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Biological thermodynamics

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https://www.readbyqxmd.com/read/28742941/solid-state-transformation-of-amorphous-calcium-carbonate-to-aragonite-captured-by-cryotem
#1
Jessica Mary Walker, Bartosz Marzec, Fabio Nudelman
Early stage reaction mechanisms for aragonite promoting systems are relatively unknown, compared to the more thermodynamically stable calcium carbonate polymorph, calcite. Using cryoTEM and SEM, we identified the early reaction stages taking place during aragonite formation in a highly supersaturated solution using an alcohol-water solvent, and described an overall particle attachment growth mechanism for the system. We provide the first evidence for the solid-state transformation of amorphous calcium carbonate to aragonite, demonstrating the co-existence of both amorphous and crystalline material within the same aragonite needle...
July 25, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28739107/hydrostatic-pressure-and-the-experimental-toxicology-of-marine-fishes-the-elephant-in-the-room
#2
Benjamin Lemaire
Hydrostatic pressure (HP) increases linearly with depth in aquatic environments, so that many fish species routinely experience moderate-to-high HP levels (i.e., from a few to dozens of MPa). Biological effects of this thermodynamic variable are evidenced by a reduced functionality of many biomolecular systems, even in barotolerant and barophilic species. It is likely that environmentally-relevant HP levels (i.e., above atmospheric) could also modulate the responsiveness to and toxic effects of pollutants in fish...
July 21, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28732943/encompassment-of-benzyl-isothiocyanate-in-cyclodextrin-using-ultrasonication-methodology-to-enhance-its-stability-for-biological-applications
#3
Shivani Uppal, Khushwinder Kaur, Rajendra Kumar, Nakshdeep Kaur Kahlon, Rachna Singh, S K Mehta
The use of methodical and innovative sonication method has been explored for the fabrication of inclusion complex of Benzyl Isothiocyanate, a potential anticancer and -antimicrobial agent. The advancement involved investigation of inclusion behaviour, characterisation and an in-depth study of thermal and UV stability of Benzyl Isothiocyanate with cyclodextrins; β-CD and hp-β-CD. The sonication driven encompassment in cyclodextrins helped to overcome the hindrance of low solubility and high volatility. Investigations of physical and thermodynamic parameters using UV-visible spectroscopy, FTIR, XRD, TGA etc confirmed stability of inclusion complexes...
November 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28725057/efficient-generation-of-single-domain-antibodies-with-high-affinities-and-enhanced-thermal-stabilities
#4
Naoya Shinozaki, Ryuji Hashimoto, Kiichi Fukui, Susumu Uchiyama
Single domain antibodies (sdAbs), made of natural single variable regions of camelid or cartilaginous fish antibodies, or unpaired variable regions of mouse or human IgGs, are some of the more promising biologic modalities. However, such conventional sdAbs have difficulties of either using unwieldy animals for immunization or having high affinity deficiencies. Herein, we offer a versatile method to generate rabbit variable domain of heavy chain (rVH) derived sdAbs with high affinities (K D values of single digit nM or less) and enhanced thermal stabilities (equal to or even higher than those of camelid derived sdAbs)...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28718281/long-distance-modulation-of-disorder-to-order-in-protein-allostery
#5
Jingheng Wang, Gregory S Custer, Dorothy Beckett, Silvina Matysiak
Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the E. coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28714505/the-antiproliferative-activity-of-di-2-pyridylketone-dithiocarbamate-is-partly-attributed-to-catalase-inhibition-detailing-the-interaction-by-spectroscopic-methods
#6
Cuiping Li, Youxun Liu, Yun Fu, Tengfei Huang, Lixia Kang, Changzheng Li
The bioactivity of drugs is attributed to their interaction with biological molecules, embodied in either their direct or indirect influence on enzyme activity and conformation. Di-2-pyridylketone hydrazine dithiocarbamate (DpdtC) exhibits significant antitumor activity in our preliminary study. We speculated that its activity may partly stem from enzyme inhibition due to strong metal chelating ability. To this end, we assessed its effect on catalase from erythrocytes and found evidence of inhibition, which was further confirmed by ROS determination in vivo...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28704608/the-electron-bifurcating-fixabcx-protein-complex-from-azotobacter-vinelandii-generation-of-low-potential-reducing-equivalents-for-nitrogenase-catalysis
#7
Rhesa Ledbetter, Amaya M Garcia-Costas, Carolyn E Lubner, David W Mulder, Monika Tokmina-Lukaszewska, Jacob H Artz, Angela Patterson, Timothy Magnuson, Zackary J Jay, H Diessel Duan, Jacquelyn Miller, Mary H Plunkett, John P Hoben, Brett M Barney, Ross P Carlson, Anne-Frances Miller, Brian Bothner, Paul W King, John W Peters, Lance C Seefeldt
The biological reduction of dinitrogen (N2) to ammonia (NH3) by nitrogenase is an energetically demanding reaction that requires low-potential electrons and ATP; however, pathways used to deliver the electrons from central metabolism to the reductants of nitrogenase, ferredoxin or flavodoxin, remain unknown for many diazotrophic microbes. The FixABCX protein complex has been proposed to reduce flavodoxin or ferredoxin using NADH as the electron donor in a process known as electron bifurcation. Herein, the FixABCX complex from Azotobacter vinelandii was purified and demonstrated to catalyze an electron bifurcation reaction: oxidation of NADH (Em= -320 mV) coupled to reduction of flavodoxin semiquinone (Em= -460 mV) and reduction of coenzyme Q (Em= +10 mV)...
July 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/28702125/self-organizing-actin-patterns-shape-cytoskeletal-cortex-organization
#8
Marco Fritzsche
Living systems rely, for biological function, on the spatiotemporal organization of their structures. Cellular order naturally emerges by dissipation of energy. Consequently, energy-consuming processes operating far from thermodynamic equilibrium are a necessary condition to enable biological systems to respond to environmental cues that allow their transitions between different steady-states. Such self-organization was predicted for the actin cytoskeleton in theoretical considerations and has repeatedly been observed in cell-free systems...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28699635/anion-capped-metallohost-allows-extremely-slow-guest-uptake-and-on-demand-acceleration-of-guest-exchange
#9
Yoko Sakata, Chiho Murata, Shigehisa Akine
The switching of molecular recognition selectivity is important for tuning molecular functions based on host-guest binding. While the switching processes in artificial functional molecules are usually driven by changes of the thermodynamic stabilities, non-equilibrium phenomena also play an important role in biological systems. Thus, here we designed a host-guest system utilizing a non-equilibrium kinetically trapped state for on-demand and time-programmable control of molecular functions. We synthesized a bis(saloph) macrocyclic cobalt(III) metallohost 1(OTf)2, which has anion caps at both sides of the cation-binding site...
July 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28694844/a-synthetic-biology-approach-to-engineering-living-photovoltaics
#10
N Schuergers, C Werlang, C M Ajo-Franklin, A A Boghossian
The ability to electronically interface living cells with electron accepting scaffolds is crucial for the development of next-generation biophotovoltaic technologies. Although recent studies have focused on engineering synthetic interfaces that can maximize electronic communication between the cell and scaffold, the efficiency of such devices is limited by the low conductivity of the cell membrane. This review provides a materials science perspective on applying a complementary, synthetic biology approach to engineering membrane-electrode interfaces...
May 1, 2017: Energy & Environmental Science
https://www.readbyqxmd.com/read/28691114/structure-and-dynamics-of-type-iii-secretion-effector-protein-exou-as-determined-by-sdsl-epr-spectroscopy-in-conjunction-with-de-novo-protein-folding
#11
Axel W Fischer, David M Anderson, Maxx H Tessmer, Dara W Frank, Jimmy B Feix, Jens Meiler
ExoU is a 74 kDa cytotoxin that undergoes substantial conformational changes as part of its function, that is, it has multiple thermodynamically stable conformations that interchange depending on its environment. Such flexible proteins pose unique challenges to structural biology: (1) not only is it often difficult to determine structures by X-ray crystallography for all biologically relevant conformations because of the flat energy landscape (2) but also experimental conditions can easily perturb the biologically relevant conformation...
June 30, 2017: ACS Omega
https://www.readbyqxmd.com/read/28680687/a-facilitated-diffusion-model-constrained-by-the-probability-isotherm-a-pedagogical-exercise-in-intuitive-non-equilibrium-thermodynamics
#12
REVIEW
Brian Chapman
This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action...
June 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28675379/non-steady-state-mass-action-dynamics-without-rate-constants-dynamics-of-coupled-reactions-using-chemical-potentials
#13
William Cannon, Scott Baker
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants...
July 4, 2017: Physical Biology
https://www.readbyqxmd.com/read/28673235/comparative-analysis-of-lincrna-in-insect-species
#14
Alberto Lopez-Ezquerra, Mark C Harrison, Erich Bornberg-Bauer
BACKGROUND: The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes...
July 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28673085/large-scale-analysis-of-breast-cancer-related-conformational-changes-in-proteins-using-silac-sprox
#15
Fang Liu, He Meng, Michael C Fitzgerald
Proteomic methods for disease state characterization and biomarker discovery have traditionally utilized quantitative mass spectrometry methods to identify proteins with altered expression levels in disease states. Here we report on the large-scale use of protein folding stability measurements to characterize different subtypes of breast cancer using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique. Protein folding stability differences were studied in a comparison of two luminal breast cancer subtypes, luminal-A and -B (i...
July 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28668517/interaction-of-a-bioactive-pyrazole-derivative-with-calf-thymus-dna-deciphering-the-mode-of-binding-by-multi-spectroscopic-and-molecular-docking-investigations
#16
Pronab Kundu, Nitin Chattopadhyay
Deoxyribonuclic acid (DNA) is the most relevant intracellular target for a wide variety of anticancer and antibiotic drugs. Elucidating the binding interaction of small bioactive molecules with DNA provides a structural guideline for designing new drugs with improved selectivity and superior clinical efficacy. In the present work interaction of a newly synthesized biologically relevant fluorophore, namely, (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) with calf thymus DNA (ctDNA) has been investigated vividly through a number of in vitro studies...
June 22, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28668024/using-force-based-adaptive-resolution-simulations-to-calculate-solvation-free-energies-of-amino-acid-sidechain-analogues
#17
Raffaele Fiorentini, Kurt Kremer, Raffaello Potestio, Aoife C Fogarty
The calculation of free energy differences is a crucial step in the characterization and understanding of the physical properties of biological molecules. In the development of efficient methods to compute these quantities, a promising strategy is that of employing a dual-resolution representation of the solvent, specifically using an accurate model in the proximity of a molecule of interest and a simplified description elsewhere. One such concurrent multi-resolution simulation method is the Adaptive Resolution Scheme (AdResS), in which particles smoothly change their resolution on-the-fly as they move between different subregions...
June 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28667640/comparative-adsorption-of-amylase-protease-and-lipase-on-znfe2o4-kinetics-isothermal-and-thermodynamics-studies
#18
Abideen Idowu Adeogun, Sarafadeen Olateju Kareeem, Oluwatobi Samson Adebayo, Saka Adebayo Balogun
The role of enzyme engineering in biotechnology, biological and pharmaceutical process cannot be over emphasized. This study compared the adsorption of digestives enzymes; amylase, protease and lipase on to Zn-ferrite (ZnFe2O4). The metal ferrite was synthesized via a sol-gel technique and characterized with scanning electron microscopy (SEM), X-ray diffraction (XRD), Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy (FTIR). The adsorption was studied in a batch process and the data were subjected to kinetics and isotherm models...
July 2017: 3 Biotech
https://www.readbyqxmd.com/read/28655198/glycosylation-of-igg-fc-a-molecular-perspective
#19
Masato Kiyoshi, Kouhei Tsumoto, Akiko Ishii-Watabe, Jose M M Caaveiro
Antibodies of the IgG class carry a pair of oligosaccharides (N-glycans) in the fragment crystallizable (Fc) region. The importance of the N-glycan is clearly demonstrated by the profound effect it has in the physicochemical and biological properties of antibodies. The term "glycoengineering" has been coined to describe contemporary strategies to improve the performance of therapeutic monoclonal antibodies on the basis of modifications in the structure and composition of the N-glycan. These methodologies have resulted in the approval and commercialization of a new generation of antibodies with improved therapeutic efficacy...
June 26, 2017: International Immunology
https://www.readbyqxmd.com/read/28654291/photocatalytic-e%C3%A2-z-isomerization-of-polarized-alkenes-inspired-by-the-visual-cycle-mechanistic-dichotomy-and-origin-of-selectivity
#20
Jan B Metternich, Denis Gennadievich Artiukhin, Mareike C Holland, Maximilian von Bremen-Kühne, Johannes Neugebauer, Ryan Gilmour
Iteratively executed with exquisite spatial and temporal control, the selective isomerization of polarized alkenes underpins a plethora of complex biological processes ranging from natural product biosynthesis through to the mammalian visual cycle. However, Nature's proficiency conceals the inherent difficulties in replicating this contra-thermodynamic transformation in the laboratory. Recently, we disclosed the first highly Z-selective isomerization of polarized alkenes, employing the cinnamoyl chromophore as a retinal surrogate under UV-irradiation (402 nm) with (-)-riboflavin (vitamin B2) as an inexpensive, organic photocatalyst (J...
June 27, 2017: Journal of Organic Chemistry
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