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Biophysical Chemistry

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https://www.readbyqxmd.com/read/30199772/differential-effect-of-multiple-kinesin-motors-on-run-length-force-and-microtubule-binding-rate
#1
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...
September 3, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30195214/molecular-mechanistic-insights-into-uncoupling-of-ion-transport-from-atp-synthesis
#2
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...
August 27, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30173103/atp-hydrolysis-inactivating-walker-b-mutation-perturbs-e-coli-clpa-self-assembly-energetics-in-the-absence-of-nucleotide
#3
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...
August 27, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30195215/an-empirical-analysis-of-enzyme-function-reporting-for-experimental-reproducibility-missing-incomplete-information-in-published-papers
#4
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...
August 24, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30218978/a-theory-of-reactant-stationary-kinetics-for-a-mechanism-of-zymogen-activation
#5
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...
August 23, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30153504/x-ray-observations-of-single-bio-supramolecular-photochirogenesis
#6
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...
August 14, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30107307/copper-ii-complexation-by-fragment-of-central-part-of-fbp28-protein-from-mus-musculus
#7
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
https://www.readbyqxmd.com/read/30099248/a-weighted-average-kinetic-equation-and-its-application-in-estimating-mass-transfer-coefficients-in-liquid-phase-adsorption
#8
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
https://www.readbyqxmd.com/read/30099247/derivation-and-numerical-profile-analysis-of-a-hierarchically-formulated-microscopic-model-of-hemoglobin-oxygen-binding
#9
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
https://www.readbyqxmd.com/read/30081240/conformational-heterogeneity-of-tau-implication-on-intrinsic-disorder-acid-stability-and-fibrillation-in-alzheimer-s-disease
#10
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
https://www.readbyqxmd.com/read/30081239/molecular-mechanistic-insights-into-coupling-of-ion-transport-to-atp-synthesis
#11
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
https://www.readbyqxmd.com/read/30077014/mechano-molecular-transduction-putting-the-pieces-together
#12
LETTER
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
https://www.readbyqxmd.com/read/30064098/carboplatin-as-an-alternative-to-cisplatin-in-chemotherapies-new-insights-at-single-molecule-level
#13
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
https://www.readbyqxmd.com/read/30036762/simulating-biological-charge-transfer-continuum-dielectric-theory-or-molecular-dynamics
#14
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
https://www.readbyqxmd.com/read/30014892/the-hydrolysis-of-6-phosphogluconolactone-in-the-second-step-of-pentose-phosphate-pathway-occurs-via-a-two-water-mechanism
#15
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
https://www.readbyqxmd.com/read/30014891/antagonistic-role-of-klotho-derived-peptides-dynamics-in-the-pancreatic-cancer-treatment-through-obstructing-wnt-1-and-frizzled-binding
#16
Muhammad Fakhar, Najumuddin, Mehreen Gul, Sajid Rashid
Klotho is an anti-aging protein that is engaged in the suppression of canonical WNT signaling. In this study, we investigated the expression pattern of human WNTs and Klotho in the pancreatic cancer. In the cancerous cells, WNT-1 exhibited much higher expression as compared to other WNTs, while no WNT expression was detected in the normal tissue. In contrast, Klotho expression was significantly low in the cancerous tissue. Based on these observations, we intended to explore Klotho binding to WNT-1 and cystein-rich domains (CRDs) of Frizzled (FZD) homologs through molecular docking and dynamics simulation assays...
September 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29957358/effects-of-lyotropic-anions-on-thermodynamic-stability-and-dynamics-of-horse-cytochrome-c
#17
Rishu Jain, Mukesh Chand Agarwal, Rakesh Kumar, Deepak Sharma, Rajesh Kumar
This paper evaluates the effect of various lyotropic anions (chloride, sulfate, perchlorate, iodide, nitrate, bromide) on the thermodynamic stability and dynamics of native cytochrome c (Cyt c) at pH 7.0. The results of equilibrium and kinetic studies revealed that: (i) at low to intermediate concentrations (≤ 0.5 M), both chaotropic and kosmotropic anions restrict the dynamics of native protein, (ii) at relatively higher concentrations (≥ 1.0 M), the denaturing effect of chaotropic anions dominates, which increases the level of structural-fluctuations responsible to unfold the protein according to Hofmeister series (perchlorate > iodide > nitrate > bromide), and (iii) the lyotropic anions affect the thermal and global stability of Cyt c according to Hofmeister series...
September 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29945014/a-theoretical-study-on-the-cross-talk-of-stress-regulatory-pathways-in-root-cells
#18
Wei Cao, Liang Luo, Ming Yi, Ya Jia
The plants developed more dedicated regulatory pathways than the animals did to response various environment stresses, since they could not run away. The cross-talk among the pathways generally introduce non-trivial regulatory behaviors, from which the plants may benefit. For better understanding the regulatory mechanism due to cross-talk, we study in this work two entangled stress regulatory pathways in root cells. A quantitative model of the regulatory network is constructed in the simplest fashion. An analytic parameter-free approach is then employed to analyse the response tendencies...
September 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29913331/unraveling-the-binding-interaction-of-a-bioactive-pyrazole-based-probe-with-serum-proteins-relative-concentration-dependent-1-1-and-2-1-probe-protein-stoichiometries
#19
Pronab Kundu, Nitin Chattopadhyay
Molecular interactions and binding of probes/drugs with biomacromolecular systems are of fundamental importance in understanding the mechanism of action and hence designing of proactive drugs. In the present study, binding interactions of a biologically potent fluorophore, (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) with two serum transport proteins, human serum albumin and bovine serum albumin, have been investigated exploiting multi-spectroscopic techniques. The spectrophotometric and fluorometric studies together with fluorescence quenching, fluorescence anisotropy, urea induced denaturation studies and fluorescence lifetime measurements reveal strong binding of DSDP with both the plasma proteins...
September 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29906639/development-of-a-machine-learning-model-to-predict-gibbs-free-energy-of-binding-for-protein-ligand-complexes
#20
Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions is still an open problem in the simulation of biological systems, and the development of a new generation machine-learning model is an active research field. In this work, we propose a novel scoring function to predict Gibbs free energy of binding (ΔG) based on the crystallographic structure of complexes involving a protein and an active ligand...
September 2018: Biophysical Chemistry
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