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Biological thermodynamics

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https://www.readbyqxmd.com/read/28636006/copper-ion-interaction-with-the-rnase-catalytic-site-fragment-of-the-angiogenin-protein-an-experimental-and-theoretical-investigation
#1
Antonio Magrì, Giovanni Tabbì, Raffaella Breglia, Luca De Gioia, Piercarlo Fantucci, Maurizio Bruschi, Raffaele P Bonomo, Diego La Mendola
The angiogenin protein (Ang) is a member of the vertebrate-specific secreted ribonucleases and one of the most potent angiogenic factors known. Ang is a normal constituent of human plasma and its concentration increases under some physiological and pathological conditions to promote neovascularization. Ang was originally identified as an angiogenic tumour factor, but its biological activity has been found to extend from inducing angiogenesis to promoting cell survival in different neurodegenerative diseases...
June 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28635269/the-reduction-potentials-of-fefe-hydrogenase-accessory-iron-sulfur-clusters-provide-insights-into-the-energetics-of-proton-reduction-catalysis
#2
Jacob H Artz, David W Mulder, Michael W Ratzloff, Carolyn E Lubner, Oleg A Zadvornyy, Axl X LeVan, S Garrett Williams, Michael W W Adams, Anne K Jones, Paul W King, John W Peters
An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28630679/molecular-interactions-of-amyloid-nanofibrils-with-biological-aggregation-modifiers-implications-for-cytotoxicity-mechanisms-and-biomaterial-design
#3
REVIEW
Durga Dharmadana, Nicholas P Reynolds, Charlotte E Conn, Céline Valéry
Amyloid nanofibrils are ubiquitous biological protein fibrous aggregates, with a wide range of either toxic or beneficial activities that are relevant to human disease and normal biology. Protein amyloid fibrillization occurs via nucleated polymerization, through non-covalent interactions. As such, protein nanofibril formation is based on a complex interplay between kinetic and thermodynamic factors. The process entails metastable oligomeric species and a highly thermodynamically favoured end state. The kinetics, and the reaction pathway itself, can be influenced by third party moieties, either molecules or surfaces...
August 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28629618/conditioning-and-robustness-of-rna-boltzmann-sampling-under-thermodynamic-parameter-perturbations
#4
Emily Rogers, David Murrugarra, Christine Heitsch
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28625482/equalizing-the-information-amounts-of-protein-and-mrna-by-information-theory
#5
Y Adiguzel
Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein...
June 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28623019/exogenous-addition-of-h2-for-an-in-situ-biogas-upgrading-through-biological-reduction-of-carbon-dioxide-into-methane
#6
Daniel Girma Mulat, Freya Mosbæk, Alastair James Ward, Daniela Polag, Markus Greule, Frank Keppler, Jeppe Lund Nielsen, Anders Feilberg
Biological reduction of CO2 into CH4 by exogenous addition of H2 is a promising technology for upgrading biogas into higher CH4 content. The aim of this work was to study the feasibility of exogenous H2 addition for an in situ biogas upgrading through biological conversion of the biogas CO2 into CH4. Moreover, this study employed systematic study with isotope analysis for providing comprehensive evidence on the underlying pathways of CH4 production and upstream processes. Batch reactors were inoculated with digestate originating from a full-scale biogas plant and fed once with maize leaf substrate...
June 13, 2017: Waste Management
https://www.readbyqxmd.com/read/28621996/transient-dissipation-and-structural-costs-of-physical-information-transduction
#7
Alexander B Boyd, Dibyendu Mandal, Paul M Riechers, James P Crutchfield
A central result that arose in applying information theory to the stochastic thermodynamics of nonlinear dynamical systems is the information-processing second law (IPSL): the physical entropy of the Universe can decrease if compensated by the Shannon-Kolmogorov-Sinai entropy change of appropriate information-carrying degrees of freedom. In particular, the asymptotic-rate IPSL precisely delineates the thermodynamic functioning of autonomous Maxwellian demons and information engines. How do these systems begin to function as engines, Landauer erasers, and error correctors? We identify a minimal, and thus inescapable, transient dissipation of physical information processing, which is not captured by asymptotic rates, but is critical to adaptive thermodynamic processes such as those found in biological systems...
June 2, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28617612/effect-of-urea-on-g-quadruplex-stability
#8
Lusine Aslanyan, Jordan Ko, Byul G Kim, Ishkhan Vardanyan, Yeva B Dalyan, Tigran V Chalikian
G-quadruplexes represent a class of noncanonical nucleic acid structures implicated in transcriptional regulation, cellular function, and disease. An understanding of the forces involved in stabilization/destabilization of the G-quadruplex conformation relative to the duplex or single-stranded conformation is a key to elucidating the biological role of G-quadruplex-based genomic switches and the quest for therapeutic means for controlled induction or suppression of a G-quadruplex at selected genomic loci. Solute-solvent interactions provide a ubiquitous and, in many cases, the determining thermodynamic force in maintaining and modulating the stability of nucleic acids...
June 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28616189/the-combined-effects-of-reactant-kinetics-and-enzyme-stability-explain-the-temperature-dependence-of-metabolic-rates
#9
J P DeLong, J P Gibert, T M Luhring, G Bachman, B Reed, A Neyer, K L Montooth
A mechanistic understanding of the response of metabolic rate to temperature is essential for understanding thermal ecology and metabolic adaptation. Although the Arrhenius equation has been used to describe the effects of temperature on reaction rates and metabolic traits, it does not adequately describe two aspects of the thermal performance curve (TPC) for metabolic rate-that metabolic rate is a unimodal function of temperature often with maximal values in the biologically relevant temperature range and that activation energies are temperature dependent...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28609097/computational-study-of-h2s-release-in-reactions-of-diallyl-polysulfides-with-thiols
#10
You-Ru Cai, Ching-Han Hu
Hydrogen sulfide (H2S) is a gasotransmitter molecule recognized for its role in cell signaling. Garlic-derived polysulfides including diallyl disulfide (DADS) and diallyl trisulfide (DATS) have been shown to release H2S. We investigated the mechanism of the reaction of DADS and DATS with biological thiols, including cysteine (Cys) and glutathione (GSH) using density functional theory. We propose that Cys and GSH react with DADS and DATS in their anionic forms. Thiol anions are much more likely to attack the sulfur atoms of DADS and DATS than the α-carbon of allyl groups...
June 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28607997/exploring-the-boundaries-of-direct-detection-and-characterization-of-labile-isomers-a-case-study-of-copper-ii-dipeptide-systems
#11
Eszter N Tóth, Nóra V May, Antal Rockenbauer, Gábor Peintler, Béla Gyurcsik
The investigation of the linkage isomers of biologically essential and kinetically labile metal complexes in aqueous solutions poses a challenge, as these microspecies cannot be separately studied. Therefore, derivatives are commonly used to initially determine the stability or spectral characteristics of at least one of the isomers. Here we directly detect the isomers, describe the metal ion coordination sphere, speciation and thermodynamic parameters by a synergistic application of temperature dependent EPR and CD spectroscopic measurements in copper(ii)-dipeptide systems including His-Gly and His-Ala ligands...
June 13, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28603672/chemical-composition-and-the-potential-for-proteomic-transformation-in-cancer-hypoxia-and-hyperosmotic-stress
#12
Jeffrey M Dick
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue ([Formula: see text]), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species...
2017: PeerJ
https://www.readbyqxmd.com/read/28601508/design-synthesis-and-biological-evaluation-of-renin-inhibitors-guided-by-simulated-annealing-of-chemical-potential-simulations
#13
Ian S Cloudsdale, John K Dickson, Thomas E Barta, Brian S Grella, Emilie D Smith, John L Kulp, Frank Guarnieri, John L Kulp
We have applied simulated annealing of chemical potential (SACP) to a diverse set of ∼150 very small molecules to provide insights into new interactions in the binding pocket of human renin, a historically difficult target for which to find low molecular weight (MW) inhibitors with good bioavailability. In one of its many uses in drug discovery, SACP provides an efficient, thermodynamically principled method of ranking chemotype replacements for scaffold hopping and manipulating physicochemical characteristics for drug development...
May 19, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28594047/base-catalyzed-diastereoselective-trimerization-of-trifluoroacetone
#14
Anthony P Silvestri, Philip E Dawson
Amphiphilic fluorocarbons have unique properties that facilitate their self assembly and adhesion to both inorganic and biological substrates. Incorporation of these moieties into valuable constructs typically require complex synthetic routes that have limited their use. Here, the base-catalyzed diastereoselective synthesis of 6-methyl-2,4,6-tris(trifluoromethyl)tetrahydro-2H-pyran-2,4-diol is reported. Trimerization of trifluoroacetone in the presence of 5 mol% KHMDS delivers one of four diastereomers selectively in 81% yield with no column chromatography...
June 28, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28590118/measuring-rapid-time-scale-reaction-kinetics-using-isothermal-titration-calorimetry
#15
Justin M Di Trani, Nicolas Moitessier, Anthony K Mittermaier
Isothermal titration calorimetry (ITC) is a powerful tool for acquiring both thermodynamic and kinetic data for biological interactions including molecular recognition and enzymatic catalysis. ITC-based kinetics measurements typically focus on reactions taking place over long time scales (tens of minutes or hours) in order to avoid complications due to the finite length of time needed detect heat flow in the calorimeter cell. While progress has been made toward analyzing more rapid reaction kinetics by ITC, the capabilities and limitations of this approach have not been thoroughly tested to date...
June 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28588198/in-vitro-assembly-of-the-rous-sarcoma-virus-capsid-protein-into-hexamer-tubes-at-physiological-temperature
#16
Soumeya A Jaballah, Graham D Bailey, Ambroise Desfosses, Jaekyung Hyun, Alok K Mitra, Richard L Kingston
During a proteolytically-driven maturation process, the orthoretroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at near-physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface...
June 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28584100/entropy-in-molecular-recognition-by-proteins
#17
José A Caro, Kyle W Harpole, Vignesh Kasinath, Jackwee Lim, Jeffrey Granja, Kathleen G Valentine, Kim A Sharp, A Joshua Wand
Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28580613/update-of-the-attract-force-field-for-the-prediction-of-protein-protein-binding-affinity
#18
Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci
Determining the protein-protein interactions is still a major challenge for molecular biology. Docking protocols has come of age in predicting the structure of macromolecular complexes. However, they still lack accuracy to estimate the binding affinities, the thermodynamic quantity that drives the formation of a complex. Here, an updated version of the protein-protein ATTRACT force field aiming at predicting experimental binding affinities is reported. It has been designed on a dataset of 218 protein-protein complexes...
June 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28575988/an-evaluation-of-colloidal-and-crystalline-properties-of-caco3-nanoparticles-for-biological-applications
#19
V Lauth, M Maas, K Rezwan
Biodegradable calcium carbonate carriers are a promising and safe nanoparticle platform which might enable various applications as an engineered nanomaterial in health care, food and cosmetics. However, engineered nanoparticles can exhibit new forms of toxicity that must be carefully evaluated before being widely adopted in consumer products or novel drug delivery systems. To this end, we studied four common calcium carbonate particle systems (calcite nanoparticles, amorphous sub-micrometer and vaterite sub-micrometer and micrometer particles) and compared their behavior in biological medium and in cell culture experiments...
September 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28573847/nickel-sequestration-by-the-host-defense-protein-human-calprotectin
#20
Toshiki G Nakashige, Emily M Zygiel, Catherine L Drennan, Elizabeth M Nolan
The human innate immune protein calprotectin (CP, S100A8/S100A9 oligomer, calgranulin A/calgranulin B oligomer, MRP-8/MRP-14 oligomer) chelates a number of first-row transition metals, including Mn(II), Fe(II), and Zn(II), and can withhold these essential nutrients from microbes. Here we elucidate the Ni(II) coordination chemistry of human CP. We present a 2.6-Å crystal structure of Ni(II)- and Ca(II)-bound CP, which reveals that CP binds Ni(II) ions at both its transition-metal-binding sites: the His3Asp motif (site 1) and the His6 motif (site 2)...
June 22, 2017: Journal of the American Chemical Society
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