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Biophysical Chemistry

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https://www.readbyqxmd.com/read/29153883/conformational-dynamics-and-free-energy-of-bhrf1-binding-to-bim-bh3
#1
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/29054581/mechanism-of-aggregation-of-uv-irradiated-glycogen-phosphorylase-b-at-a-low-temperature-in-the-presence-of-crowders-and-trimethylamine-n-oxide
#2
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...
October 18, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29046256/capping-effects-on-polymorphic-a%C3%AE-16-21-amyloids-depend-on-their-size-a-molecular-dynamics-simulation-study
#3
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...
October 10, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28965786/mesoscopic-modelling-of-cy3-and-cy5-dyes-attached-to-dna-duplexes
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28893424/quantifying-the-influence-of-5-rna-modifications-on-rna-polymerase-i-activity
#11
Francis D Appling, Aaron L Lucius, David A Schneider
For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28887045/the-molten-globule-residual-structure-is-critical-for-reflavination-of-glucose-oxidase
#12
Katarína Garajová, Martina Zimmermann, Martina Petrenčáková, Lenka Dzurová, Michal Nemergut, Ľudovít Škultéty, Gabriel Žoldák, Erik Sedlák
Glucose oxidase (GOX) is a homodimeric glycoprotein with tightly bound one molecule of FAD cofactor per monomer of the protein. GOX has numerous applications, but the preparation of biotechnologically interesting GOX sensors requires a removal of the native FAD cofactor. This process often leads to unwanted irreversible deflavination and, as a consequence, to the low enzyme recovery. Molecular mechanisms of reversible reflavination are poorly understood; our current knowledge is based only on empiric rules, which is clearly insufficient for further development...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28887044/biochemical-and-biophysical-properties-of-positively-supercoiled-dna
#13
Yingting Liu, Andrea M Berrido, Zi-Chun Hua, Yuk-Ching Tse-Dinh, Fenfei Leng
In this paper we successfully developed a procedure to generate the (+) supercoiled (sc) plasmid DNA template pZXX6 in the milligram range. With the availability of the (+) sc DNA, we are able to characterize and compare certain biochemical and biophysical properties of (+) sc, (-) sc, and relaxed (rx) DNA molecules using different techniques, such as UV melting, circular dichroism, and fluorescence spectrometry. Our results show that (+) sc, (-) sc, and rx DNA templates can only be partially melted due to the fact that these DNA templates are closed circular DNA molecules and the two DNA strands cannot be completely separated upon denaturation at high temperatures...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28882384/two-ion-theory-of-energy-coupling-in-atp-synthesis-rectifies-a-fundamental-flaw-in-the-governing-equations-of-the-chemiosmotic-theory
#14
Sunil Nath
The vital coupled processes of oxidative phosphorylation and photosynthetic phosphorylation synthesize molecules of adenosine-5'-triphosphate (ATP), the universal biological energy currency, and sustain all life on our planet. The chemiosmotic theory of energy coupling in oxidative and photophosphorylation was proposed by Mitchell >50years ago. It has had a contentious history, with part of the accumulated body of experimental evidence supporting it, and part of it in conflict with the theory. Although the theory was strongly criticized by many prominent scientists, the controversy has never been resolved...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28851547/key-factors-regulating-protein-carbonylation-by-%C3%AE-%C3%AE-unsaturated-carbonyls-a-structural-study-based-on-a-retrospective-meta-analysis
#15
Giulio Vistoli, Chiara Mantovani, Silvia Gervasoni, Alessandro Pedretti, Giancarlo Aldini
Protein carbonylation represents one of the most important oxidative-based modifications involving nucleophilic amino acids and affecting protein folding and function. Protein carbonylation is induced by electrophilic carbonyl species and is an highly selective process since few nucleophilic residues are carbonylated within each protein. While considering the great interest for protein carbonylation, few studies investigated the factors which render a nucleophilic residue susceptible to carbonylation. Hence, the present study is aimed to delve into the factors which modulate the reactivity of cysteine, histidine and lysine residues towards α,β unsaturated carbonyls by a retrospective analysis of the available studies which identified the adducted residues for proteins, the structure of which was resolved...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28843429/ultracompact-states-of-native-proteins
#16
Leandro Grille Coronel, Juan P Acierno, Mario R Ermácora
A statistical analysis of circa 20,000 X-ray structures evidenced the effects of temperature of data collection on protein intramolecular distances and degree of compaction. Identical chains with data collected at cryogenic ultralow temperatures (≤160K) showed a radius of gyration (Rg) significantly smaller than at moderate temperatures (≥240K). Furthermore, the analysis revealed the existence of structures with a Rg significantly smaller than expected for cryogenic temperatures. In these ultracompact cases, the unusually small Rg could not be specifically attributed to any experimental parameter or crystal features...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28818314/comparison-of-disaggregative-effect-of-a-type-egcg-dimer-and-egcg-monomer-on-the-preformed-bovine-insulin-amyloid-fibrils
#17
Rong-Zu Nie, Wei Zhu, Jin-Ming Peng, Zhen-Zhen Ge, Chun-Mei Li
In the present study, the disruptive effects of epigallocatechin-3-gallate (EGCG) and A-type dimeric epigallocatechin-3-gallate (A-type EGCG dimer) on the preformed bovine insulin amyloid fibrils were studied by several biophysical methods including thioflavin-T (ThT) fluorescence assay, 1-anilinonaphthalene-8-sulfonic (ANS) fluorescence assay, Congo red (CR) binding assay, dynamic light scattering (DLS), transmission electron microscopy (TEM), Gel electrophoresis (SDS-PAGE) and Bradford assay. Our results demonstrated that A-type EGCG dimer showed significantly more potential disaggregative effects on the bovine insulin amyloid fibrils than EGCG...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28818312/thermodynamic-and-spectroscopic-study-of-al-3-interaction-with-glycine-l-cysteine-and-tranexamic-acid-in-aqueous-solution
#18
Paola Cardiano, Fausta Giacobello, Ottavia Giuffrè, Silvio Sammartano
In this paper a thermodynamic and spectroscopic study on the interaction between Al(3+) and glycine (Gly), l-cysteine (Cys), tranexamic acid (Tranex) is reported. Speciation models have been obtained by processing potentiometric titration data to determine stability constants of the species formed in aqueous solution at T=298.15K, 0.15≤I/molL(-1)≤1 in NaCl. Thermodynamic formation parameters have been obtained from calorimetric titration data, at T=298.15K, I=0.15molL(-1) using NaCl as ionic medium. Al(3+)-Cys system was also investigated by spectrophotometric and (1)H NMR measurements...
November 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28941613/sibpa-under-the-tuscan-sun-introduction-to-the-sibpa-xxiii-special-issue
#19
EDITORIAL
Daniela Giacomazza, Cristiano Viappiani, Enrico Di Cera, Carlo Musio
The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIII National Congress in the gorgeous Tuscan town of Cortona, Italy, on September 18-21, 2016. This special issue features a selection of contributions from the Congress in the areas of molecular, applied, cellular and computational biophysics. Cutting-edge developments in nanoscale biophysics were introduced for the first time in the program. SIBPA continues its successful promotion of biophysical disciplines at the national and international levels, with added strength from its partnership with Biophysical Chemistry and Elsevier...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28818313/controlled-single-cell-cyclic-compression-and-transcription-analysis-a-pilot-study
#20
Paola Gavazzo, Loredana Petecchia, Paolo Facci, Massimo Vassalli, Federica Viti
An innovative platform for the study of the molecular mechanisms at the basis of mechanotransduction has been implemented, developing an experimental approach capable of providing controlled dynamic compression stimuli and retrieving the biomolecular response with single-cell sensitivity. The system provides the ability to perform compression-release cycles on single cells with controlled forces in the nN range and a user-defined repetition rate. Experimental procedures to perform qPCR from a small set of single cells were finely tuned...
October 2017: Biophysical Chemistry
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