4,973 results match your criteria Biophysical chemistry[Journal]


The complex role of the N-terminus and acidic residues of HdeA as pH-dependent switches in its chaperone function.

Biophys Chem 2020 May 19;264:106406. Epub 2020 May 19.

Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America. Electronic address:

HdeA is a small acid-stress chaperone protein found in the periplasm of several pathogenic gram-negative bacteria. In neutral pH environments HdeA is an inactive folded homodimer but when exposed to strong acidic environments it partially unfolds and, once activated, binds to other periplasmic proteins, protecting them from irreversible aggregation. Here we use a combination of hydrogen/deuterium exchange NMR experiments and constant pH molecular dynamics simulations to elucidate the role of HdeA's N-terminus in its activation mechanism. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106406DOI Listing

Characterizing osmolyte chemical class hierarchies and functional group requirements for thermal stabilization of proteins.

Biophys Chem 2020 Jun 12;264:106410. Epub 2020 Jun 12.

Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA. Electronic address:

Osmolytes are naturally occurring organic compounds that protect cellular proteins and other macromolecules against various forms of stress including temperature extremes. While biological studies have correlated the accumulation of certain classes of osmolytes with specific forms of stress, including thermal stress, it remains unclear whether or not these observations reflect an intrinsic chemical class hierarchy amongst the osmolytes with respect to effects on protein stability. In addition, very little is known in regards to the molecular elements of the osmolytes themselves that are essential for their functions. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106410DOI Listing

Gallotannins are uncompetitive inhibitors of pancreatic lipase activity.

Biophys Chem 2020 Jun 3;264:106409. Epub 2020 Jun 3.

Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera Gustavo Enrique Astiazarán Rosas No. 46, Col. La Victoria, Hermosillo, Sonora 83304, Mexico. Electronic address:

Inhibition of pancreatic lipase (PL) is used to treat dyslipidemias and obesity. Phenolic compounds are highly bioactive molecules that can inhibit various enzymes. Our aim was to evaluate the inhibitory activity of selected phenolic compounds of increasing molecular complexity, namely, phenolic acids, mangiferin, penta-O-galloyl-β-d-glucose (PGG) and tannic acid (TA) against porcine PL, according to in vitro and in silico methodologies. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106409DOI Listing

Erratum: High pressure response of H NMR chemical shifts of purine nucleotides.

Biophys Chem 2020 Jun 6:106408. Epub 2020 Jun 6.

University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2020.106408DOI Listing

The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective.

Biophys Chem 2020 Aug 22;263:106394. Epub 2020 May 22.

Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India. Electronic address:

Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO, SO and NO that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106394DOI Listing

Amino acid-functionalized borospherenes as drug delivery systems.

Biophys Chem 2020 Aug 20;263:106407. Epub 2020 May 20.

Arizona State University, Tempe, United States.

Here we report a density functional theory study on the pristine and amino acid-functionalized C4B32 borospherene as drug delivery systems. Inspired by a fascinating finding of novel borospherenes which were designed by doping four carbon atoms in the B cluster (CB), we suggest the pristine and alanine-functionalized CB clusters as high-efficient drug delivery systems. The main objective of the present work is to investigate the interaction of pristine and alanine-conjugated borospherenes with an anticancer drug (hydroxyurea) by means of the density functional theory. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106407DOI Listing

Green synthesis of FeO-Ag nanocomposite using Psidium guajava leaf extract: An eco-friendly and recyclable adsorbent for remediation of Cr(VI) from aqueous media.

Biophys Chem 2020 Aug 11;263:106392. Epub 2020 May 11.

School of Applied Sciences, Centurion University of Technology and Management, Odisha, India. Electronic address:

An environmental friendly and cost effective method was used for the preparation of silver‑iron oxide (α-FeO-Ag) nanocomposite using guava (Psidium guajava) leaf extract, which can be used as an adsorbent for decontamination of chromium (VI) ions from aqueous media. XRD analysis revealed that both Iron oxide and silver nanoparticles are crystalline in nature with face-centered cubic and rhombohedral geometry respectively. The FESEM micrographs of FeO-Ag nanocomposite displayed irregular shaped particles with an average size of 50-90 nm. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106392DOI Listing

Molecular dynamics of an asymmetric form of GabR, a bacterial transcriptional regulator.

Biophys Chem 2020 Jul 27;262:106380. Epub 2020 Apr 27.

Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy. Electronic address:

GabR is a bacterial transcription regulator with a dimeric structure in which each subunit includes a wHTH (winged Helix-Turn-Helix) domain connected through a peptide linker to a large C-terminal domain folded as the enzyme aspartate aminotransferase (AAT). In Bacillus subtilis, GabR activates the genes involved in the metabolism of γ-amino butyric acid (GABA) upon formation of a PLP-GABA adduct. Recently, the crystallographic structure of an asymmetric form of GabR has been solved. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106380DOI Listing

Avenanthramide-C prevents amyloid formation of bovine serum albumin.

Biophys Chem 2020 Aug 5;263:106391. Epub 2020 May 5.

Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Ciencias Genomicas, San Nicolas de los Garza, N.L. Mexico 66451, Mexico. Electronic address:

The misfolding of protein and its assembly into amyloid fibrils with a characteristic β-sheet-rich secondary structure, cause a lot of illnesses. Polyphenols have been extensively studied as a class of amyloid inhibitors, whose effect depends on the position and number of hydroxyl groups around the flavone backbone. In this study, we used bovine serum albumin (BSA) as an amyloid model to test the anti-amyloid effects of Avenanthramide-C (Avn-C), a molecule with a long aliphatic linker between two aromatic rings. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106391DOI Listing

Membrane morphology effects in quartz crystal microbalance characterization of antimicrobial peptide activity.

Biophys Chem 2020 Apr 23;262:106381. Epub 2020 Apr 23.

La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia. Electronic address:

The mechanism of action of membrane disrupting antimicrobial peptides (AMPs) and the basis of their specificity and selectivity to pathogens are often studied by using biomimetic model membranes. It is often assumed that all model membrane morphologies, e.g. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106381DOI Listing

Binding of Nox5's EF-Hand domain to the peptides corresponding to the phosphorylatable region and regulatory inhibitory loop in its dehydrogenase domain.

Biophys Chem 2020 Apr 14;262:106379. Epub 2020 Apr 14.

Department of Chemistry, College of Arts and Sciences, Southern Illinois University Edwardsville, Edwardsville, IL 62026, USA.

Reactive oxygen species (ROS) produced by NADPH oxidase 5 (Nox5) are regulated by Ca flux through the interactions of its self-contained EF-hand domain (EFD), dehydrogenase domain (DH), and transmembrane domain. Studies suggest that the regulatory EF-hand binding domain (REFBD) and phosphorylatable (PhosR) sequences within DH play an important role in Nox5's superoxide-generating activity. However, the interplay of the EFD-DH interaction is largely unclear. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106379DOI Listing

Comparative study of the interaction of some meso-substituted anionic cyanine dyes with human serum albumin.

Biophys Chem 2020 Jun 10;261:106378. Epub 2020 Apr 10.

N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.

Spectral-fluorescent properties of the meso-substituted anionic cyanine dye 3,3'-di-(γ-sulfopropyl)-4,5,4',5'-dibenzo-9-methylthiacarbocyanine betaine (DMC) were studied in solutions and in the presence of human serum albumin (HSA). The properties of DMC were compared with those of the previously studied meso-substituted anionic dyes 3,3'-di(γ-sulfopropyl)-4,5,4',5'-dibenzo-9-ethylthiacarbocyanine betaine (DEC), 3,3'-di-(γ-sulfopropyl)-9-methylthiacarbocyanine betaine (MTC) and 3,3'-di-(γ-sulfopropyl)-5,5'-diphenyl-9-ethyloxacarbocyanine betaine (OCC), which were studied here in more detail. In aqueous solutions, DMC, like DEC, is prone to dimerization; it also forms H- and J-aggregates. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106378DOI Listing

Differences in cytosolic glucose dynamics in astrocytes and adipocytes measured by FRET-based nanosensors.

Biophys Chem 2020 Jun 10;261:106377. Epub 2020 Apr 10.

Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, University of Ljubljana, Faculty of Medicine, 1000 Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, 1000 Ljubljana, Slovenia. Electronic address:

The cellular response to fluctuations in blood glucose levels consists of integrative regulation of cell glucose uptake and glucose utilization in the cytosol, resulting in altered levels of glucose in the cytosol. Cytosolic glucose is difficult to be measured in the intact tissue, however recently methods have become available that allow measurements of glucose in single living cells with fluorescence resonance energy transfer (FRET) based protein sensors. By studying the dynamics of cytosolic glucose levels in different experimental settings, we can gain insights into the properties of plasma membrane permeability to glucose and glucose utilization in the cytosol, and how these processes are modulated by different environmental conditions, agents and enzymes. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106377DOI Listing

Protonation states of central amino acids in a zinc metalloprotease complexed with inhibitor: Molecular mechanics optimizations and ab initio molecular orbital calculations.

Biophys Chem 2020 Jun 1;261:106368. Epub 2020 Apr 1.

Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan. Electronic address:

The zinc-metalloprotease pseudolysin (PLN) secreted from bacteria degrades extracellular proteins to produce bacterial nutrition. Since PLN has a Zn ion at the inhibitor-binding site, the interactions between Zn and PLN residues as well as inhibitor can be significantly changed depending on the protonation states of PLN residues at the inhibitor-binding site. To determine stable protonation states of these residues, we here considered different protonation states for Glu and His residues located around Zn and investigated the electronic states of the PLN + inhibitor complex, using ab initio molecular simulations. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106368DOI Listing

Unbinding events of amino acids and peptides from water-pyrite interfaces: A case study of life's origin on mineral surfaces.

Biophys Chem 2020 May 26;260:106338. Epub 2020 Feb 26.

Chemical Evolution Lab Unit, Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan. Electronic address:

Selective binding of aqueous-phase amino acids to mineral surfaces is regarded as a plausible first step in oligopeptide formation on early Earth. To clarify the strength and underlying mechanism of amino acid binding to pyrite surfaces, we measured the unbinding (pull-off) force of ten amino acids and two oligo-peptides from water-pyrite interfaces using atomic force microscopy (AFM). The most probable unbinding force could be described by a linearly increasing function with the size of the amino acid and a characteristic offset. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106338DOI Listing

Inhibition effect of thiol-type antioxidants on protein oxidative aggregation caused by free radicals.

Biophys Chem 2020 May 19;260:106367. Epub 2020 Mar 19.

Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy Sichuan University, Chengdu 610041, PR China. Electronic address:

This study was aimed to investigate the inhibition effect of thiol-type antioxidants on protein oxidative aggregation caused by free radicals and the underlying mechanisms using six different thiol-type antioxidants (N-acetyl-L-cysteine, methionine, taurine, alpha-lipoic acid, glutathione and thioproline), Cu-HO as a free radical generator (mainly a hydroxyl radical generator) and bovine serum albumin as the model protein. The inhibition effect of these antioxidants on protein oxidative aggregation and protective effect against oxidative damage in mouse brain tissues were investigated using SDS-PAGE, intrinsic fluorescence, simultaneous fluorescence, thioflavin T fluorescence, Congo red absorbance and inverted microscope. The results showed that all six antioxidants could inhibit protein oxidative aggregation by scavenging free radicals. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106367DOI Listing

Coarse-grained MD simulations reveal beta-amyloid fibrils of various sizes bind to interfacial liquid-ordered and liquid-disordered regions in phase separated lipid rafts with diverse membrane-bound conformational states.

Biophys Chem 2020 May 5;260:106355. Epub 2020 Mar 5.

Department of Neuroscience, Trinity University, United States; Department of Physics, Trinity University, United States. Electronic address:

The membrane binding behaviors of beta-amyloid fibrils, dimers to pentamers, from solution to lipid raft surfaces, were investigated using coarse-grained (CG) MD simulations. Our CG rafts contain phospholipid, cholesterol (with or without tail- or headgroup modifications), and with or without asymmetrically distributed monosialotetrahexosylganglioside (GM1). All rafts exhibited liquid-ordered (Lo), liquid-disordered (Ld), and interfacial Lo/Ld (Lod) domains, with domain sizes depending on cholesterol structure. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7254575PMC

Reconstitution of full-length human caveolin-1 into phospholipid bicelles: Validation by analytical ultracentrifugation.

Biophys Chem 2020 04 26;259:106339. Epub 2020 Feb 26.

Department of Chemistry, Lehigh University, 6 E Packer Ave, Bethlehem, PA, USA. Electronic address:

A significant hurdle in obtaining biophysical information on membrane proteins is developing a successful strategy for their reconstitution into a suitable membrane mimic. In particular, utilization of the more 'native-like' membrane mimics such as bicelles is generally more challenging than simple micellar solubilization. Caveolin-1, an integral membrane protein involved in membrane curvature, endocytosis, mechano-protection, and signal transduction, has been shown to be particularly recalcitrant to standard reconstitution protocols due to its highly hydrophobic characteristics. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106339DOI Listing

Conformational properties of LOV2 domain and its C450A variant within broad pH region.

Biophys Chem 2020 04 25;259:106337. Epub 2020 Feb 25.

Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia. Electronic address:

LOV2 (Light-Oxygen-Voltage) domain from Avena sativa phototropin 1 (AsLOV2) belongs to the superfamily of PAS (Per-Arnt-Sim) domains, members of which function as signaling sensors. AsLOV2 undergoes a conformational change upon blue-light absorption by its FMN cofactor. AsLOV2 wild type (wt) is intensively studied as a photo-switchable element in conjugation with various proteins. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106337DOI Listing

Investigation of redox mechanism and DNA binding of novel 2-(x-nitrophenyl)-5-nitrobenzimidazole (x = 2, 3 and 4).

Biophys Chem 2020 03 27;258:106316. Epub 2019 Dec 27.

Department of Science Education, Faculty of Education, Iqbal Open University, Islamabad, Pakistan.

The present study describes the investigation of the binding modes of potential anti-cancerous nitrophenyl derivatives of 2-(x-nitrophenyl)-5-nitrobenzimidazole with calf thymus DNA. The -2-(x-nitrophenyl)-5-nitrobenzimidazoles under investigation differ only in position x of nitro group in nitrophenyl substituent relative to benzimidazole moiety leading to 1-NPNB (x = 2), 2-NPNB (x = 3) and 3-NPNB (x = 4). The DFT calculations predicted that derivatives were electrochemically reducible which was then confirmed by cyclic voltammetry. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106316DOI Listing

Standard Gibbs energy of metabolic reactions: IV. Triosephosphate isomerase reaction.

Biophys Chem 2020 03 13;258:106330. Epub 2020 Jan 13.

Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany. Electronic address:

The glycolytic pathway is present in most organisms and represents a central part of the energy production mechanism in a cell. For a general understanding of glycolysis, the investigation from a thermodynamic point of view is essential and allows realising thermodynamic feasibility analyses under in vivo conditions. However, available literature standard Gibbs energies of reaction, Δg', are calculated using equilibrium-molality ratios K', which might lead to a misinterpretation of the glycolytic pathway. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106330DOI Listing

Editorial "High-pressure biophysical chemistry: Exploring the dynamical landscape of biomolecular systems by pressure perturbation".

Authors:
Roland Winter

Biophys Chem 2020 03 16;258:106328. Epub 2020 Jan 16.

TU Dortmund University, Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, Otto-Hahn Str. 4a, D-44227 Dortmund, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2020.106328DOI Listing

Plasticity or elasticity? Relating elastic moduli with secondary structural features of mixed films of polypeptides at air/fluid and fluid/solid interfaces.

Biophys Chem 2020 03 11;258:106329. Epub 2020 Jan 11.

Advanced Materials Lab., CSIR-CLRI, Adyar, Chennai 600020, India. Electronic address:

Viscoelastic properties of molecular assemblies formed by mixing poly (l-lysine) (PLL) and poly (l-glutamic acid) (PGA) at pH = 7.5 have been studied using Quartz crystal microbalance with dissipation (QCM-D). The inter-molecular complex between PLL and PGA arising from strong electrostatic interaction, leads to local changes in secondary structure resulting in intra-molecular complexes. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106329DOI Listing

Formation of a bovine serum albumin diligand complex with rutin for the suppression of heme toxicity.

Biophys Chem 2020 03 7;258:106327. Epub 2020 Jan 7.

Key Laboratory of Functional Small Organic Molecule, Ministry of Education; Key Laboratory of Green Chemistry, Jiangxi Province and College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, China. Electronic address:

Serum albumin binds avidly to heme to form heme-serum albumin complex and can protect against the potentially toxic effects of heme. Rutin is a glycoside of the bioflavonoid quercetin with various protective effects due to its antioxidant ability. Clarification of the interaction mechanisms between serum albumin and bioactive components (such as heme and flavonoid) is important to develop effective carriers for encapsulation of heme and suppression of its toxicity. Read More

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http://dx.doi.org/10.1016/j.bpc.2020.106327DOI Listing

Naïve balance between structural stability and DNA-binding ability of c-Myb R2R3 under physiological ionic conditions.

Biophys Chem 2020 03 2;258:106319. Epub 2020 Jan 2.

Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan. Electronic address:

The minimum functional unit of c-Myb for specific DNA binding, c-Myb R2R3, fluctuates largely in solution which is critical for its DNA-binding function. The thermal stability of R2R3 increases with increasing NaCl concentrations and upon DNA binding as well. The DNA-binding affinity of R2R3 is stringently dependent on NaCl concentration, and decreases both with an increase or decrease in NaCl concentration from the physiological levels. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106319DOI Listing

Interaction of amphotericin B and saturated or unsaturated phospholipid monolayers containing cholesterol or ergosterol at the air-water interface.

Biophys Chem 2020 03 16;258:106317. Epub 2019 Dec 16.

Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi'an 710123, China.

The antimicrobial activity of amphotericin B (AmB) depends on its interaction with ergosterol-containing cell membranes of fungus. Cholesterol is a sterol in mammalian cell membrane, and its structure is very similar to ergosterol, which caused to the toxic of amphotericin B to mammalian or human cell membranes. Even so, it is still the gold standard for the treatment of fungal infections. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106317DOI Listing

Thermodynamic, viscoelastic and electrical properties of lipid membranes in the presence of astaxanthin.

Biophys Chem 2020 03 24;258:106318. Epub 2019 Dec 24.

Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland.

Among numerous compounds found in marine organisms, astaxathin has received considerable research interest due to beneficial impact on health such as anti-inflammatory, antioxidant and neuroprotective activity. Recently new functionalities of this xanthophyll have been revealed indicating important applications in nutrition and pharmacy. However, astaxanthin, as the bioactive, has limited value without a protecting carrier that provides controlled release in a human body. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106318DOI Listing

Pressure-dependent electronic structure calculations using integral equation-based solvation models.

Biophys Chem 2020 02 27;257:106258. Epub 2019 Aug 27.

Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany. Electronic address:

Recent methodological progress in quantum-chemical calculations using the "embedded cluster reference interaction site model" (EC-RISM) integral equation theory is reviewed in the context of applying it as a solvation model for calculating pressure-dependent thermodynamic and spectroscopic properties of molecules immersed in water. The methodology is based on self-consistent calculations of electronic and solvation structure around dissolved molecules where pressure enters the equations via an appropriately chosen solvent response function and the pure solvent density. Besides specification of a dispersion-repulsion force field for solute-solvent interactions, the EC-RISM approach derives the electrostatic interaction contributions directly from the wave function. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106258DOI Listing
February 2020

Functional changes of biomolecules and organocatalysts as a probe for pressure effects in solution.

Biophys Chem 2020 02 11;257:106280. Epub 2019 Nov 11.

Institute of Organic Chemistry, University Regensburg Universitätsstr, 31, 93053 Regensburg, Germany. Electronic address:

High pressure acts as a mild and non-destructive activation mode for chemical reactions. However, in the context of organo-/biocatalysis, high pressure activation, has not been investigated systematically, although there are significant benefits such as rate acceleration, increased selectivity and the possibility of suppressing side product formation. The influence of hydrostatic pressure in solution on the catalytic performance of enzymes and small molecule organocatalysts such as amino acids, peptides, amines, cinchona alkaloids and thioureas is evaluated in this review, taking reactivity and selectivity as a probe to identify pressure effects on biomolecules. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106280DOI Listing
February 2020

Quasi-native transition and self-diffusion of proteins in water-glycerol mixture.

Biophys Chem 2020 02 26;257:106274. Epub 2019 Nov 26.

School of Chemistry, University of Hyderabad, Hyderabad, 500046, India. Electronic address:

An orderly investigation of the levels of secondary and tertiary structures, kinetics of tertiary structural changes, and self diffusion coefficient of lysozyme and cytochrome c in the 0-70% (weight/volume) range of glycerol is reported. While secondary structural propensity of both proteins is larger in glycerol, results for tertiary structure and translational diffusion coefficient with increasing glycerol provide two contrasting depictions - lysozyme becomes increasingly compact, plausibly due to disulfide bridge constraints, but cytochrome c expands and loses the tertiary structure. The chain expansion and contraction corresponding to loss and reformation of tertiary structure of cytochrome c are ultrafast that occur in the submillisecond bin. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106274DOI Listing
February 2020

NMR studies on oligonucleotide - Methylene blue conjugates targeting double-helical nucleic acids.

Biophys Chem 2020 02 5;257:106314. Epub 2019 Dec 5.

University of Surabaya, Faculty of Biotechnology, Surabaya, Indonesia; University of Greifswald, Institute of Biochemistry, 17489 Greifswald, Germany. Electronic address:

Methylene blue (MB) - nucleic acid interactions are of considerable interest due to the photosensitizing activity of the dye with potential applications in medicine and biotechnology. Covalent attachment of the MB to an oligonucleotide through a flexible heptamethylene linker enabled a positioning of the dye moiety to specific sites through triplex formation with a target duplex. NMR studies demonstrated interactions of MB with the nucleic acids. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106314DOI Listing
February 2020

Enthalpically-driven ligand recognition and cavity solvation of bovine odorant binding protein.

Biophys Chem 2020 02 9;257:106315. Epub 2019 Dec 9.

Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México 04510, Mexico. Electronic address:

Lipocalins are a widely distributed family of extracellular proteins typically involved in the transport of small hydrophobic molecules. To gain new insights into the molecular basis that governs ligand recognition by this ancient protein family, the binding properties of the domain-swapped dimer bovine odorant binding protein (bOBP) and its monomeric mutant bOBP were characterized using calorimetric techniques and molecular dynamics simulations. Thermal unfolding profiles revealed that the isolated bOBP subunits behave as a cooperative folding unit. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106315DOI Listing
February 2020

A molecular dynamics study proposing the existence of statistical structural heterogeneity due to chain orientation in the POPC-cholesterol bilayer.

Biophys Chem 2020 02 24;257:106275. Epub 2019 Oct 24.

Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México Av. Universidad s/n Cuernavaca, Morelos, 62251, Mexico. Electronic address:

We performed molecular dynamics simulations of a lipid bilayer consisting of POPC and cholesterol at temperatures from 283 to 308K and cholesterol concentrations from 0 to 50% mol/mol. The purpose of this study was to look for the existence of structural differences in the region delimited by these parameters and, in particular, in a region where coexistence of liquid disordered and liquid ordered phases has been proposed. Our interest in this range of concentration and temperature responds to the fact that polyene ionophore activity varies considerably along it. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106275DOI Listing
February 2020

Refutation of the cation-centric torsional ATP synthesis model and advocating murburn scheme for mitochondrial oxidative phosphorylation.

Biophys Chem 2020 02 18;257:106278. Epub 2019 Nov 18.

Satyamjayatu: The Science & Ethics Foundation, Shoranur-2 PO, Palakkad District, Kerala 679122, India. Electronic address:

The acclaimed explanation for mitochondrial oxidative phosphorylation (mOxPhos) is a proton or cation centric scheme. Such ideas were recently disclaimed and in lieu, an evidence-based oxygen-centric explanation, murburn concept, was proposed. The new understanding vouches for catalytic roles of diffusible reactive oxygen species (DROS). Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106278DOI Listing
February 2020

Consolidation of Nath's torsional mechanism of ATP synthesis and two-ion theory of energy coupling in oxidative phosphorylation and photophosphorylation.

Authors:
Sunil Nath

Biophys Chem 2020 02 14;257:106279. Epub 2019 Nov 14.

Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address:

In a recent publication, Manoj raises criticisms against consensus views on the ATP synthase. The radical statements and assertions are shown to contradict a vast body of available knowledge that includes i) pioneering single-molecule biochemical and biophysical studies from the respected experimental groups of Kinosita, Yoshida, Noji, Börsch, Dunn, Gräber, Frasch, and Dimroth etc., ii) state-of-the-art X-ray and EM/cryo-EM structural information garnered over the decades by the expert groups of Leslie-Walker, Kühlbrandt, Mueller, Meier, Rubinstein, Sazanov, Duncan, and Pedersen on ATP synthase, iii) the pioneering energy-based computer simulations of Warshel, and iv) the novel theoretical and experimental works of Nath. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106279DOI Listing
February 2020

Vibrational (FT-IR, Raman) analysis of tea catechins based on both theoretical calculations and experiments.

Biophys Chem 2020 01 14;256:106282. Epub 2019 Nov 14.

Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China. Electronic address:

Structural investigations, based on density functional theory (DFT) calculations, are performed on tea catechins, including 4-aminobutyric acid (GABA), L-theanine (Thea), caffeine (CAF), theobromine (TB), theophylline (TP), catechin (C), epicatechin (EC), gallocatechin (GC), epigallocatechin (EGC), catechin gallate (CG), epicatechin gallate (ECG), gallocatechin gallate (GCG) and epigallocatechin gallate (EGCG). With an identified lowest energy conformer of investigated molecules, FTIR and FT-Raman spectra have been assigned according to DFT calculations in the way of B3LYP/6-31 + G (d, p). Normal spectra of these catechin powders are also measured by Raman spectrometers. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106282DOI Listing
January 2020

Computational investigation of the binding characteristics of β-amyloid fibrils.

Biophys Chem 2020 01 14;256:106281. Epub 2019 Nov 14.

Department of Chemical Sciences, University of Johannesburg, P. O. Box 17011, Doornfontein Campus, 2028 Johannesburg, South Africa. Electronic address:

Timely and accurate diagnosis of Alzheimer's disease (AD) remains a major challenge in the medical arena. β-amyloid (Aβ) imaging techniques such as positron emission tomography and single photon emission computed tomography require the use of an imaging probe. To date, only flutemetamol, florbetaben and florbetapir have been approved for clinical use as imaging probes. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106281DOI Listing
January 2020

Protein isoelectric point distribution in the interactomes across the domains of life.

Biophys Chem 2020 01 25;256:106269. Epub 2019 Oct 25.

MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College, St. Mary's Campus, Norfolk Place, London W2 1PG, UK.

The distribution of the protein isoelectric point (pI) in the protein-protein interaction (PPI) networks across the domains of life has not been investigated yet. This work attempts to correlate the pI with the number of direct interacting partners in the experimentally supported networks involving 226.085 PPIs from 14 various organisms including human, mouse, yeast, bacteria, viruses and 53. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106269DOI Listing
January 2020

Explaining leak states in the proton pump of heme-copper oxidases observed in single-molecule experiments.

Biophys Chem 2020 01 2;256:106276. Epub 2019 Nov 2.

SMBNOS, University of Bari 'Aldo Moro', Bari, Italy. Electronic address:

Heme-copper oxidases couple the exergonic oxygen reduction with the endergonic proton translocation. Redox-linked structural changes have been localized in deeply buried regions of the protein, near the low-potential heme. How these movements can modulate distant gating events along the intramolecular proton path, where the entry (exit) of pumped proton occurs, is a major concern for the proton pump models. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106276DOI Listing
January 2020

Retraction notice to "Symmetrical interactions in K+ channel" [Biophys. Chem. 254 (2019) 106259].

Authors:
Yuval Ben-Abu

Biophys Chem 2019 11 8;254:106277. Epub 2019 Nov 8.

Department of Physics and Project Unit, Sapir Academic College, Sderot, Hof Ashkelon 79165, Israel.

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http://dx.doi.org/10.1016/j.bpc.2019.106277DOI Listing
November 2019

Formation of a bovine serum albumin diligand complex with rutin and single-walled carbon nanotubes for the reduction of cytotoxicity.

Biophys Chem 2020 01 24;256:106268. Epub 2019 Oct 24.

Key Laboratory of Functional Small Organic Molecule, Ministry of Education, Key Laboratory of Green Chemistry, Jiangxi Province and College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, China. Electronic address:

Carbon nanotubes (CNTs) are extensively used in the area of biotechnology and biomedicine, and the binding of proteins to CNTs plays an important role in the potential toxicity of nanomaterials. Rutin is a glycoside of the bioactive quercetin with various health-improving effects due to its antioxidant ability. Demonstration of the interaction between serum albumin and bioactive components is important to design effective carriers for the suppression of CNTs' toxicity. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106268DOI Listing
January 2020

Stability of the different arms of a DNA tetrahedron and its interaction with a minor groove ligand.

Biophys Chem 2020 01 21;256:106270. Epub 2019 Oct 21.

School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom. Electronic address:

DNA strands can be designed to assemble into stable three-dimensional structures, based on Watson-Crick base pairing rules. The simplest of these is the DNA tetrahedron that is composed of four oligonucleotides. We have re-designed the sequence of a DNA tetrahedron so that it contains a single (AATT) binding site for the minor groove binding ligand Hoechst 33258. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106270DOI Listing
January 2020

GM1 Ganglioside role in the interaction of Alpha-synuclein with lipid membranes: Morphology and structure.

Biophys Chem 2019 12 18;255:106272. Epub 2019 Oct 18.

Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy.

Alpha-Synuclein (AS) is the protein playing the major role in Parkinson's disease (PD), a neurological disorder characterized by the degeneration of dopaminergic neurons and the accumulation of AS into amyloid plaques. The aggregation of AS into intermediate aggregates, called oligomers, and their pathological relation with biological membranes are considered key steps in the development and progression of the disease. Here we propose a multi-technique approach to study the effects of AS in its monomeric and oligomeric forms on artificial lipid membranes containing GM1 ganglioside. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106272DOI Listing
December 2019

SIBPA on the crest of the Adriatic Sea wave: Introduction to the SIBPA XXIV (2018 congress) special issue.

Biophys Chem 2019 12 18;255:106273. Epub 2019 Oct 18.

CNR Institute of Biophysics, Trento Unit, Via alla Cascata 56/C, 38123 Trento, Italy. Electronic address:

The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIV National Congress in the beautiful seaside town of Ancona, Italy, on September 10-13, 2018. This special issue features a selection of contributions from the Congress in all areas of modern biophysics including molecular, cellular, applied, computational and nanoscale biophysics. SIBPA pursues its institutional tasks and carries on its successful promotion of biophysical disciplines at the national and international levels, also trough the consolidation of its partnership with Biophysical Chemistry and Elsevier. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106273DOI Listing
December 2019
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Modern theory of energy coupling and ATP synthesis. Violation of Gauss's law by the chemiosmotic theory and validation of the two-ion theory.

Authors:
Sunil Nath

Biophys Chem 2019 12 17;255:106271. Epub 2019 Oct 17.

Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India. Electronic address:

Adenosine triphosphate (ATP) is the universal biological energy fuel, or nature's gasoline. The vast quantities of ATP required for sustenance of living processes in cells are synthesized by oxidative phosphorylation and photosynthesis. The chemiosmotic theory of energy coupling was proposed by Mitchell more than 50 years ago but has a contentious history. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106271DOI Listing
December 2019

Investigation of the binding between olfactory receptors and odorant molecules in C. elegans organism.

Biophys Chem 2019 12 11;255:106264. Epub 2019 Sep 11.

Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy. Electronic address:

The molecular mechanisms regulating the complex sensory system that underlies olfaction are still not completely understood. The compounds formed from the interaction of Olfactory Receptors (ORs) with volatile molecules play a crucial role in producing the sense of olfaction. Therefore, it is necessary to investigate the binding mechanisms between these receptors and small ligands. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106264DOI Listing
December 2019

Amyloid fibril formation in the presence of water structure-affecting solutes.

Biophys Chem 2019 11 12;254:106265. Epub 2019 Sep 12.

Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland.

The impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106265DOI Listing
November 2019

Understanding membrane remodelling initiated by photosensitized lipid oxidation.

Biophys Chem 2019 11 5;254:106263. Epub 2019 Sep 5.

Applied Physics Department, Institute of Physics, University of São Paulo, SP, Brazil. Electronic address:

In this review, we describe how photooxidation changes membrane properties that can ultimately lead to permanent membrane damage. Lipid photooxidation occurs in the presence of reactive oxygen species such as singlet oxygen and by direct reactions of lipids with a photosensitizer in the excited state. Indeed, lipid oxidation triggers chemical transformations that can alter lipid packing; change the membrane surface area, thickness and elastic modulus; and induce pore formation and phase separation. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106263DOI Listing
November 2019

Response to the "Comments on 'Statistical thermodynamics of casein aggregation: Effects of salts and water' [Biophys Chem. 247 (2019) 34-42]".

Biophys Chem 2020 01 13;256:106267. Epub 2019 Sep 13.

York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2019.106267DOI Listing
January 2020

Molecular dynamics simulations of mechanical stress on oxidized membranes.

Biophys Chem 2019 11 13;254:106266. Epub 2019 Sep 13.

Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil. Electronic address:

Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106266DOI Listing
November 2019