cosolute- and salt-dependent manner. Perturbation with NaCl in the absence of non-ionic cosolute showed that preferential hydration water was released upon formation of the DB1976/DNA complex. As salt probes counter-ion release from charged groups such as the DNA backbone, we propose that the preferential hydration uptake in DB1976/DNA binding observed in the presence of osmolytes reflects the exchange of preferentially bound cosolute with hydration water in the environs of the bound DNA, rather than a net uptake of hydration waters by the complex.

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Datum: 20.02.2018


Comparative analysis on inactivation kinetics of between piezotolerant and piezosensitive mutant strains of Saccharomyces cerevisiae under combinations of high hydrostatic pressure and temperature

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Kazuki Nomura, Yuki Kuwabara, Wataru Kuwabara, Hiroyuki Takahashi, Kanako Nakajima, Mayumi Hayashi, Akinori Iguchi, Toru Shigematsu

We previously obtained a pressure-tolerant (piezotolerant) and a pressure sensitive (piezosensitive) mutant strain, under ambient temperature, from Saccharomyces cerevisiae strain KA31a. The inactivation kinetics of these mutants were analyzed at 150 to 250MPa with 4 to 40°C. By a multiple regression analysis, the pressure and temperature dependency of the inactivation rate constants k values of both mutants, as well as the parent strain KA31a, were well approximated with high correlation coefficients (0.92 to 0.95). For both mutants, as well as strain KA31a, the lowest k value was shown at a low pressure levels with around ambient temperature. The k value approximately increased with increase in pressure level, and with increase and decrease in temperature. The piezosensitive mutant strain a924E1 showed piezosensitivity at all pressure and temperature levels, compared with the parent strain KA31a. In contrast, the piezotolerant mutant strain a2568D8 showed piezotolerance at 4 to 20°C, but did not show significant piezotolerance at 40°C. These results of the variable influence of temperature on pressure inactivation of these strains would be important for better understanding of piezosensitive and piezotolerant mechanisms, as well as the pressure inactivation mechanism of S. cerevisiae.

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Datum: 20.02.2018


Study of Al3+ interaction with AMP, ADP and ATP in aqueous solution

Publication date: March 2018
Source:Biophysical Chemistry, Volume 234

Author(s): Paola Cardiano, Claudia Foti, Fausta Giacobello, Ottavia Giuffrè, Silvio Sammartano

The interaction of Al3+ and nucleotide ligands, namely adenosine-5′-monophosphate, (AMP), adenosine-5′-diphosphate, (ADP), adenosine-5′-triphosphate, (ATP), has been studied in aqueous solution at T = 298.15 K and I = 0.15 mol L−1 in NaCl (only for Al3+-ATP system at I = 0.1 mol L−1). Formation constants and speciation models for the species formed are discussed on the basis of potentiometric results. The speciation models found for the three systems include ML and ML2 species in all the cases, and for Al3+-ADP and ATP systems, MLH, MLOH and ML2OH species as well. The formation constant value for ML species shows the trend, AMP < ADP < ATP. 1H NMR spectroscopy was also employed for the study of Al3+-ATP system. The 1H NMR results are in agreement with the speciation model obtained from analysis of potentiometric titration data, confirming the stabilities of the main species. Enthalpy change values were obtained by titration calorimetry; for the main Al3+-ATP species (at T = 298.15 K and I = 0.1 mol L−1 in NaCl), they resulted always higher than zero, as typical for hard-hard interactions. The dependence of formation constants on ionic strength over the range I = 0.1 to 1 mol L−1 in NaCl is also reported for Al3+-ATP system. The sequestering ability of the nucleotides under study towards Al3+ was also evaluated by the empirical parameter pL0.5.

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Datum: 20.02.2018


Effect of high pressure on the saccharification of starch in the tuberous root of sweet potato (Ipomoea batatas)

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Toru Shigematsu, Naho Furukawa, Ryo Takaoka, Mayumi Hayashi, Shoji Sasao, Shigeaki Ueno, Kanako Nakajima, Miyuki Kido, Kazuki Nomura, Akinori Iguchi

We analyzed the effect of high hydrostatic pressure (HHP) treatment on reducing sugar production in the tuberous root of sweet potato (Ipomoea batatas), based on pressure-gelatinization of starch and subsequent saccharification by internal amylases. HHP treatment at up to 600MPa at ambient temperature for 10min did not apparently affect the reducing sugar concentration in tuberous root. However, HHP treatment at 100 to 500MPa and 60°C or 70°C for 10min increased reducing sugar concentration as both the pressure and temperature increased. The reducing sugar concentration after HHP treatment at 500MPa and 70°C for 10min was roughly comparable to that of the thermal treatment control (80°C for 10min under atmospheric pressure). HHP treatment enabled the gelatinization and enzymatic saccharification of starch in the tuberous root of sweet potato, at a lower temperature than required by thermal treatment at atmospheric pressure.

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Datum: 20.02.2018


Low crowding agent concentration destabilizes against pressure unfolding

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): J. Somkuti, Z. Török, F. Pfalzgraf, L. Smeller

The concentration of macromolecules inside a cell is very high, which can affect the behavior of the enzymes, and consequently influence vital biological processes. This is called macromolecular crowding. Since the most important effect of macromolecular crowding is the excluded volume, we performed pressure experiments, where the volume (as conjugate parameter to the pressure) is the crucial factor. We measured the temperature and pressure stability of bovine serum albumin and lysozyme with various concentrations of crowding agents, dextran, Ficoll™ and lysozyme itself. Our most interesting finding is that low concentration of all the studied crowding agents decreases the pressure stability of the proteins. We explain this by the reduced hydration volume change in the crowded environment. Furthermore, we discuss the volumetric parameters and emphasize the difference between the partial volume of the protein and the volume it influences, and their relation to the excluded volume which is responsible for the macromolecular crowding.

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Datum: 20.02.2018


Stability of different influenza subtypes: How can high hydrostatic pressure be a useful tool for vaccine development?

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Carlos Henrique Dumard, Shana P.C. Barroso, Ana Clara V. Santos, Nathalia S. Alves, José Nelson S.S. Couceiro, Andre M.O. Gomes, Patricia S. Santos, Jerson L. Silva, Andréa C. Oliveira

Background Avian influenza A viruses can cross naturally into mammals and cause severe diseases, as observed for H5N1. The high lethality of human infections causes major concerns about the real risk of a possible pandemic of severe diseases to which human susceptibility may be high and universal. High hydrostatic pressure (HHP) is a valuable tool for studies regarding the folding of proteins and the assembly of macromolecular structures such as viruses; furthermore, HHP has already been demonstrated to promote viral inactivation. Methods Here, we investigated the structural stability of avian and human influenza viruses using spectroscopic and light-scattering techniques. We found that both particles have similar structural stabilities and that HHP promotes structural changes. Results HHP induced slight structural changes to both human and avian influenza viruses, and these changes were largely reversible when the pressure returned to its initial level. The spectroscopic data showed that H3N2 was more pressure-sensitive than H3N8. Structural changes did not predict changes in protein function, as H3N2 fusion activity was not affected, while H3N8 fusion activity drastically decreased. The fusion activity of H1N1 was also strongly affected by HHP. In all cases, HHP caused inactivation of the different influenza viruses. Conclusions HHP may be a useful tool for vaccine development, as it induces minor and reversible structural changes that may be associated with partial preservation of viral biological activities and may potentiate their immunogenic response while abolishing their infectivity. We also confirmed that, although pressure does not promote drastic changes in viral particle structure, it can distinctly affect viral fusion activity.

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Datum: 20.02.2018


Inhibition of amyloid fibrillation of lysozyme by bisdemethoxycurcumin and diacetylbisdemethoxycurcumin

Publication date: Available online 12 February 2018
Source:Biophysical Chemistry

Author(s): Fakhrossadat Mohammadi, Marzieh Moeeni, Afshin Mahmudian, Leila Hassani

Amyloid deposition, arising from the fibrillogenesis of proteins in organs and tissues of the body, causes several neurodegenerative disorders. One therapeutic approach is based on the use of polyphenols and their derivatives for suppressing and inhibiting the accumulation of these toxic fibrils in tissues. In the present study, the anti-amyloidogenic activities of bisdemethoxycurcumin (BDMC), a natural polyphenolic compound, and diacetylbisdemethoxycurcumin (DABC), a synthetic derivative of curcumin, on the amyloid fibrillation of hen egg white lysozyme (HEWL) is studied in depth using thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), circular dichroism spectroscopy (CD), molecular docking and Ligplot calculations. The binding parameters such as binding constants and the number of substantive binding sites were obtained experimentally. It could be shown from docking simulation that four hydrogen bonds via the two phenolic OH groups of BDMC and two β-diketone moiety of BDMC are formed with the Asp-101, Trp-63, Asn-59 and Glu-35 of HEWL, whereas, two hydrogen bonds formed via two β-diketone moiety of DABC with Asn-39 and Trp-63 of HEWL. The short Fӧrster's distance (r) between donor and acceptor, the binding constant values and also the nature of interaction, demonstrate strong interaction between these two curcuminoids and lysozyme. According to amyloid fibrillation and binding results, the interaction of BDMC with HEWL is stronger than that of DABC and amyloid fibrillation of HEWL was inhibited more effectively by BDMC than DABC. It can be suggested that the more inhibitory activity of BDMC than DABC is correlated to the stronger interaction of BDMC with HEWL. These natural polyphenolic compounds are thus good candidates for inhibiting of amyloid formation. The inhibitory activities of BDMC and DABC can be used in drug formulation against the dangerous amyloid-related diseases and provide health promotion for organs and tissues of the body.

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Datum: 20.02.2018


Simulated pressure denaturation thermodynamics of ubiquitin

Publication date: December 2017
Source:Biophysical Chemistry, Volume 231

Author(s): Elizabeth A. Ploetz, Paul E. Smith

Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.

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Datum: 20.02.2018


 


Category: Current Chemistry Research

Last update: 04.01.2018.






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