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Biological thermodynamics

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https://www.readbyqxmd.com/read/28540680/computational-prediction-of-microrna-target-genes-target-prediction-databases-and-web-resources
#1
Justin T Roberts, Glen M Borchert
MicroRNA (miRNA) mediated silencing and repression of mRNA molecules requires complementary base pairing between the "seed" region of the miRNA and the "seed match" region of target mRNAs. While this mechanism is fairly well understood, accurate prediction of valid miRNA targets remains challenging due to factors such as imperfect sequence specificity, target site availability, and the thermodynamic stability of the mRNA structure itself. As knowledge of what genes are being targeted by each miRNA is arguably the most important facet of miRNA biology, many approaches have been developed to address the need for reliable prediction and ranking of putative targets, with most using a combination of various strategies such as evolutionary conservation, statistical inference, and distinct features of the target sequences themselves...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540040/dna-secondary-structure-formation-by-dna-shuffling-of-the-conserved-domains-of-the-cry-protein-of-bacillus-thuringiensis
#2
Efrain H Pinzon, Daniel A Sierra, Miguel O Suarez, Sergio Orduz, Alvaro M Florez
BACKGROUND: The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy [Formula: see text] were determined by an in silico analysis using different experimental DNA shuffling scenarios...
2017: BMC Biophysics
https://www.readbyqxmd.com/read/28538167/understanding-the-bioavailability-and-sequestration-of-different-metal-cations-in-the-presence-of-a-biodegradable-chelant-mgda-in-biological-fluids-and-natural-waters
#3
Clemente Bretti, Rosalia Maria Cigala, Concetta De Stefano, Gabriele Lando, Silvio Sammartano
Thermodynamic information about the metal-ligand interaction between Fe(3+), Zn(2+), Cu(2+) and Sn(2+), and a biodegradable ligand as MGDA is reported. The speciation scheme was obtained by means of potentiometric measurements and isothermal titration calorimetry (to determine enthalpy changes) in NaCl medium. The formation of the ML and MLOH species was evidenced for all the metal cations, and for Fe(3+) also the ML2 and ML(OH)2 were found. The relative stability, for the ML species, follows the order: Sn(2+) > Fe(3+) > Cu(2+) > Zn(2+)...
May 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28537604/multiscale-simulations-for-understanding-the-evolution-and-mechanism-of-hierarchical-peptide-self-assembly
#4
Chengqian Yuan, Shukun Li, Qianli Zou, Ying Ren, Xuehai Yan
Hierarchical self-assembly, abundant in biological systems, has been explored as an effective bottom-up method to fabricate highly ordered functional superstructures from elemental building units. Biomolecules, especially short peptides consisting of several amino acids, are a type of elegant building blocks due to their advantages of structural, mechanical, and functional diversity as well as high biocompatibility and biodegradability. The hierarchical self-assembly of peptides is a spontaneous process spanning multiple time and length scales under certain thermodynamics and kinetics conditions...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28537305/study-of-antiradical-mechanisms-with-dihydroxybenzenes-using-reaction-force-and-reaction-electronic-flux
#5
Cristina Ortega-Moo, Rocio Durán, Bárbara Herrera, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Rubicelia Vargas
Phenolic compounds represent an important category of antioxidants because they help inhibit the oxidation process of organic compounds, while also acting as antiradicals in many biological processes. In this work, we analyze the transfer mechanisms for a set of catechols and resorcinols of a single electron, proton and hydrogen, with the radical peroxyl (˙OOH) and with different electron withdrawing and donating groups as substituents. By using the M05-2X exchange correlation functional within the Density Functional Theory framework combined with the 6-311++G(d,p) basis set, we were able to compute the Gibbs free energies for all mechanisms and compounds...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28528093/kinetic-and-thermodynamic-compensation-a-current-and-practical-review-for-foods
#6
REVIEW
Alfonso Garvín, Raquel Ibarz, Albert Ibarz
Kinetic and thermodynamic compensations have been reported in many chemical, physical, biological and food processes. Kinetic compensation can be found for any process and when it takes place, it gives information about the reaction mechanism and whether the reaction is controlled by enthalpy or entropy. It consists of the linear relationship between the logarithm of the frequency factor (lnk0) and the activation energy (Ea), both previously obtained from the Arrhenius equation for different values of an environmental variable (e...
June 2017: Food Research International
https://www.readbyqxmd.com/read/28518057/on-the-mechanistic-nature-of-epistasis-in-a-canonical-cis-regulatory-element
#7
Mato Lagator, Tiago Paixao, Nick Barton, Jonathan P Bollback, Călin C Guet
Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites...
May 18, 2017: ELife
https://www.readbyqxmd.com/read/28515874/universal-expressions-of-population-change-by-the-price-equation-natural-selection-information-and-maximum-entropy-production
#8
Steven A Frank
The Price equation shows the unity between the fundamental expressions of change in biology, in information and entropy descriptions of populations, and in aspects of thermodynamics. The Price equation partitions the change in the average value of a metric between two populations. A population may be composed of organisms or particles or any members of a set to which we can assign probabilities. A metric may be biological fitness or physical energy or the output of an arbitrarily complicated function that assigns quantitative values to members of the population...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28510440/fundamental-characterization-of-the-micellar-self-assembly-of-sophorolipid-esters
#9
Amanda Koh, Katherine Todd, Ezekiel Sherbourne, Richard A Gross
Surfactants are ubiquitous constituents of commercial and biological systems that function based on complex structure-dependent interactions. Sophorolipid (SL) n-alkyl esters (SL-esters) comprise a group of modified naturally derived glycolipids from Candida bombicola. Herein, micellar self-assembly behavior as a function of SL-ester chain length was studied. Surface tensions as low as 31.2 mN/m and critical micelle concentrations (CMCs) as low as 1.1µM were attained for diacetylated SL-decyl ester (dASL-DE) and SL-octyl ester, respectively...
May 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28510051/proteins-in-binary-solvents
#10
REVIEW
Francesco Spinozzi, Paolo Mariani, Maria Grazia Ortore
Proteins in living organisms exist in complex aqueous solutions or embedded in membranes. In solution, proteins are surrounded by a tightly bound hydration layer, which is more ordered and less mobile than bulk water. As a consequence, water plays a major role in controlling protein structure stability, conformational flexibility, dynamics, and functionality, but it also appears that protein surface regulates the structuring of the surrounding water. The presence of cosolvents can modify the hydration layer characteristics and then the whole protein structural and dynamical properties...
June 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28509549/heterogeneous-backbone-foldamer-mimics-of-zinc-finger-tertiary-structure
#11
Kelly L George, W Seth Horne
A variety of oligomeric backbones with compositions deviating from biomacromolecules can fold in defined ways. Termed "foldamers," these agents have diverse potential applications. A number of protein-inspired secondary structures (e.g., helices, sheets) have been produced from unnatural backbones, yet examples of tertiary folds combining several secondary structural elements in a single entity are rare. One promising strategy to address this challenge is the systematic backbone alteration of natural protein sequences, through which a subset of the side chains is displayed on an unnatural building block to generate a heterogeneous backbone...
May 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28508129/development-and-characterization-of-magnetite-poly-butylcyanoacrylate-nanoparticles-for-magnetic-targeted-delivery-of-cancer-drugs
#12
Margarita López-Viota, Mazen M El-Hammadi, Laura Cabeza, José Prados, Consolación Melguizo, M Adolfina Ruiz Martinez, José L Arias, Ángel V Delgado
A great attention is presently paid to the design of drug delivery vehicles based on surface-modified magnetic nanoparticles. They can, in principle, be directed to a desired target area for releasing their drug payload, a process triggered by pH, temperature, radiation, or even magnetic field. To this, the possibility of forming part of diagnostic tools by enhanced magnetic resonance imaging or that of further treatment by magnetic hyperthermia can be added. Bare particles are rapidly eliminated from the bloodstream by the phagocyte mononuclear system, leading to short biological half-life...
May 15, 2017: AAPS PharmSciTech
https://www.readbyqxmd.com/read/28505838/correlations-induced-by-depressing-synapses-in-critically-self-organized-networks-with-quenched-dynamics
#13
João Guilherme Ferreira Campos, Ariadne de Andrade Costa, Mauro Copelli, Osame Kinouchi
In a recent work, mean-field analysis and computer simulations were employed to analyze critical self-organization in networks of excitable cellular automata where randomly chosen synapses in the network were depressed after each spike (the so-called annealed dynamics). Calculations agree with simulations of the annealed version, showing that the nominal branching ratio σ converges to unity in the thermodynamic limit, as expected of a self-organized critical system. However, the question remains whether the same results apply to the biological case where only the synapses of firing neurons are depressed (the so-called quenched dynamics)...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28497967/interactions-of-metal-based-and-ligand-based-electronic-spins-in-neutral-tripyrrindione-%C3%AF-dimers
#14
Ritika Gautam, Andrei V Astashkin, Tsuhen M Chang, Jason Shearer, Elisa Tomat
The ability of tetrapyrrolic macrocycles to stabilize unpaired electrons and engage in π-π interactions is essential for many electron-transfer processes in biology and materials engineering. Herein, we demonstrate that the formation of π dimers is recapitulated in complexes of a linear tripyrrolic analogue of naturally occurring pigments derived from heme decomposition. Hexaethyltripyrrindione (H3TD1) coordinates divalent transition metals (i.e., Pd, Cu, Ni) as a stable dianionic radical and was recently described as a robust redox-active ligand...
May 12, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28497330/development-of-nanoemulsion-from-vitex-negundo-l-essential-oil-and-their-efficacy-of-antioxidant-antimicrobial-and-larvicidal-activities-aedes-aegypti-l
#15
Sundararajan Balasubramani, Thamaraiselvi Rajendhiran, Anil Kumar Moola, Ranjitha Kumari Bollipo Diana
It is believed that nanoemulsions were emerged as a promising candidate to improve the qualities of natural essential oil towards antimicrobial and insecticidal applications. In the present study, we have focused on the encapsulation of Vitex negundo L. leaf essential oil using Polysorbate80 for its different biological activities including antioxidant, bactericidal and larvicidal activity against dengue fever vector Aedes aegypti L. Initially, the nanoemulsion was prepared by low energy method and droplet size of the formulated nanoemulsion was characterized by using Dynamic Light Scattering analysis...
May 11, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28497135/unscrambling-micro-solvation-of-cooh-and-nh-groups-in-neat-dimethyl-sulfoxide-insights-from-1-h-nmr-spectroscopy-and-computational-studies
#16
Panteleimon G Takis, Konstantinos D Papavasileiou, Loukas D Peristeras, Georgios C Boulougouris, Vasilios S Melissas, Anastassios N Troganis
Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via(1)H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i...
May 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28490602/processes-on-the-emergent-landscapes-of-biochemical-reaction-networks-and-heterogeneous-cell-population-dynamics-differentiation-in-living-matters
#17
REVIEW
Sui Huang, Fangting Li, Joseph X Zhou, Hong Qian
The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat...
May 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28490061/the-inclusion-complex-of-oxyresveratrol-in-modified-cyclodextrins-a-thermodynamic-structural-physicochemical-fluorescent-and-computational-study
#18
Adrián Matencio, Francisco García-Carmona, José Manuel López-Nicolás
The interaction between oxyresveratrol (a type of stilbene with high biological activity) and modified cyclodextrins (CDs) was studied. Using HPLC-RP, was seen to form a 1:1 complex with all the CDs tested. The best CD in this respect was MβCD (KF=606.65±30.18M(-1)), the complexation showing a strong dependence on pH and temperature: The complexation constant (KF) decreased as the pH and temperature increased. The thermodynamic parameters studied (ΔH°, ΔS° and ΔG°) showed negative entropy, enthalpy and Gibbs free energy change at 25°C...
October 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28489408/thermodynamics-and-mechanisms-of-the-interactions-between-ultra-small-fluorescent-gold-nanoclusters-and-human-serum-albumin-%C3%AE-globulins-and-transferrin-a-spectroscopic-approach
#19
Miao-Miao Yin, Ping Dong, Wen-Qi Chen, Shi-Ping Xu, Liyun Yang, Feng-Lei Jiang, Yi Liu
Noble metal nanoclusters (NCs) show great promise as nanoprobes for bioanalysis and cellular imaging in biological applications due to ultra-small size, good photophysical properties and excellent biocompatibility. In order to achieve a comprehensive understanding of possible biological implications, a series of spectroscopic measurements were conducted under different temperatures to investigate the interactions of Au NCs (~1.7 nm) with three model plasmatic proteins (human serum albumin (HSA), γ-globulins and transferrin)...
May 10, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28487761/how-and-why-kinetics-thermodynamics-and-chemistry-induce-the-logic-of-biological-evolution
#20
Addy Pross, Robert Pascal
Thermodynamic stability, as expressed by the Second Law, generally constitutes the driving force for chemical assembly processes. Yet, somehow, within the living world most self-organisation processes appear to challenge this fundamental rule. Even though the Second Law remains an inescapable constraint, under energy-fuelled, far-from-equilibrium conditions, populations of chemical systems capable of exponential growth can manifest another kind of stability, dynamic kinetic stability (DKS). It is this stability kind based on time/persistence, rather than on free energy, that offers a basis for understanding the evolutionary process...
2017: Beilstein Journal of Organic Chemistry
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