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Biophysical Chemistry

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https://www.readbyqxmd.com/read/28318906/analysis-of-molecular-mechanisms-of-atp-synthesis-from-the-standpoint-of-the-principle-of-electrical-neutrality
#1
REVIEW
Sunil Nath
Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis...
March 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28314628/petit-high-pressure-carbon-dioxide-stress-increases-synthesis-of-s-adenosylmethionine-and-phosphatidylcholine-in-yeast-saccharomyces-cerevisiae
#2
Liyuan Niu, Kazuki Nomura, Hitoshi Iwahashi, Hiroyuki Matsuoka, Satoshi Kawachi, Yoshihisa Suzuki, Katsuhiro Tamura
Petit-High Pressure Carbon Dioxide (p-HPCD) is a promising nonthermal technology for foods pasteurization. Cluster analysis of gene expression profiles of Saccharomyces cerevisiae exposed to various stresses exhibited that gene expression profile for p-HPCD stress (0.5MPa, 25°C) was grouped into a cluster including profiles for Sodium Dodecyl Sulfate and Roundup herbicide. Both are detergents that can disorder membrane structurally and functionally, which suggests that cell membrane may be a target of p-HPCD stress to cause cell growth inhibition...
March 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28318905/thermodynamic-properties-of-amyloid-fibrils-in-equilibrium
#3
Tomaz Urbic, Sara Najem, Cristiano L Dias
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e...
March 7, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28318907/the-effects-of-mutating-tyr9-and-arg15-on-the-structure-stability-conformational-dynamics-and-mechanism-of-gsta3-3
#4
Gary J Robertson, Stoyan H Stoychev, Yasien Sayed, Ikechukwu Achilonu, Heini W Dirr
Glutathione S-transferase A3-3 is the most catalytically efficient steroid isomerase enzyme known in humans, transforming Δ(5)-androstene-3-17-dione into Δ(4)-androstene-3-17-dione. GSTA3-3 catalyzes this reaction with ten-fold greater efficiency than GSTA1-1, its closest competitor in the Alpha class of GSTs. In order to examine the differences between Alpha class GSTs and to better elucidate the mechanism of GSTA3-3 the roles of Tyr9 and Arg15 were examined. Tyr9 is the major catalytic residue of Alpha class GSTs and Arg15 is proposed to be catalytically important to GSTA3-3 but never before experimentally examined...
March 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28282626/standard-gibbs-energy-of-metabolic-reactions-ii-glucose-6-phosphatase-reaction-and-atp-hydrolysis
#5
Florian Meurer, Hoang Tam Do, Gabriele Sadowski, Christoph Held
ATP (adenosine triphosphate) is a key reaction for metabolism. Tools from systems biology require standard reaction data in order to predict metabolic pathways accurately. However, literature values for standard Gibbs energy of ATP hydrolysis are highly uncertain and differ strongly from each other. Further, such data usually neglect the activity coefficients of reacting agents, and published data like this is apparent (condition-dependent) data instead of activity-based standard data. In this work a consistent value for the standard Gibbs energy of ATP hydrolysis was determined...
March 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28283210/osmolyte-depletion-viewed-in-terms-of-the-dividing-membrane-and-its-work-of-expansion-against-osmotic-pressure
#6
Seishi Shimizu, Nobuyuki Matubayasi
How osmolytes enhance the folding, binding, and self-assembly of biological macromolecules at a microscopic scale has long been a matter of debate. Ambiguities persist on the key interpretive concepts, such as the "effective membrane" (which marks the boundary of the volume from which osmolytes are excluded) and the "free energy of exclusion" of osmolytes from biomolecular surfaces. In this paper, we formulate these elusive concepts based upon chemical thermodynamics and rigorous statistical thermodynamics (the Kirkwood-Buff theory)...
February 27, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28249763/solution-nmr-investigation-of-the-response-of-the-lactose-repressor-core-domain-dimer-to-hydrostatic-pressure
#7
Brian Fuglestad, Matthew A Stetz, Zachary Belnavis, A Joshua Wand
Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change...
February 24, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28188007/volumetric-contributions-of-loop-regions-of-g-quadruplex-dna-to-the-formation-of-the-tertiary-structure
#8
Shuntaro Takahashi, Naoki Sugimoto
DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆Vtr, of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75...
February 6, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28187351/identifying-binding-modes-of-two-synthetic-derivatives-of-adrenalin-to-the-%C3%AE-2c-adrenoceptor-by-using-molecular-modeling-insights-into-the-%C3%AE-2c-adrenoceptor-activation
#9
Samira Gholami, A Khalegh Bordbar, Amir Lohrasebi
Although, α2C adrenergic receptor (AR) mediates a number of physiological functions in vivo and has great therapeutic potential, the absence of its crystal structure is a major difficulty in the activation mechanism studies and drug design endeavors. Here, a homology model of α2C AR has been presented by means of multiple sequence alignment. The used templates were the latest crystal structures of the other ARs (Protein Data Bank IDs: 2R4R, 2RH1, 4GPO, 3P0G, 4BVN and 4LDO) that have 38.4% identity with the query...
February 2, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28183008/potentiometric-uv-and-1-h-nmr-study-on-the-interaction-of-penicillin-derivatives-with-zn-ii-in-aqueous-solution
#10
Paola Cardiano, Rosalia Maria Cigala, Francesco Crea, Concetta De Stefano, Ottavia Giuffrè, Silvio Sammartano, Giuseppina Vianelli
The interaction of Zn(II) with ampicillin [(2S,5R,6R)-6-([(2R)-2-amino-2-phenylacetyl]amino)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2- carboxylic acid] and amoxicillin [(2S,5R,6R)-6-{[(2R)-2-amino-2-(4-hydroxyphenyl)-acetyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-24-carboxylic acid] in NaCl aqueous solution at different ionic strengths and at t=25°C was investigated by potentiometric, UV and (1)H NMR techniques. Fairly similar speciation models were obtained for the two systems...
January 31, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28282625/phosphorylation-of-the-regulatory-domain-of-human-tyrosine-hydroxylase-1-monitored-using-non-uniformly-sampled-nmr
#11
Petr Louša, Hana Nedozrálová, Erik Župa, Jiří Nováček, Jozef Hritz
Human tyrosine hydroxylase 1 (hTH1) activity is regulated by phosphorylation of its regulatory domain (RD-hTH1) and by an interaction with the 14-3-3 protein. The RD-hTH1 is composed of a structured region (66-169) preceded by an intrinsically disordered protein region (IDP, hTH1_65) containing two phosphorylation sites (S19 and S40) which are highly relevant for its increase in activity. The NMR signals of the IDP region in the non-phosphorylated, singly phosphorylated (pS40) and doubly phosphorylated states (pS19_pS40) were assigned by non-uniformly sampled spectra with increased dimensionality (5D)...
January 27, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28162829/the-role-of-loops-and-cation-on-the-volume-of-unfolding-of-g-quadruplexes-related-to-htel
#12
Yang Yun Li, David N Dubins, Dianna My Nhi Thi Le, Karen Leung, Robert B Macgregor
In aqueous solutions containing sodium or potassium cations, oligodeoxyribonucleotides (ODNs) rich in guanine form four-stranded DNA structures called G-quadruplexes (G4s). These structures are destabilized by elevated hydrostatic pressure. Here, we use pressure to investigate the volumetric changes arising from the formation of G4 structures. G4s display a great deal of structural heterogeneity that depends on the stabilizing cation as well as the oligonucleotide sequence. Using UV thermal unfolding at different pressures, we have investigated the volume change of the helix-coil equilibrium of a series of ODNs whose sequences are related to the G-rich ODN HTel (d[A(GGGTTA)3GGG]), which contains four repeats of the human telomeric sequence...
January 6, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28081859/hydrostatic-pressure-effect-on-pnipam-cononsolvency-in-water-methanol-solutions
#13
Andrea Pica, Giuseppe Graziano
When methanol is added to water at room temperature and 1atm, poly (N-isopropylacrylamide), PNIPAM, undergoes a coil-to-globule collapse transition. This intriguing phenomenon is called cononsolvency. Spectroscopic measurements have shown that application of high hydrostatic pressure destroys PNIPAM cononsolvency in water-methanol solutions. We have developed a theoretical approach that identifies the decrease in solvent-excluded volume effect as the driving force of PNIPAM collapse on increasing the temperature...
January 5, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28092802/signal-and-binding-i-physico-chemical-response-to-macromolecule-ligand-interactions
#14
REVIEW
Wlodzimierz Bujalowski, Maria J Jezewska, Paul J Bujalowski
Obtaining a detailed knowledge about energetics of ligand-macromolecule interactions is a prerequisite for elucidation of the nature, behavior, and activities of the formed complexes. The most commonly used methods in characterizing molecular interactions are physico-chemical techniques based mainly on spectroscopic, calorimetric, hydrodynamic, etc., measurements. The major advantage of the physico-chemical methods is that they do not require large quantities of material and, if performed carefully, do not perturb examined reactions...
January 3, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28095333/effect-of-resveratrol-on-platelet-aggregation-by-fibrinogen-protection
#15
Claudia Bonechi, Stefania Lamponi, Alessandro Donati, Gabriella Tamasi, Marco Consumi, Gemma Leone, Claudio Rossi, Agnese Magnani
The effect of resveratrol (RSV) in inhibiting platelet adhesion and aggregation, as well as fibrinogen (FBG) conformational changes promoted by epinephrine (EP), were studied, by using complementary experimental techniques. NMR and IR spectroscopies were used to investigate possible protective effects by RSV towards FBG, in presence of EP. The protective effect of RSV towards FBG was highlighted by spin nuclear relaxation experiments that were interpreted for determining the thermodynamic equilibrium constants of FBG-EP interaction, and by infrared measurements, that showed EP-induced conformational changes of FBG...
January 2, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28095332/signal-and-binding-ii-converting-physico-chemical-responses-to-macromolecule-ligand-interactions-into-thermodynamic-binding-isotherms
#16
REVIEW
Wlodzimierz Bujalowski, Maria J Jezewska, Paul J Bujalowski
Physico-chemical titration techniques are the most commonly used methods in characterizing molecular interactions. These methods are mainly based on spectroscopic, calorimetric, hydrodynamic, etc., measurements. However, truly quantitative physico-chemical methods are absolutely based on the determination of the relationship between the measured signal and the total average degree of binding in order to obtain meaningful interaction parameters. The relationship between the observed physico-chemical signal of whatever nature and the degree of binding must be determined and not assumed, based on some ad hoc intuitive relationship/model, leading to determination of the true binding isotherm...
December 30, 2016: Biophysical Chemistry
https://www.readbyqxmd.com/read/28187350/conformational-selection-and-induced-fit-as-a-useful-framework-for-molecular-motor-mechanisms
#17
REVIEW
Eric A Galburt, Eric J Tomko
The linkage between macromolecular binding and conformational change that is ubiquitous in biological molecules can be understood in the context of the mechanisms of conformational selection and induced fit. Here, we explore mappings between these mechanisms of ligand binding and those underlying the translocation of molecular motors and the nucleic acid unwinding of helicases. The mechanism of biased motion exhibited by molecular motors is typically described as either a thermal ratchet or a power-stroke and nucleic acid helicases are characterized by either active or passive unwinding mechanisms...
April 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/27992841/structural-analyses-of-the-nucleosome-complexes-with-human-testis-specific-histone-variants-hth2a-and-hth2b
#18
Sivaraman Padavattan, Viswanathan Thiruselvam, Toshie Shinagawa, Kazuya Hasegawa, Takashi Kumasaka, Shunsuke Ishii, Thirumananseri Kumarevel
Th2a and Th2b are the testis-specific histone variants highly expressed during spermatogenesis. Approximately 4% of the genome is retained in nucleosomes in mature human sperm, which is enriched at loci of developmental importance. Our recent studies revealed that the mouse histone variant homologs TH2a and TH2b are involved in reprogramming. In the present work, we report three nucleosome structures (NCPs) with human testis-specific histone variants hTh2a and hTh2b, [hGcH (hTh2a-hTh2b-H3-H4), hGcHV1 (hTh2a-H2b-H3-H4) and hGcHV2 (H2a-hTh2b-H3-H4)] and a 146-base pair (bp) duplex DNA fragment at ~3...
February 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/27951444/modified-poisson-equations-for-calculating-solvation-free-energy
#19
Pei-Kun Yang
The dielectric polarization (P) is the key factor in calculating the solvation free energy. P can be decomposed into the product of the electric dipole per solvent (p) and the relative solvent molecular density (g). p can be calculated from the electric field (E), and g can be calculated from the mean force (F), where the electric component of F is calculated from ∇xE. The Poisson equations were modified for E and ∇xE. Strategies to estimate the boundary conditions of E and ∇xE were proposed. The dependences of P and g on the parameters used for the numerical analysis were explored...
February 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/27912144/elucidation-of-%C3%AE-s-dynamics-of-domain-iii-of-human-serum-albumin-during-the-chemical-and-thermal-unfolding-a-fluorescence-correlation-spectroscopic-investigation
#20
Bhaswati Sengupta, Nilimesh Das, Pratik Sen
The local structural dynamics and denaturation profile of domain-III of HSA against guanidine hydrochloride (GnHCl) and temperature has been studied using a coumarin based solvatochromic fluorescent probe p-nitrophenyl coumarin ester (NPCE), covalently tagged to Tyr-411 residue. By the steady state, time-resolved and single molecular level fluorescence studies it has been established that the domain-III of HSA is very sensitive to GnHCl but somewhat resistant to temperature and the domain specific unfolding proceeds in an altered way as compared to the overall unfolding of HSA...
February 2017: Biophysical Chemistry
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