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Biological thermodynamics

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https://www.readbyqxmd.com/read/28094993/the-biophysics-of-artificially-expanded-genetic-information-systems-thermodynamics-of-dna-duplexes-containing-matches-and-mismatches-involving-2-amino-3-nitropyridin-6-one-z-and-imidazo-1-2-a-1-3-5-triazin-4-8h-one-p
#1
Xiaoyu Wang, Shuichi Hoshika, Raymond J Peterson, Myong-Jung Kim, Steven A Benner, Jason D Kahn
Synthetic nucleobases presenting non-Watson Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent of the standard A:T and G:C pairs. The pair between 2-amino-3-nitropyridin-6-one 2'-deoxyriboside (presenting a {donor-donor-acceptor} hydrogen bonding pattern on the Watson-Crick face of the small component, trivially designated Z) and imidazo[1,2-a]-1,3,5-triazin-4(8H)one 2'-deoxyriboside (presenting an {acceptor-acceptor-donor} hydrogen bonding pattern on the large component, trivially designated P) is one of these extra pairs for which a substantial amount of molecular biology has been developed...
January 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28080028/a-grand-avenue-to-au-nanocluster-electrochemiluminescence
#2
Mahdi Hesari, Zhifeng Ding
In most cases of semiconductor quantum dot nanocrystals, the inherent optical and electrochemical properties of these interesting nanomaterials do not translate into expected efficient electrochemiluminescence or electrogenerated chemiluminescence (ECL) because of the surface-state induction effect. Thus, their low ECL efficiencies, while very interesting to explore, limit their applications. As their electrochemistry is not well-defined, insight into their ECL mechanistic details is also limited. Alternatively, gold nanoclusters possess monodispersed sizes with atomic precision, low and well defined HOMO-LUMO energy gaps, and stable optical and electrochemical properties that make them suitable for potential ECL applications...
January 12, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28074209/cu-i-and-ag-i-complex-formation-with-the-hydrophilic-phosphine-1-3-5-triaza-7-phosphadamantane-in-different-ionic-media-how-to-estimate-the-effect-of-a-complexing-medium
#3
Francesco Endrizzi, Plinio Di Bernardo, Pier Luigi Zanonato, Francesco Tisato, Marina Porchia, Abdirisak Ahmed Isse, Andrea Melchior, Marilena Tolazzi
The complexes of Cu(i) and Ag(i) with 1,3,5-triaza-7-phosphadamantane (PTA) are currently studied for their potential clinical use as anticancer agents, given the cytotoxicity they exhibited in vitro towards a panel of several human tumor cell lines. These metallodrugs are prepared in the form of [M(PTA)4](+) (M = Cu(+), Ag(+)) compounds and dissolved in physiological solution for their administration. However, the nature of the species involved in the cytotoxic activity of the compounds is often unknown. In the present work, the thermodynamics of formation of the complexes of Cu(i) and Ag(i) with PTA in aqueous solution is investigated by means of potentiometric, spectrophotometric and microcalorimetric methods...
January 11, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28067274/computational-and-biochemical-characterization-of-two-partially-overlapping-interfaces-and-multiple-weak-affinity-k-ras-dimers
#4
Priyanka Prakash, Abdallah Sayyed-Ahmad, Kwang-Jin Cho, Drew M Dolino, Wei Chen, Hongyang Li, Barry J Grant, John F Hancock, Alemayehu A Gorfe
Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060517/thermodynamics-of-helix-coil-transitions-of-polyalanine-in-open-carbon-nanotubes
#5
Dylan Suvlu, Seneviratne Samaratunga, Dave Thirumalai, Jayendran C Rasaiah
Understanding structure formation in polypeptide chains and synthetic polymers encapsulated in pores is important in biology and no technology. We present replica exchange molecular dynamics studies of the phase diagram for alpha-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters, which surprisingly is comparable to the width of the ribosome tunnel. Increasing the hydrophobicity enhances helicity in the NT...
January 6, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28055193/model-of-the-mitoneet-2fe-2s-cluster-shows-proton-coupled-electron-transfer
#6
Marie Bergner, Sebastian Dechert, Serhiy Demeshko, Claudia Kupper, James M Mayer, Franc Meyer
MitoNEET is an outer membrane protein whose exact function remains unclear, though a role of this protein in redox and iron sensing as well as in controlling maximum mitochondrial respiratory rates has been discussed. It was shown to contain a redox active and acid labile [2Fe-2S] cluster which is ligated by one histidine and three cysteine residues. Herein we present the first synthetic analogue with biomimetic {SN/S2} ligation which could be structurally characterized in its diferric form, 5(2-). In addition to being a high fidelity structural model for the biological cofactor, the complex is shown to mediate proton coupled electron transfer (PCET) at the {SN} ligated site, pointing at a potential functional role of the enzyme's unique His ligand...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28053085/inhibition-of-mammalian-glycoprotein-ykl-40-identification-of-the-physiological-ligand
#7
Abhishek A Kognole, Christina M Payne
YKL-40 is a mammalian glycoprotein associated with progression, severity, and prognosis of chronic inflammatory diseases and a multitude of cancers. Despite this well-documented association, identification of the lectin's physiological ligand, and accordingly, biological function, has proven experimentally difficult. YKL-40 has been shown to bind chito-oligosaccharides; however, the production of chitin by the human body has not yet been documented. Possible alternative ligands include proteoglycans, polysaccharides, and fibers like collagen, all of which makeup the extracellular matrix...
January 4, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28045501/the-advancement-of-the-emerging-field-of-rna-nanotechnology
#8
Daniel Jasinski, Farzin Haque, Daniel W Binzel, Peixuan Guo
The field of RNA nanotechnology has advanced rapidly during the last decade. A variety of programmable RNA nanoparticles with defined shape, size, and stoichiometry have been developed for diverse applications in nanobiotechnology. The rising popularity of RNA nanoparticles is due to a number of factors: (1) Removing the concern of RNA degradation in vitro and in vivo by introducing chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; (2) Confirming the concept that RNA displays very high thermodynamic stability and is suitable for in vivo trafficking and other applications; (3) Obtaining the knowledge to tune the immunogenic properties of synthetic RNA constructs for in vivo applications; (4) Increased understanding of the 4D structure and intermolecular interaction of RNA molecules; (5) Developing methods to control shape, size and stoichiometry of RNA nanoparticles; (6) Increasing knowledge of unique regulation and processing functions of RNA in cells; (7) Decreasing cost of RNA production by biological and chemical synthesis; and (8) Proving the concept that RNA is a safe and specific therapeutic modality for cancer and other diseases with little or no accumulation in vital organs...
January 3, 2017: ACS Nano
https://www.readbyqxmd.com/read/28024603/physicochemical-characterization-of-in-situ-drug-polymer-nanocomplex-formed-between-zwitterionic-drug-and-ionomeric-material-in-aqueous-solution
#9
Constain H Salamanca, Duvan F Castillo, Juan D Villada, Gustavo R Rivera
Biocompatible polymeric materials with the potential to form functional structures, in association with different therapeutic molecules, in physiological media, represent a great potential for biological and pharmaceutical applications. Therefore, here the formation of a nano-complex between a synthetic cationic polymer and model drug (ampicillin trihydrate) was studied. The formed complex was characterized by size and zeta potential measurements, using dynamic light scattering and capillary electrophoresis...
March 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28013501/calorimetry-methods-to-study-membrane-interactions-and-perturbations-induced-by-antimicrobial-host-defense-peptides
#10
Mauricio Arias, Elmar J Prenner, Hans J Vogel
Biological membranes play an important role in determining the activity and selectivity of antimicrobial host defense peptides (AMPs). Several biophysical methods have been developed to study the interactions of AMPs with biological membranes. Isothermal titration calorimetry and differential scanning calorimetry (ITC and DSC, respectively) are powerful techniques as they provide a unique label-free approach. ITC allows for a complete thermodynamic characterization of the interactions between AMPs and membranes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28001043/biological-insights-of-the-dopaminergic-stabilizer-acr16-at-the-binding-pocket-of-dopamine-d2-receptor
#11
Ramin Ekhteiari Salmas, Philip Seeman, Busecan Aksoydan, Matthias Stein, Mine Yurtsever, Serdar Durdagi
The dopamine D2 receptor (D2R) plays an important part in the human central nervous system and is considered to be a focal target of antipsychotic agents. It is structurally modeled in active and inactive states, in which homo-dimerization reaction of the D2R monomers is also applied. The ASP2314 (also known as ACR16) ligand, a D2R stabilizer, is used in tests to evaluate how dimerization and conformational changes may alter the ligand binding space and to provide information on alterations in inhibitory mechanisms upon activation...
December 21, 2016: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/27999184/chiral-twist-drives-raft-formation-and-organization-in-membranes-composed-of-rod-like-particles
#12
Louis Kang, Tom C Lubensky
Lipid rafts are hypothesized to facilitate protein interaction, tension regulation, and trafficking in biological membranes, but the mechanisms responsible for their formation and maintenance are not clear. Insights into many other condensed matter phenomena have come from colloidal systems, whose micron-scale particles mimic basic properties of atoms and molecules but permit dynamic visualization with single-particle resolution. Recently, experiments showed that bidisperse mixtures of filamentous viruses can self-assemble into colloidal monolayers with thermodynamically stable rafts exhibiting chiral structure and repulsive interactions...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27994029/applicability-of-a-computational-design-approach-for-synthetic-riboswitches
#13
Gesine Domin, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F Stadler, Mario Mörl
Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand-dependent transcription termination in Escherichia coli Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers...
December 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27993002/recycling-in-asymmetric-catalysis
#14
Christina Moberg
Cyclic reaction networks consisting of an enantioselective product-forming step and a reverse reaction of the undesired enantiomer back to starting reactant are important for the generation of compounds with high enantiomeric purity. In order to avoid an equilibrium racemic state, a unidirectional cyclic process where product formation and regeneration of starting reactant proceed through different mechanistic pathways is required. Such processes must necessarily include a thermodynamically unfavorable step, since the product of the forward reaction is the reactant of the reverse reaction and vice versa...
December 20, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27992421/selective-nitrogen-capture-by-porous-hybrid-materials-containing-accessible-transition-metal-ion-sites
#15
Ji Woong Yoon, Hyunju Chang, Seung-Joon Lee, Young Kyu Hwang, Do-Young Hong, Su-Kyung Lee, Ji Sun Lee, Seunghun Jang, Tae-Ung Yoon, Kijeong Kwac, Yousung Jung, Renjith S Pillai, Florian Faucher, Alexandre Vimont, Marco Daturi, Gérard Férey, Christian Serre, Guillaume Maurin, Youn-Sang Bae, Jong-San Chang
Selective dinitrogen binding to transition metal ions mainly covers two strategic domains: biological nitrogen fixation catalysed by metalloenzyme nitrogenases, and adsorptive purification of natural gas and air. Many transition metal-dinitrogen complexes have been envisaged for biomimetic nitrogen fixation to produce ammonia. Inspired by this concept, here we report mesoporous metal-organic framework materials containing accessible Cr(III) sites, able to thermodynamically capture N2 over CH4 and O2. This fundamental study integrating advanced experimental and computational tools confirmed that the separation mechanism for both N2/CH4 and N2/O2 gas mixtures is driven by the presence of these unsaturated Cr(III) sites that allows a much stronger binding of N2 over the two other gases...
December 19, 2016: Nature Materials
https://www.readbyqxmd.com/read/27989191/determinants-of-fe-2-over-m-2-m-mg-mn-zn-selectivity-in-non-heme-iron-proteins
#16
Todor Dudev, Valia Nikolova
Iron cations are indispensable players in a number of vital biological processes such as respiration, cell division, nitrogen fixation, oxygen transport, nucleotide synthesis, oxidant protection, O2 activation in the metabolism of various organic substrates, gene regulation, and protein structure stabilization. The basic mechanisms and factors governing the competition between Fe(2+) and other metal species from the cellular fluids such as Mg(2+), Mn(2+), and Zn(2+) are, however, not well understood, and several outstanding questions remain...
December 19, 2016: Inorganic Chemistry
https://www.readbyqxmd.com/read/27986633/unraveling-the-interaction-of-hemoglobin-with-a-biocompatible-and-cleavable-oxy-diester-functionalized-gemini-surfactant
#17
Mohd Akram, Sana Anwar, Imtiyaz Ahmad Bhat, Kabir-Ud-Din
Surfactant-protein mixtures have attracted considerable research interest in recent years at the interface of chemical biology and medicinal chemistry. Herein, the interaction between a green gemini surfactant (C16-E2O-C16) and a redox protein hemoglobin was examined through a series of in vitro experimental techniques with an attempt to provide a comprehensive knowledge of the surfactant-protein binding interactions. Quantitative appraisal of the fluorescence/CV data showed that the binding of C16-E2O-C16 to Hb leads to the formation of thermodynamically favorable non-covalent adduct with 1:1 stoichiometry...
December 14, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27984146/deciphering-the-interaction-of-bovine-heart-cystatin-with-zno-nanoparticles-spectroscopic-and-thermodynamic-approach
#18
Aamir Sohail, Mohd Faraz, Hussain Arif, Sheraz Ahmad Bhat, Azad Alam Siddiqui, Bilqees Bano
ZnO-NPs have been widely used in biomedical fields such as therapeutics, cellular imaging, and drug delivery. However, the risk of exposure of nanoparticles to the biological system is not well understood. Nanoparticle-protein interaction is pivotal to understand their biological behavior and predict nanoparticle toxicity that is crucial for its safer applications. In the present study zinc oxide nanoparticles (ZnO-NPs) were synthesized and subjected to interact with buffalo heart cystatin (BHC), purified from buffalo heart, to assess the effect(s) of ZnO-NPs on the structure and function of BHC...
February 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27982621/template-directed-copolymerization-random-walks-along-disordered-tracks-and-fractals
#19
Pierre Gaspard
In biology, template-directed copolymerization is the fundamental mechanism responsible for the synthesis of DNA, RNA, and proteins. More than 50 years have passed since the discovery of DNA structure and its role in coding genetic information. Yet, the kinetics and thermodynamics of information processing in DNA replication, transcription, and translation remain poorly understood. Challenging issues are the facts that DNA or RNA sequences constitute disordered media for the motion of polymerases or ribosomes while errors occur in copying the template...
December 2, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27967118/vibration-induced-coherence-enhancement-of-the-performance-of-a-biological-quantum-heat-engine
#20
Hong-Bin Chen, Pin-Yi Chiu, Yueh-Nan Chen
Photosynthesis has been a long-standing research interest due to its fundamental importance. Recently, studies on photosynthesis processes also have inspired attention from a thermodynamical aspect when considering photosynthetic apparatuses as biological quantum heat engines. Quantum coherence is shown to play a crucial role in enhancing the performance of these quantum heat engines. Based on the experimentally reported structure, we propose a quantum heat engine model with a non-Markovian vibrational mode...
November 2016: Physical Review. E
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