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Biophysical Chemistry

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https://www.readbyqxmd.com/read/29328990/the-amyloidogenicity-of-the-influenza-virus-pb1-derived-peptide-sheds-light-on-its-antiviral-activity
#1
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
https://www.readbyqxmd.com/read/29306652/influence-of-the-surrounding-environment-in-re-naturalized-%C3%AE-barrel-membrane-proteins
#2
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
https://www.readbyqxmd.com/read/29287184/photosystem-i-when-excited-in-the-chlorophyll-qy-absorption-band-feeds-on-negative-entropy
#3
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
https://www.readbyqxmd.com/read/29287183/electronic-properties-of-dna-description-of-weak-interactions-in-tata-box-like-chains
#4
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...
December 12, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29232602/cooperative-protein-unfolding-a-statistical-mechanical-model-for-the-action-of-denaturants
#5
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...
December 5, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29227791/dynamic-content-exchange-between-liprotides
#6
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...
December 5, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29207358/sequence-length-dependence-in-arginine-phenylalanine-oligopeptides-implications-for-self-assembly-and-cytotoxicity
#7
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...
November 29, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29304477/wpbmb-entrez-an-interface-to-ncbi-entrez-for-wordpress
#8
LETTER
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...
November 26, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29174505/protective-effect-of-quercetin-and-rutin-encapsulated-liposomes-on-induced-oxidative-stress
#9
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...
November 22, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29169687/understanding-the-inhibitory-mechanism-of-bit225-drug-against-p7-viroporin-using-computational-study
#10
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...
November 16, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29153883/conformational-dynamics-and-free-energy-of-bhrf1-binding-to-bim-bh3
#11
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...
November 10, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29331201/impact-of-polymer-geometry-on-the-interactions-of-protein-peg-conjugates
#12
Jonathan Zarzar, Whitney Shatz, Nikhil Peer, Rosalynn Taing, Brian McGarry, Yun Liu, Daniel G Greene, Isidro E Zarraga
The conjugation of high molecular weight polyethylene glycol (PEG) to an active pharmaceutical ingredient (API) is an attractive strategy for the modification of biophysical and biodistribution properties of the API. Indeed, several therapeutic proteins conjugated to PEG have been safely administered in the clinic. While there have been studies on the configuration of these conjugates in solution, investigations on the impact of PEG geometry on protein-PEG conjugate interactions is limited. In this study, we use dynamic light scattering (DLS), rheology, and small-angle neutron scattering (SANS) to investigate the biophysical solution and interaction behavior of a 50kDa Fab protein attached to either a linear or tetrameric (branched) 40kDa PEG molecule...
November 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29173654/editorial-high-pressure-bioscience-and-biotechnology
#13
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
December 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28965786/mesoscopic-modelling-of-cy3-and-cy5-dyes-attached-to-dna-duplexes
#14
Pâmella Miranda, Luciana M Oliveira, Gerald Weber
Cy3 and Cy5 dyes linked to the 5' end of a double stranded DNA molecule are known to attach to both strands in a way that is very similar to an additional base pair and has a stabilizing effect on the oligonucleotide. Here we adapt the Peyrard-Bishop mesoscopic model to incorporate cyanine dyes and use the technique of thermal equivalence to obtain the appropriate parameters from existing melting temperatures. We have found that the stacking parameters are in the same range of ordinary AT and CG base pairs, in particular Cy3-A was found to be most rigidly stacked...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28965785/bioactive-compounds-from-extra-virgin-olive-oils-correlation-between-phenolic-content-and-oxidative-stress-cell-protection
#15
G Presti, V Guarrasi, E Gulotta, F Provenzano, A Provenzano, S Giuliano, M Monfreda, M R Mangione, R Passantino, P L San Biagio, M A Costa, D Giacomazza
When compared with other edible vegetable oils, the extra virgin olive oil (EVOO) exhibits excellent nutritional properties due to the presence of biophenolic compounds. Although they constitute only a very small amount of the unsaponifiable fraction of EVOO, biophenols strongly contribute to the sensorial properties of this precious food conferring it, for example, the bitter or pungent taste. Furthermore, it has been found that biophenols possess beneficial effects against many human pathologies such as oxidative stress, inflammation, cardiovascular diseases, cancer and aging-related illness...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28958449/investigation-of-structural-dynamics-of-thrombocytopenia-cargeeg-mutants-of-human-apoptotic-cytochrome-c-a-molecular-dynamics-simulation-approach
#16
Gurusamy Muneeswaran, Subramanian Kartheeswaran, Manickam Pandiaraj, Kaliappan Muthukumar, Muniyandi Sankaralingam, Saravanavadivu Arunachalam
Naturally occurring mutations to cytochrome c (cyt-c) have been identified recently in patients with mild autosomal dominant thrombocytopenia (low platelet levels), which yield cyt-c mutants with enhanced apoptotic activity. However, the molecular mechanism underlying this low platelet production and enhanced apoptosis remain unclear. Therefore, an attempt is made herein for the first time to investigate the effects of mutations of glycine 41 by serine (G41S) and tyrosine 48 by histidine (Y48H) on the conformational and dynamic changes of apoptotic (Fe(3+)) cyt-c using all atom molecular dynamics (MD) simulations in explicit water solvent...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28947300/towards-understanding-the-e-coli-pnp-binding-mechanism-and-fret-absence-between-e-coli-pnp-and-formycin-a
#17
Małgorzata Prokopowicz, Bartosz Greń, Joanna Cieśla, Borys Kierdaszuk
The aim of this study is threefold: (1) augmentation of the knowledge of the E. coli PNP binding mechanism; (2) explanation of the previously observed 'lack of FRET' phenomenon and (3) an introduction of the correction (modified method) for FRET efficiency calculation in the PNP-FA complexes. We present fluorescence studies of the two E. coli PNP mutants (F159Y and F159A) with formycin A (FA), that indicate that the aromatic amino acid is indispensable in the nucleotide binding, additional hydroxyl group at position 159 probably enhances the strength of binding and that the amino acids pair 159-160 has a great impact on the spectroscopic properties of the enzyme...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28941815/effect-of-protonation-on-the-mechanism-of-phosphate-monoester-hydrolysis-and-comparison-with-the-hydrolysis-of-nucleoside-triphosphate-in-biomolecular-motors
#18
Hammad Ali Hassan, Sadaf Rani, Tabeer Fatima, Farooq Ahmad Kiani, Stefan Fischer
Hydrolysis of phosphate groups is a crucial reaction in living cells. It involves the breaking of two strong bonds, i.e. the OaH bond of the attacking water molecule, and the POl bond of the substrate (Oa and Ol stand for attacking and leaving oxygen atoms). Mechanism of the hydrolysis reaction can proceed either by a concurrent or a sequential mechanism. In the concurrent mechanism, the breaking of OaH and POl bonds occurs simultaneously, whereas in the sequential mechanism, the OaH and POl bonds break at different stages of the reaction...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28941814/sequence-selective-binding-of-c8-conjugated-pyrrolobenzodiazepines-pbds-to-dna
#19
Mohammad A Basher, Khondaker Miraz Rahman, Paul J M Jackson, David E Thurston, Keith R Fox
DNA footprinting and melting experiments have been used to examine the sequence-specific binding of C8-conjugates of pyrrolobenzodiazepines (PBDs) and benzofused rings including benzothiophene and benzofuran, which are attached using pyrrole- or imidazole-containing linkers. The conjugates modulate the covalent attachment points of the PBDs, so that they bind best to guanines flanked by A/T-rich sequences on either the 5'- or 3'-side. The linker affects the binding, and pyrrole produces larger changes than imidazole...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28916410/kinetic-stability-and-sequence-structure-studies-of-urine-derived-bence-jones-proteins-from-multiple-myeloma-and-light-chain-amyloidosis-patients
#20
Luis M Blancas-Mejía, Emily B Martin, Angela Williams, Jonathan S Wall, Marina Ramirez-Alvarado
It is now accepted that the ability of a protein to form amyloid fibrils could be associated both kinetic and thermodynamic protein folding parameters. A recent study from our laboratory using recombinant full-length (encompassing the variable and constant domain) immunoglobulin light chains found a strong kinetic control of the protein unfolding for these proteins. In this study, we are extending our analysis by using urine-derived Bence Jones proteins (BJPs) from five patients with light chain (AL) amyloidosis and four patients with multiple myeloma (MM)...
November 2017: Biophysical Chemistry
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