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Biological thermodynamics

Sashka Krumova, Svetla Todinova, Deyan Mavrov, Pencho Marinov, Vassia Atanassova, Krassimir Atanassov, Stefka G Taneva
BACKGROUND: Biological microcalorimetry has entered into a phase where its potential for disease diagnostics is readily recognized. A wide variety of oncological and immunological disorders have been characterized by differential scanning calorimetry (DSC) and characteristic thermodynamic profiles were reported. Now the challenge before DSC is not the experimental data collection but the development of analysis protocols for reliable data stratification/classification and discrimination of disease specific features (calorimetric markers)...
October 15, 2016: Biochimica et Biophysica Acta
Qin Wang, Katherine J Franz
Metal ions are essential for a wide range of physiological processes, but they can also be toxic if not appropriately regulated by a complex network of metal trafficking proteins. Intervention in cellular metal distribution with small-molecule or peptide chelating agents has promising therapeutic potential to harness metals to fight disease. Molecular outcomes associated with forming metal-chelate interactions in situ include altering the concentration and subcellular metal distribution, inhibiting metalloenzymes, enhancing the reactivity of a metal species to elicit a favorable biological response, or passivating the reactivity of a metal species to prevent deleterious reactivity...
October 17, 2016: Accounts of Chemical Research
Gayan Senavirathne, Santosh K Mahto, Jeungphill Hanne, Daniel O'Brian, Richard Fishel
Wrapping of genomic DNA into nucleosomes poses thermodynamic and kinetic barriers to biological processes such as replication, transcription, repair and recombination. Previous biochemical studies have demonstrated that in the presence of adenosine triphosphate (ATP) the human RAD51 (HsRAD51) recombinase can form a nucleoprotein filament (NPF) on double-stranded DNA (dsDNA) that is capable of unwrapping the nucleosomal DNA from the histone octamer (HO). Here, we have used single molecule Förster Resonance Energy Transfer (smFRET) to examine the real time nucleosome dynamics in the presence of the HsRAD51 NPF...
October 13, 2016: Nucleic Acids Research
Matthew A Richards, Thomas J Lie, Juan Zhang, Stephen W Ragsdale, John A Leigh, Nathan D Price
: Hydrogenotrophic methanogenesis occurs in multiple environments ranging from the intestinal tracts of animals to anaerobic sediments and hot springs. Energy conservation in hydrogenotrophic methanogens was long a mystery; only within the last decade, it was reported that net energy conservation for growth depends on electron bifurcation. In this work we focus on Methanococcus maripaludis, a well-studied hydrogenotrophic marine methanogen. To better understand hydrogenotrophic methanogenesis and compare it with methylotrophic methanogenesis that utilizes oxidative phosphorylation rather than electron bifurcation, we have built iMR539, a genome scale metabolic reconstruction that accounts for 539 of the 1722 protein-coding genes of M...
October 10, 2016: Journal of Bacteriology
F Gorrini, M Cazzanelli, N Bazzanella, R Edla, M Gemmi, V Cappello, J David, C Dorigoni, A Bifone, A Miotello
Nanodiamonds are the subject of active research for their potential applications in nano-magnetometry, quantum optics, bioimaging and water cleaning processes. Here, we present a novel thermodynamic model that describes a graphite-liquid-diamond route for the synthesis of nanodiamonds. Its robustness is proved via the production of nanodiamonds powders at room-temperature and standard atmospheric pressure by pulsed laser ablation of pyrolytic graphite in water. The aqueous environment provides a confinement mechanism that promotes diamond nucleation and growth, and a biologically compatible medium for suspension of nanodiamonds...
October 12, 2016: Scientific Reports
Jose Maria Carnerero, Aila Jimenez-Ruiz, Paula Margarita Castillo, Rafael Prado-Gotor
The interactions of DNA, whether long, hundred base pair chains or short-chained oligonucleotides, with ligands play a key role in the field of structural biology. Its biological activity not only depends on the thermodynamic properties of DNA-ligand complexes, but can and often is conditioned by the formation kinetics of those complexes. On the other hand, gold nanoparticles (AuNPs) have long been known to present excellent biocompatibility with biomolecules and are themselves remarkable for their structural, electronic, magnetic, optical and catalytic properties, radically different from those of their counterpart bulk materials, and which make them an important asset in multiple applications...
October 10, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Elena Ragnoni, Francesca Palombo, Ellen Green, C Peter Winlove, Mariangela Di Donato, Andrea Lapini
Elastin is the main protein to confer elasticity to biological tissues, through the formation of a hierarchical network of fibres. α-Elastin, a soluble form of the protein, is widely used in studies of the biosynthesis of human elastic tissue and exhibits coacervation in solution. This process involves the association of α-elastin molecules through a liquid-liquid phase transition, which is reversible unless the temperature is driven sufficiently high to induce the formation of insoluble aggregates. The thermodynamics of this process have attracted interest over many years and in the present work we used ultrafast nonlinear infrared spectroscopy of the amide I protein backbone vibration to resolve the secondary structural changes occurring during coacervation and probe the protein dynamics on a picosecond time scale...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
Indah Primadona, Yin-Hung Lai, Rey Y Capangpangan, Rofeamor P Obena, Mei-Chun Tseng, Ming-Feng Huang, Huan-Tsung Chang, Shiou-Ting Li, Chung-Yi Wu, Wei-Ting Chien, Chun-Cheng Lin, Yi-Sheng Wang, Yu-Ju Chen
Glycoconjugates are ubiquitously present and play a critical role in various biological processes. Due to their low stability and incredibly high degree of structural diversity, the structural characterization of glycan generally requires chemical derivatization and sophisticated instrumentation. Herein, we report a method for complicated glycan characterization in a single assay by employing 2,5-dihydroxybenzoic acid functionalized mercury telluride nanoparticles (HgTe@DHB NPs) as a dual ionization-dissociation element in matrix-assisted laser desorption/ionization mass spectrometry...
September 14, 2016: Analyst
Eun Beul Park, Kwang Jong Kim, Hui Rak Jeong, Jae Kyun Lee, Hyoung Ja Kim, Hwi Ho Lee, Ji Woong Lim, Ji-Sun Shin, Andreas Koeberle, Oliver Werz, Kyung-Tae Lee, Jae Yeol Lee
In our previous research, a novel series of phenylsulfonyl hydrazide derivatives were found to reduce LPS-induced PGE2 levels in RAW 264.7 macrophage cells via an inhibition of mPGES-1 enzyme. Recently, it was found that a regioisomeric mixture of phenylsulfonyl hydrazide was formed depending on the reaction conditions, which favor either of two regioisomers. One regioisomer corresponds to a kinetic product (7a-7c) and the other regioisomer corresponds to a thermodynamic product (8a-8c). Among them, the structure of kinetic product 7b was confirmed by measuring single X-ray crystallography...
September 29, 2016: Bioorganic & Medicinal Chemistry Letters
Marko Jusup, Tânia Sousa, Tiago Domingos, Velimir Labinac, Nina Marn, Zhen Wang, Tin Klanjšček
We review the most comprehensive metabolic theory of life existing to date. A special focus is given to the thermodynamic roots of this theory and to implications that the laws of physics-such as the conservation of mass and energy-have on all life. Both the theoretical foundations and biological applications are covered. Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work...
September 9, 2016: Physics of Life Reviews
Ana Amić, Bono Lučić, Višnja Stepanić, Zoran Marković, Svetlana Marković, Jasmina M Dimitrić Marković, Dragan Amić
Reaction energetics of the double (2H(+)/2e(-)), i.e., the first 1H(+)/1e(-) (catechol→ phenoxyl radical) and the second 1H(+)/1e(-) (phenoxyl radical→ quinone) free radical scavenging mechanisms of quercetin and its six colonic catecholic metabolites (caffeic acid, hydrocaffeic acid, homoprotocatechuic acid, protocatechuic acid, 4-methylcatechol, and catechol) were computationally studied using density functional theory, with the aim to estimate the antiradical potency of these molecules. We found that second hydrogen atom transfer (HAT) and second sequential proton loss electron transfer (SPLET) mechanisms are less energy demanding than the first ones indicating 2H(+)/2e(-) processes as inherent to catechol moiety...
March 1, 2017: Food Chemistry
Joshua J Cardiel, Daisuke Takagi, Hsieh-Fu Tsai, Amy Q Shen
Understanding the formation and instability behavior of membranes is of fundamental interest and practical relevance to various biotechnological applications and self-assembly systems. Surfactant micellar membranes serve as a simple model system when surfactant molecules self-assemble into micellar structures under flow, but observing such process in real time is a major challenge due to limitations in spatiotemporal resolutions. We use a simple T-shaped microchannel to capture the formation and flow behavior of an ionic surfactant micro-micellar-membrane (μMM) when an aqueous stream of organic salt sodium salicylate (NaSal) meets a stream of cationic surfactant cetyltrimethylammonium bromide (CTAB)...
October 4, 2016: Soft Matter
Robert P Johnson, Rukshan T Perera, Aaron M Fleming, Cynthia J Burrows, Henry S White
Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix...
September 20, 2016: Faraday Discussions
David A Quint, Ajay Gopinathan, Gregory M Grason
Motivated to understand the behavior of biological filaments interacting with membranes of various types, we employ a theoretical model for the shape and thermodynamics of intrinsically helical filaments bound to curved membranes. We show that filament-surface interactions lead to a host of nonuniform shape equilibria, in which filaments progressively unwind from their native twist with increasing surface interaction and surface curvature, ultimately adopting uniform-contact curved shapes. The latter effect is due to nonlinear coupling between elastic twist and bending of filaments on anisotropically curved surfaces such as the cylindrical surfaces considered here...
October 4, 2016: Biophysical Journal
R Delgado-Buscalioni
A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U((1))-U((0)) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials...
November 13, 2016: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Pierre Gaspard
Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization...
November 13, 2016: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Marco Deiana, Bastien Mettra, Katarzyna Matczyszyn, Delphine Pitrat, Joanna Olesiak-Banska, Cyrille Monnereau, Chantal Andraud, Marek Samoc
We report the synthesis, spectroscopy, and the DNA binding properties of a biocompatible, water-soluble, polycationic two-photon absorbing anthracenyl derivative (Ant-PIm) specifically designed for bio-related applications. Detailed insights into the Ant-PIm-DNA binding interaction are provided by using several spectroscopic approaches, including UV-VIS absorption, circular dichroism (CD), Fourier-transform infrared spectroscopy (FTIR), steady-state and time-resolved fluorescence techniques. Absorption and fluorescence quantitative data analysis show a strong Ant-PIm-duplex interaction with binding constants of: Kf = 4...
October 3, 2016: Biomacromolecules
Sanliang Ling, Maciej Gutowski
Computational results have been reported for 2'-deoxycytidine (dC), its gas phase isomers, tautomers, and their conformers, as well as for the crystalline phase. In addition to the neutral gas phase molecules, we have also considered associated radical anions and cations. The structural calculations were performed at the density functional and MP2 levels of theory. Vertical electron ionization energies and excess electron binding energies were determined using electron propagator theory. The α-anomer proved to be more stable by a fraction of kcal/mol than the biologically relevant canonical β-anomer...
October 6, 2016: Journal of Physical Chemistry. A
Silvina Cerveny, Izaskun Combarro-Palacios, Jan Swenson
Studies of protein dynamics at low temperatures are generally performed on hydrated powders and not in biologically realistic solutions of water because of water crystallization. However, here we avoid the problem of crystallization by reducing the size of the biomolecules. We have studied oligomers of the amino acid l-lysine, fully dissolved in water, and our dielectric relaxation data show that the glass transition-related dynamics of the oligomers is determined by the water dynamics, in a way similar to that previously observed for solvated proteins...
October 4, 2016: Journal of Physical Chemistry Letters
Shaveta Kanoria, William Rennie, Chaochun Liu, C Steven Carmack, Jun Lu, Ye Ding
MicroRNAs (miRNAs) are a class of endogenous short noncoding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs), which results in translational repression and/or mRNA degradation. As regulatory molecules, miRNAs are involved in many mammalian biological processes and also in the manifestation of certain human diseases. As miRNAs play central role in the regulation of gene expression, understanding miRNA-binding patterns is essential to gain an insight of miRNA mediated gene regulation and also holds promise for therapeutic applications...
2016: Methods in Molecular Biology
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