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https://www.readbyqxmd.com/read/29778882/insight-into-the-interactions-of-proteinase-inhibitor-alpha-2-macroglobulin-with-hypochlorite-thermal-analysis-and-biophysical-approach
#1
Tooba Siddiqui, Mohammad Khalid Zia, Syed Saqib Ali, Haseeb Ahsan, Fahim Halim Khan
Hypochlorous acid, an active bleaching agent is one of the major oxidants produced by neutrophils under physiological conditions. It is a potent reactive oxygen species (ROS) which causes oxidation of biomolecules. Treatment of proteins with hypochlorite results in direct oxidative damage to proteins. Alpha-2-macroglobulin is a major proteinase inhibitor and it can inhibit proteinase of any kind regardless of specificity and catalytic mechanism. The proteinase-antiproteinase balance plays an important role in mediating inflammation associated tissue destruction...
May 17, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29778689/network-analysis-of-a-proposed-exit-pathway-for-protons-to-the-p-side-of-cytochrome-c-oxidase
#2
Xiuhong Cai, Kamran Haider, Jianxun Lu, Slaven Radic, Chang Yun Son, Qiang Cui, M R Gunner
Cytochrome c Oxidase (CcO) reduces O2 , the terminal electron acceptor, to water in the aerobic respiration electron transport chain. The energy released by O2 reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior...
May 17, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29778404/plasma-assisted-synthesis-of-%C3%AE-alumina-from-waste-aluminium-dross
#3
R Saravanakumar, K Ramachandran, Lintu G Laly, P V Ananthapadmanabhan, S Yugeswaran
Aluminium dross, a waste generated from aluminium melting process, contains aluminium metal, aluminium oxide, aluminium oxy-nitride and impurities such as sodium chloride and potassium chloride. Since aluminium dross is land filled without treatment, it is hazardous to the environment. Conventional methods for the metal recovery from the recycling of aluminium dross involve chemicals and are time consuming. In this study, an attempt was made to treat aluminium dross using plasma arc melting process. The aluminium dross was melted and evaporated by the plasma arc established between a crucible anode and a rod type hollow cathode made of graphite...
May 16, 2018: Waste Management
https://www.readbyqxmd.com/read/29777393/oxygen-reduction-reaction-on-ptco-nanocatalyst-bi-sulfate-anion-poisoning
#4
Jie Liu, Yan Huang
Pt alloy electrocatalysts are susceptible to anion adsorption in the working environment of fuel cells. In this work, the unavoidable bisulfate and sulfate ((bi)sulfate) poisoning of the oxygen reduction reaction (ORR) on a common PtCo nanocatalyst was studied by the rotating disk electrode (RDE) technique, for the first time to the best of our knowledge. The specific activity decreases linearly with the logarithm of (bi)sulfate concentration under various high potentials. This demonstrates that the (bi)sulfate adsorption does not affect the free energy of ORR activation at a given potential...
May 18, 2018: Nanoscale Research Letters
https://www.readbyqxmd.com/read/29777197/the-transition-state-structure-for-binding-between-taz1-of-cbp-and-the-disordered-hif-1%C3%AE-cad
#5
Ida Lindström, Eva Andersson, Jakob Dogan
Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1α (Hif-1α CAD)...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776125/post-transcriptional-bursting-in-genes-regulated-by-small-rna-molecules
#6
Guillermo Rodrigo
Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776093/impact-of-hydrodynamic-interactions-on-protein-folding-rates-depends-on-temperature
#7
Fabio C Zegarra, Dirar Homouz, Yossi Eliaz, Andrei G Gasic, Margaret S Cheung
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α/β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β-barrel α-spectrin Src-homology 3 domain (SH3) protein...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776077/reconstructing-free-energy-landscapes-for-nonequilibrium-periodic-potentials
#8
N J López-Alamilla, Michael W Jack, K J Challis
We present a method for reconstructing the free-energy landscape of overdamped Brownian motion on a tilted periodic potential. Our approach exploits the periodicity of the system by using the k-space form of the Smoluchowski equation and we employ an iterative approach to determine the nonequilibrium tilt. We reconstruct landscapes for a number of example potentials to show the applicability of the method to both deep and shallow wells and near-to- and far-from-equilibrium regimes. The method converges logarithmically with the number of Fourier terms in the potential...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776070/analysis-and-optimization-of-population-annealing
#9
Christopher Amey, Jonathan Machta
Population annealing is an easily parallelizable sequential Monte Carlo algorithm that is well suited for simulating the equilibrium properties of systems with rough free-energy landscapes. In this work we seek to understand and improve the performance of population annealing. We derive several useful relations between quantities that describe the performance of population annealing and use these relations to suggest methods to optimize the algorithm. These optimization methods were tested by performing large-scale simulations of the three-dimensional (3D) Edwards-Anderson (Ising) spin glass and measuring several observables...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775455/atomic-resolution-mechanism-of-ligand-binding-to-a-solvent-inaccessible-cavity-in-t4-lysozyme
#10
Jagannath Mondal, Navjeet Ahalawat, Subhendu Pandit, Lewis E Kay, Pramodh Vallurupalli
Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive...
May 18, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29774472/uncooked-spaghetti-in-a-colander-injection-of-semiflexible-polymers-in-a-nanopore
#11
Thomas Auger, Loïc Auvray, Jean-Marc Di Meglio, Fabien Montel
We study the flow injection of semiflexible polymers in a nanopore with a diameter smaller than the persistence length of the macromolecules. The suction model from de Gennes and Brochard is modified to take into account the effect of the rigidity of the polymer in the Odijk regime. We show that in this case of extreme confinement the flow threshold vanishes slowly and that in the limit of infinitely small nanopore the free energy barrier eventually disappears.
May 17, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29772403/theoretical-study-of-the-intermolecular-recognition-mechanism-between-survivin-and-substrate-based-on-conserved-binding-mode-analysis
#12
Chao Wu, Liguang Mao, Xie Huang, Weitao Fu, Xiong Cai, Yuepiao Cai, Liqun Shen, Xiaoxia Ye
Survivin is the smallest member of IAP (inhibitor of apoptosis protein) family, which plays important roles in both mitosis and apoptosis. It has become an attractive drug target due to its overexpression in many human cancers. Survivin has been proven to bind to Smac/DIABLO protein that indirectly inhibits apoptosis. Meanwhile, it is the key subunit of chromosome passenger complex (CPC) which bind to the N-terminal tail of phosphorylated histone H3T3ph during mitosis. Up to now, Survivin directly targeting inhibitor has yet to merge since the difficulty of disrupting the protein-protein interactions (PPIs) between Survivin and its substrate proteins...
May 8, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29771936/assigning-crystallographic-electron-densities-with-free-energy-calculations-the-case-of-the-fluoride-channel-fluc
#13
Igor Ariz-Extreme, Jochen S Hub
Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious...
2018: PloS One
https://www.readbyqxmd.com/read/29771515/the-link-between-membrane-composition-and-permeability-to-drugs
#14
Chi Hang Tse, Jeffrey Comer, Yi Wang, Christophe Chipot
Prediction of membrane permeability to small molecules represents an important aspect of drug discovery. First-principle calculations of this quantity require an accurate description of both the thermodynamics and kinetics that underlie translocation of the permeant across the lipid bilayer. In this contribution, the membrane permeability to three drugs, or drug-like molecules, namely, 9-anthroic acid (ANA), 2',3'-dideoxyadenosine (DDA) and hydrocortisone (HYL) are estimated in a pure 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and in a POPC:cholesterol (2:1) mixture...
May 17, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29771167/transcript-free-energy-positively-correlates-with-codon-usage-bias-in-mitochondrial-genes-of-calypogeia-species-calypogeiaceae-marchantiophyta
#15
Sudipa Das, Arif Uddin, Debjyoti Bhattacharyya, Supriyo Chakraborty
The present study attempts to focus on the pattern of codon usage bias (CUB) in mitochondrial genes among four species of Calypogeia viz. C. arguta, C. integristipula, C. neogaea and C. suecica along with the factors influencing their CUB as no work was reported yet. The four taxa exhibit noticeable difference in their morphological features, habitat preference and growth forms. To understand the patterns of codon usage in Calypogeia mitochondrial genomes, we used bioinformatic tools to analyze the mitochondrial protein-coding sequences of four Calypogeia...
May 17, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29771130/thermodynamics-of-mixing-primary-alkanolamines-with-water
#16
Abdenacer Idrissi, Pal Jedlovszky
The volume, energy, entropy, and Helmholtz free energy of mixing of the seven simplest primary alkanolamine molecules, i.e., MEA, MIPA, 2A1P, ABU, AMP, AMP2, and 1A2B with water is investigated by extensive computer simulations and thermodynamic integration. To check the force field dependence of the results, all calculations are repeated with two commonly used water models, namely SPC/E and TIP4P. The obtained results show that the thermodynamics of mixing of alkanolamines and water is largely independent from the type of the alkanolamine molecule...
May 17, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29770561/investigating-the-interaction-of-anticancer-drug-temsirolimus-with-human-transferrin-molecular-docking-and-spectroscopic-approach
#17
Anas Shamsi, Azaj Ahmed, Mohd Shahnawaz Khan, Fohad Mabood Husain, Samreen Amani, Bilqees Bano
In our present study, binding between an important anti renal cancer drug temsirolimus and human transferrin (hTF) was investigated employing spectroscopic and molecular docking approach. In the presence of temsirolimus, hyper chromaticity is observed in hTF in UV spectroscopy suggestive of complex formation between hTF and temsirolimus. Fluorescence spectroscopy revealed the occurrence of quenching in hTF in the presence of temsirolimus implying complex formation taking place between hTF and temsirolimus. Further, the mode of interaction between hTF and temsirolimus was revealed to be static by fluorescence quenching analysis at 3 different temperatures...
May 16, 2018: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29770397/nitrogen-electroreduction-and-hydrogen-evolution-on-cubic-molybdenum-carbide-a-density-functional-study
#18
Ivana Matanovic, Fernando H Garzon
We report herein a density functional theory study of the nitrogen electroreduction and hydrogen evolution reactions on cubic molybdenum carbide (MoC) in order to investigate the viability of using this material as an electro-catalyst for ammonia synthesis. Free energy diagrams for associative and dissociative Heyrovsky mechanisms showed that nitrogen reduction on cubic MoC(111) can proceed via an associative mechanism and that small negative potentials of -0.3 V vs. standard hydrogen electrode can onset the reduction of nitrogen to ammonia...
May 17, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29769585/simple-analytical-model-of-the-effect-of-high-pressure-on-the-critical-temperature-and-other-thermodynamic-properties-of-superconductors
#19
Mateusz Krzyzosiak, Ryszard Gonczarek, Adam Gonczarek, Lucjan Jacak
Within the general conformal transformation method a simplified analytical model is proposed to study the effect of external hydrostatic pressure on low- and high-temperature superconducting systems. A single fluctuation in the density of states, placed away from the Fermi level, as well as external pressure are included in the model to derive equations for the superconducting gap, free energy difference, and specific heat difference. The zero- and sub-critical temperature limits are discussed by the method of successive approximations...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29768915/relative-ligand-binding-free-energies-calculated-from-multiple-short-qm-mm-md-simulations
#20
Casper Steinmann, Martin A Olsson, Ulf Ryde
We have devised a new efficient approach to compute combined quantum mechanical (QM) and molecular mechanical (MM, i.e. QM/MM) ligand-binding relative free energies. Our method employs the reference-potential approach with free-energy perturbation both at the MM level (between the two ligands) and from MM to QM/MM (for each ligand). To ensure that converged results are obtained for the MM→QM/MM perturbations, explicit QM/MM molecular dynamics (MD) simulations are performed with two intermediate mixed states...
May 17, 2018: Journal of Chemical Theory and Computation
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