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Biological thermodynamics

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https://www.readbyqxmd.com/read/28443654/quantifying-the-self-assembly-behavior-of-anisotropic-nanoparticles-using-liquid-phase-transmission-electron-microscopy
#1
Binbin Luo, John W Smith, Zihao Ou, Qian Chen
For decades, one of the overarching objectives of self-assembly science has been to define the rules necessary to build functional, artificial materials with rich and adaptive phase behavior from the bottom-up. To this end, the computational and experimental efforts of chemists, physicists, materials scientists, and biologists alike have built a body of knowledge that spans both disciplines and length scales. Indeed, today control of self-assembly is extending even to supramolecular and molecular levels, where crystal engineering and design of porous materials are becoming exciting areas of exploration...
April 26, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28439831/predicting-functional-microrna-mrna-interactions
#2
Zixing Wang, Yin Liu
MicroRNAs (miRNAs) are small RNA molecules that play key regulatory roles in general biological processes and disease pathogenesis. These small RNA molecules interact with their target mRNAs to induce mRNA degradation and/or inhibit the translation of mRNAs into proteins. Therefore, identifying miRNA targets is an essential step to fully understand the regulatory effects of miRNAs. Here, we describe a regularized regression approach that integrates the sequence information with the miRNA and mRNA expression profiles for detecting miRNA targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28436453/functional-thermodynamics-structural-and-biological-studies-of-in-silico-identified-inhibitors-of-mycobacterium-tuberculosis-enoyl-acp-coa-reductase-enzyme
#3
Leonardo K B Martinelli, Mariane Rotta, Anne D Villela, Valnês S Rodrigues-Junior, Bruno L Abbadi, Rogério V Trindade, Guilherme O Petersen, Giuliano M Danesi, Laura R Nery, Ivani Pauli, Maria M Campos, Carla D Bonan, Osmar Norberto de Souza, Luiz A Basso, Diogenes S Santos
Novel chemotherapeutics agents are needed to kill Mycobacterium tuberculosis, the main causative agent of tuberculosis (TB). The M. tuberculosis 2-trans-enoyl-ACP(CoA) reductase enzyme (MtInhA) is the druggable bona fide target of isoniazid. New chemotypes were previously identified by two in silico approaches as potential ligands to MtInhA. The inhibition mode was determined by steady-state kinetics for seven compounds that inhibited MtInhA activity. Dissociation constant values at different temperatures were determined by protein fluorescence spectroscopy...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28435868/label-free-optical-detection-of-single-enzyme-reactant-reactions-and-associated-conformational-changes
#4
Eugene Kim, Martin D Baaske, Isabel Schuldes, Peter S Wilsch, Frank Vollmer
Monitoring the kinetics and conformational dynamics of single enzymes is crucial to better understand their biological functions because these motions and structural dynamics are usually unsynchronized among the molecules. However, detecting the enzyme-reactant interactions and associated conformational changes of the enzyme on a single-molecule basis remains as a challenge to established optical techniques because of the commonly required labeling of the reactants or the enzyme itself. The labeling process is usually nontrivial, and the labels themselves might skew the physical properties of the enzyme...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28432354/structural-and-functional-analysis-of-lysozyme-after-treatment-with-dielectric-barrier-discharge-plasma-and-atmospheric-pressure-plasma-jet
#5
Sooho Choi, Pankaj Attri, Inhwan Lee, Jeongmin Oh, Ji-Hye Yun, Ji Hoon Park, Eun Ha Choi, Weontae Lee
The variation in the biological function of proteins plays an important role in plasma medicine and sterilization. Several non-thermal plasma sources with different feeding gases are used worldwide for plasma treatment, including dielectric barrier discharge (DBD) and atmospheric-pressure plasma jet (APPJ) as the most commonly used sources. Therefore, in the present work, we used both DBD and APPJ plasma sources with N2 and air as feeding gases to evaluate the effects on the structural, thermodynamic, and activity changes of enzymes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431312/melatonin-charge-transfer-complex-with-2-3-dichloro-5-6-dicyano-1-4-benzoquinone-molecular-structure-dft-studies-thermal-analyses-evaluation-of-biological-activity-and-utility-for-determination-of-melatonin-in-pure-and-dosage-forms
#6
Gehad G Mohamed, Maher M Hamed, Nadia G Zaki, Mohamed M Abdou, Marwa El-Badry Mohamed, Abanoub Mosaad Abdallah
A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL(-1) ML. The solid form of the CT complex was structurally characterized by means of different spectral methods...
April 4, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28427899/energy-and-information-flows-in-biological-systems-bioenergy-transduction-of-v1-atpase-rotary-motor-and-dynamics-of-thermodynamic-entropy-in-information-flows
#7
REVIEW
Ichiro Yamato, Takeshi Murata, Andrei Khrennikov
We classify research fields in biology with respect to flows of materials, energy, and information. We investigate energy transducing mechanisms in biology, using as a representative the typical molecular rotary motor V1-ATPase from a bacterium Enterococcus hirae. The structures of several intermediates of the rotary motor are described and the molecular mechanism of the motor converting chemical energy into mechanical energy is discussed. Comments and considerations on the information flows in biology, especially on the thermodynamic entropy in quantum physical and biological systems, are presented in section 3 in a biologist friendly manner...
April 17, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28425930/the-peculiar-glycolytic-pathway-in-hyperthermophylic-archaea-understanding-its-whims-by-experimentation-in-silico
#8
Yanfei Zhang, Theresa Kouril, Jacky L Snoep, Bettina Siebers, Matteo Barberis, Hans V Westerhoff
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28421749/design-of-multi-functional-nanogate-in-response-to-multiple-external-stimuli-using-amphiphilic-diblock-copolymer
#9
Kai Huang, Igal Szleifer
Nature uses the interplay between hydrophobic and electrostatic interactions of disordered proteins to orchestrate complicated molecular gate such as the nuclear pore complex to control the transport of biological masses. Inspired by nature, we here theoretically show that well-defined gate shape, sensitive response to pH and salt concentration, and selectivity in cargo transport can be simultaneously achieved by grafting amphiphilic diblock copolymers made of sequence-controlled hydrophobic and ionizable monomers on the inner surface of solid-state nanopore...
April 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28419089/erroneous-energy-generating-cycles-in-published-genome-scale-metabolic-networks-identification-and-removal
#10
Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J Lercher
Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database...
April 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28414224/carbanion-translocations-via-intramolecular-proton-transfers-a%C3%A2-quantum-chemical-study
#11
Yi Wang, Pei-Jun Cai, Zhi-Xiang Yu
Intramolecular proton transfers are important processes in chemical reactions and biological transformations. In particular, the translocation of reactive carbanion centers can be achieved through 1,n-proton transfer in either a direct or an assisted manner (via the protonation/deprotonation mechanism). Despite some mechanistic investigations on proton transfers within zwitterionic species, no guiding principles have been summarized for carbanion-induced intramolecular proton transfers. Herein, we report our quantum chemical study on the carbanion translocations via intramolecular proton transfers...
April 17, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28412570/ecology-science-or-philately-an-interdisciplinary-analysis-of-sustainability-by-exploring-if-it-is-possible-to-get-more-and-more-information-by-reducing-collateral-environmental-damages
#12
Ricardo A Rodríguez, Rodrigo Riera, Juan D Delgado
We herein explore the connections between the current condition of ecology concerning to sustainable development and the statement of Rutherford regarding the importance of physics to understand sustainability and biological conservation. The recent emergence of organic biophysics of ecosystems (OBEC) may constitute a feasible alternative to fill the gap between conventional ecological thinking and physics, especially thermodynamics. However, our comprehension of sustainability and biological conservation is influenced by the interactions between information and entropy, because we tend to exclude parts of the biosphere as well as their relationships among them...
April 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28401569/influences-on-viral-replication-and-sensitivity-to-gls4-a-hap-compound-of-naturally-occurring-t109-v124-mutations-in-hepatitis-b-virus-core-protein
#13
Jianghua Wang, Haiying Zhang, Yingjun Zhang, Dong Jiang, Jing Li, Siegfried Goldmann, Qingyun Ren, Ran Fei, Xueyan Wang, Lai Wei
Heteroaryldihydropyrimidine (HAP) compounds inhibit HBV replication by binding to a hydrophobic pocket at the interface between hepatitis B virus core protein (HBcAg) dimer, which interrupts capsid assembly by changing the kinetics and thermodynamics during this process. Structure biological studies have identified several amino acids in HBcAg crucial for compound binding. Here we investigated the polymorphisms of T109 and V124 amino acids in HBV sequences submitted to GenBank database. Naturally occurring T109 and V124 and/or possible compensatory mutations in neighbored amino acids were introduced into HBV-expressing plasmids...
April 12, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28395770/chiral-recognition-and-determination-of-enantiomeric-excess-by-mass-spectrometry-a-review
#14
REVIEW
Xiangying Yu, Zhong-Ping Yao
Chiral analysis is of great importance to fundamental and applied research in chemical, biological and pharmaceutical sciences. Due to the superiority of mass spectrometry (MS) over other analytical methods in terms of speed, specificity and sensitivity, chiral analysis by MS has attracted much interest in recent years. Chiral analysis by MS typically involves introduction of a chiral selector to form diastereomers with analyte enantiomers, and comparison of the behaviors of diastereomers in MS. Chiral differentiation can be achieved by comparing the relative abundances of diastereomers, the thermodynamic or kinetic constants of ion-molecule reactions of diastereomers in the gas phase, the dissociation of diastereomers in MS/MS, or the mobility of diastereomers in ion mobility mass spectrometry...
May 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28394885/mechanistic-insights-into-energy-conservation-by-flavin-based-electron-bifurcation
#15
Carolyn E Lubner, David P Jennings, David W Mulder, Gerrit J Schut, Oleg A Zadvornyy, John P Hoben, Monika Tokmina-Lukaszewska, Luke Berry, Diep M Nguyen, Gina L Lipscomb, Brian Bothner, Anne K Jones, Anne-Frances Miller, Paul W King, Michael W W Adams, John W Peters
The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction...
April 10, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28389512/theoretical-and-biological-evaluation-of-the-link-between-low-exercise-capacity-and-disease-risk
#16
Lauren Gerard Koch, Steven L Britton
Large-scale epidemiological studies show that low exercise capacity is the highest risk factor for all-cause morbidity and mortality relative to other conditions including diabetes, hypertension, and obesity. This led us to formulate the energy transfer hypothesis (ETH): Variation in capacity for energy transfer is the central mechanistic determinant of the divide between disease and health. As a test of this hypothesis, we predicted that two-way selective breeding of genetically heterogeneous rats for low and high intrinsic treadmill running capacity (a surrogate for energy transfer) would also produce rats that differ for disease risks...
April 7, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28388089/critical-comparison-of-biomembrane-force-fields-protein-lipid-interactions-at-the-membrane-interface
#17
Angelica Sandoval-Perez, Kristyna Pluhackova, Rainer A Böckmann
Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e...
April 20, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28387474/growth-of-silver-nanowires-from-controlled-silver-chloride-seeds-and-their-application-for-fluorescence-enhancement-based-on-localized-surface-plasmon-resonance
#18
Sunwoong Bae, Hyeji Han, Jin Gook Bae, Eun Yeol Lee, Sang Hyuk Im, Do Hyun Kim, Tae Seok Seo
A "Polyol" method has granted low-cost and facile process-controllability for silver-nanowire (Ag-NW) synthesis. Although homogenous and heterogeneous nucleation and growth during Ag-NW synthesis are possible using polyol methods, heterogeneous nucleation and growth of Ag NW guarantees highly selective growth of nanostructures using silver chloride (AgCl) seeds, which provides a stable source of chloride ions (Cl-) and thermodynamic reversibility. In this paper, a microdroplet has been adopted to synthesize uniform AgCl seeds with different diameter that are used for seed-mediated Ag-NW synthesis...
April 7, 2017: Small
https://www.readbyqxmd.com/read/28386073/modelling-the-three-dimensional-structure-of-the-right-terminal-domain-of-pospiviroids
#19
Gerhard Steger
Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28380044/mechanics-thermodynamics-and-kinetics-of-ligand-binding-to-biopolymers
#20
Javier Jarillo, José A Morín, Elena Beltrán-Heredia, Juan P G Villaluenga, Borja Ibarra, Francisco J Cao
Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i...
2017: PloS One
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