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Biophysical Chemistry

Lucas M B Yoshihara, Elizabeth P G Arêas
The coacervation of carboxymethylcellulose (CMC) and hen egg white lysozyme (HEWL) was investigated. The work focused on the effects of pH, ionic strength, I, temperature, T, and mass fraction of the macromolecular components on the coacervation process by spectrophotometry, and on characteristics of the resulting coacervate phase by rheology in the linear and non-linear regimes. Coacervation was found to be highest at HEWL mass fraction ≈0.25 with very slight dependence on pH in the range from 5 to 9. The process was favored at I < 0...
March 2, 2018: Biophysical Chemistry
Armando Carpaneto, Antonella Gradogna
Plant two-pore channels (TPCs) are non-selective cation channels permeable both to monovalent potassium and divalent calcium. We previously developed a technique that allowed the simultaneous determination of the fluxes of these two ions across the channel by a combined use of patch-clamp and fluorescence. In this paper we studied how potassium and calcium fluxes were influenced by modification of cytosolic concentrations of K+ and Ca2+ . A decrease in cytosolic calcium from 2 to 0.5 mM led to a shift of the activation curve of about +60 mV; although at positive potentials currents were very similar, calcium ion permeation was significantly reduced and the ratio between the total and calcium-mediated current increased about two-fold...
February 24, 2018: Biophysical Chemistry
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...
February 12, 2018: Biophysical Chemistry
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-NH 2 (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...
February 11, 2018: Biophysical Chemistry
Xiaoqing Liu, Lihui Hu, Na Pan, Laurence Grimaud, Eric Labbé, Olivier Buriez, Jérôme Delacotte, Frédéric Lemaître, Manon Guille-Collignon
Applications of the Fluorescent False Neurotransmitter FFN102, an analog of biogenic neurotransmitters and a suitable probe for coupled amperometry and TIRFM (total internal reflexion fluorescence microscopy) investigations of exocytotic secretion, were considered here. The electroactivity of FFN102 was shown to very likely arise from the oxidation of its phenolic group through a CE (Chemical-Electrochemical) mechanism. Evidences that the aminoethyl group of FFN102 is the key recognition element by BON N13 cells were also provided...
February 8, 2018: Biophysical Chemistry
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...
February 8, 2018: Biophysical Chemistry
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...
February 6, 2018: Biophysical Chemistry
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...
February 1, 2018: Biophysical Chemistry
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...
January 31, 2018: Biophysical Chemistry
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...
January 30, 2018: Biophysical Chemistry
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...
January 25, 2018: Biophysical Chemistry
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...
January 8, 2018: Biophysical Chemistry
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...
January 6, 2018: Biophysical Chemistry
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...
January 2, 2018: Biophysical Chemistry
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...
December 19, 2017: Biophysical Chemistry
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...
February 2018: Biophysical Chemistry
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...
February 2018: Biophysical Chemistry
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...
February 2018: Biophysical Chemistry
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...
February 2018: Biophysical Chemistry
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...
January 2018: Biophysical Chemistry
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