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Biophysical Chemistry

Sindy Müller, Maximilian Kind, Kai Gruhle, Gerd Hause, Annette Meister, Simon Drescher
Liposomes are a promising class of drug delivery vehicles. However, no liposomal formulation has been approved for an oral application so far, due to stability issues of the liposomes in the gastrointestinal tract. Herein, we investigate the miscibility of three novel single-chain alkyl-branched bolalipids PC-C32(1,32Cn)-PC (n = 3, 6, 9) with either saturated or unsaturated phosphatidylcholines by means of differential scanning calorimetry (DSC), transmission electron microscopy (TEM) of stained samples, vitrified specimens, or replica of freeze-fractured samples, and dynamic light scattering (DLS)...
October 24, 2018: Biophysical Chemistry
Mario C Foti, Riccardo Amorati, Andrea Baschieri, Concetta Rocco
A dimer of quercetin prepared through a Mannich reaction protects pyridinium bisretinoid A2E from photooxidation at 430 nm in aqueous medium at pH 7.4. In the presence of light and O2 , A2E is quickly attacked by 1 O2 produced in situ (by excited A2E) to give nonaoxirane and other oxygenated compounds which can be involved in diseases of the macula. Peroxyl radicals might have only a marginal role on the photooxidation of A2E. The dimer is actually a potent quencher of 1 O2 with a rate constant kQ of 8...
December 2018: Biophysical Chemistry
Eva Dušeková, Katarína Garajová, Rukiye Yavaşer, Rastislav Varhač, Erik Sedlák
Effect of Hofmeister sodium salts, sulfate, chloride, bromide and perchlorate, on catalytic properties and stability of chymotrypsin has been studied by absorbance and circular dichroism spectroscopies. To address Hofmeister effect on activity of chymotrypsin, two different substrates, N-benzoyl-L-tyrosine ethyl ester and amide N-succinyl-L-phenylalanine-p-nitroanilide, were used. Catalytic activity of chymotrypsin is dependent on salt concentration and position of anion in Hofmeister series. The enzyme activity for both substrates is only slightly affected by chaotropic anions and increases with kosmotropic nature of anions...
December 2018: Biophysical Chemistry
Alexander M Matyushenko, Sergey Y Kleymenov, Denis S Susorov, Dmitrii I Levitsky
We applied differential scanning calorimetry (DSC) to investigate the structural properties of three isoforms of tropomyosin (Tpm), α, β, and γ, expressed from different genes in human skeletal muscles. We compared specific features of the thermal unfolding of αα, ββ, and γγ Tpm homodimers, as well as of αβ and γβ Tpm heterodimers. The results show that the thermal stability of γγ homodimer is much higher than that of αα homodimer which, in turn, is much more thermostable than the ββ homodimer...
December 2018: Biophysical Chemistry
Kehinde Onwochei Okonjo
The functional properties of most fish hemoglobins are more complex than those of human hemoglobin. This complexity arises in the form of the Root effect, in which the oxygen affinity of such fish hemoglobins decreases rapidly with pH relative to that of human hemoglobin. Cooperative ligand binding is also diminished below pH ≈ 6.5. The Bohr effect, determined by acid-base titration, has been reported for the Root effect carp and anodic eel hemoglobins. Unlike for mammalian hemoglobins, the Wyman equation for the Bohr effect fails to account quantitatively for these Bohr data...
November 2018: Biophysical Chemistry
Justin Eilertsen, Wylie Stroberg, Santiago Schnell
A theoretical analysis is performed on the nonlinear ordinary differential equations that govern the dynamics of a reaction mechanism of zymogen activation. The reaction consists of a primary non-observable zymogen activation reaction that it is coupled to an indicator (observable) reaction. The product of the first reaction is the enzyme of the indicator reaction, and both reactions are governed by the Michaelis-Menten reaction mechanism. Using singular perturbation methods, we derive asymptotic solutions that are valid under the quasi-steady-state and reactant-stationary assumptions...
November 2018: Biophysical Chemistry
Braulio Gutiérrez-Medina, Mónica Buendía Padilla, Alejandra Judith Gutiérrez-Esparza, Alma Rosa Oaxaca Camacho
The in vitro transport of cargo by motor proteins constitutes a model system to understand mechanisms of vesicle trafficking inside cells. Here we apply the classic bead assay with a short, stiff kinesin protein to test the effect of multiple motors on essential transport parameters: distance, force and microtubule binding rate. Measurements of unloaded run length show that the transition from single- to multiple-motor behavior can be characterized by the appearance of extended runs, in accordance with a recently proposed model that quantifies the probability of multiple-motor engagement...
November 2018: Biophysical Chemistry
Peter Halling, Paul F Fitzpatrick, Frank M Raushel, Johann Rohwer, Santiago Schnell, Ulrike Wittig, Roland Wohlgemuth, Carsten Kettner
A key component of enzyme function experiments is reporting of considerable metadata, to allow other researchers to replicate, interpret properly or use fully the results. This paper evaluates the completeness of enzyme function data reporting for reproducibility. We present a detailed examination of 11 recent papers (and their supplementary material) from two leading journals. We found that in every paper we were not able to collect some critical information necessary to reproduce the enzyme function findings...
November 2018: Biophysical Chemistry
Sunil Nath
A procedure is evolved to assess the maximum uncoupling activity of the classical unsubstituted phenolic uncouplers of mitochondrial oxidative phosphorylation (OX PHOS) 2,4-dinitrophenol and 2,6-dinitrophenol. The uncoupler concentrations, C, required for maximum uncoupling efficacy are found to be a strong function of the pH, and a linear relationship of pC with pH is obtained between pH 5 to pH 9. The slopes of the uncoupler concentrations in the aqueous and lipid phases as a function of pH have been estimated...
November 2018: Biophysical Chemistry
Elizabeth C Duran, Aaron L Lucius
E. coli ClpA is an AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins for the purposes of proper proteome maintenance. Biologically active ClpA hexamers contain two nucleotide binding domains (NBD) per protomer, D1 and D2. Despite extensive study, complete understanding of how the twelve NBDs within a ClpA hexamer coordinate ATP binding and hydrolysis to polypeptide translocation is currently lacking. To examine nucleotide binding and coordination at D1 and D2, ClpA Walker B variants deficient in ATP hydrolysis at one or both NBDs have been employed in various studies...
November 2018: Biophysical Chemistry
Jaewon Chang, Masaki Nishijima, Hiroshi Sekiguchi, Kohei Ichiyanagi, Masahiro Kuramochi, Yoshihisa Inoue, Yuji C Sasaki
The binding and photochirogenic behaviour of 2-anthracenecarboxylate (AC) with human serum albumin (HSA) have hitherto been investigated and comprehended as time-averaged statistical events by spectroscopic examinations and product analyses. In this study, we employed a diffracted X-ray tracking (DXT) technique to visualize the single-molecular dynamics of free and AC-loaded HSA (AC:HSA = 0, 1, 5 and 10), as well as the AC-HSA complex under photoirradiation, all of which were tethered to gold nanocrystals and hence traceable in real time by DXT...
November 2018: Biophysical Chemistry
Joanna Makowska, Krzysztof Żamojć, Dariusz Wyrzykowski, Wiesław Wiczk, Lech Chmurzyński
Steady-state and time-resolved fluorescence spectroscopy, UV spectrophotometry and isothermal titration calorimetry techniques were used to study the coordinating properties of the 17aa peptide fragment (D17) derived from the central part of the mouse formin binding protein (FBP28 with the PDB code: 1E0L) towards Cu2+ ions. All the measurements were run in the 2-(N-morpholino)ethanesulfonic acid buffer (20 mM, pH 6.0). Under experimental conditions the formation of the 1:1 complex of Cu2+ ions with D17 is an entropy-driven process...
October 2018: Biophysical Chemistry
Chuncai Yao, Tianjiao Chen
The pseudo-first-order (PFO) and pseudo-second-order (PSO) models are widely used to describe liquid phase adsorption kinetics due to their simplicity and easy application. But these models do not take into account the diffusion or mass transfer effects that exist in adsorption. In this work a new weighted average (WA) kinetic model is presented. The model parameters are related to mass transfer coefficients, which allows for the estimation of the film mass transfer and surface diffusion coefficients from adsorption kinetic data...
October 2018: Biophysical Chemistry
William G Gutheil
To address complex thermodynamic systems with multiple interacting events, we have developed the concept of hierarchical thermodynamic interactions. In this study, this concept is extended to protein-ligand systems with similar but not identical protein subunits, and applied to the analysis of previously published NMR and UV-vis monitored hemoglobin oxygen binding data. Non-linear regression provided estimated errors for statistically significant parameters, but not for null (zero) valued parameters. A numerical/graphical profiling approach was therefore used to assess confidence intervals and correlations for both the statistically significant and nulled valued parameters in this model...
October 2018: Biophysical Chemistry
Benita Jebarupa, Monita Muralidharan, Arumugaperumal Arun, Amit Kumar Mandal, Gopa Mitra
The self-assembly of intrinsically disordered protein tau into paired helical filament forms one of the hallmarks of Alzheimer's disease. However, the facets of innately disordered structure of tau and its conversion to a β-sheet-rich fibril during several tauopathies are poorly understood. Here, we provide a direct insight into the ensemble of highly heterogeneous conformational families of tau at physiological pH, by nano-electrospray mass spectrometry coupled with ion mobility. The average collision cross section of the most unfolded conformer was higher by >2 fold than that of the most folded one...
October 2018: Biophysical Chemistry
Sunil Nath
A wealth of molecular mechanistic insights has been provided into the coupling of ion transport to ATP synthesis based on a two-ion theory of biological energy coupling. A kinetic scheme that considers the mode of functioning of a single F1 FO -ATP synthase molecule with H+ -A- cotransport and unidirectional rotation of the c-rotor in the membrane-bound FO -portion of the enzyme has been developed. Mathematical analysis leads to a detailed enzyme kinetic model applicable to a population of molecules which is compared with experimental data on the pH dependence of ATP synthesis...
October 2018: Biophysical Chemistry
Amit Ron
When subjected to extracellular mechanical loads, cells express a variety of responses ranging from differentiation to apoptosis. The transducing mechanism between the physical stimulus and the molecular response is known as mechanotransduction. In this study, a mechano-molecular model is established that facilitates the integration of cellular mechanics with molecular signaling. It reveals a unique coupling mechanism between the physical stimuli, the extracellular mechanical properties, and the Rho signaling pathway...
October 2018: Biophysical Chemistry
L Oliveira, J M Caquito, M S Rocha
Here we report a new study performed at single molecule level on the interaction of the antineoplastic drug Carboplatin and the DNA molecule - the main target of the drug inside cells in cancer chemotherapies. By using optical tweezers, we measure how the mechanical properties of the DNA-Carboplatin complexes changes as a function of the drug concentration in the sample, for two different ionic strengths ([Na] = 150 mM and [Na] = 1 mM). From these measurements, the binding mechanism and the physicochemical (binding) parameters of the interaction were inferred and directly compared to those obtained for the precursor drug Cisplatin under equivalent conditions...
October 2018: Biophysical Chemistry
David Gnandt, Sehee Na, Thorsten Koslowski
We study the thermodynamic parameters of Marcus's theory of charge transfer, the driving forces and the reorganization energies, using two widely applied approaches to bioenergetic problems that seem to be radically different: continuum dielectric theory via a numerical solution of Poisson's equation, and the thermodynamic integration approach based upon classical Newtonian molecular dynamics, as perfomed by Na et al., PCCP 19, 18,938 (2017). With application to a nitrite reductase NrfHA protein heterodimer, we obtain an excellent agreement between the respective driving forces with an r...
October 2018: Biophysical Chemistry
Tabeer Fatima, Sadaf Rani, Stefan Fischer, Thomas Efferth, Farooq Ahmad Kiani
Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown...
September 2018: Biophysical Chemistry
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