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Biological thermodynamics

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https://www.readbyqxmd.com/read/29148817/specific-recognition-of-g-quadruplexes-over-duplex-dna-by-a-macromolecular-nir-two-photon-fluorescent-probe
#1
Marco Deiana, Bastien Mettra, Lara Martinez-Fernandez, Leszek Mateusz Mazur, Krzysztof Pawlik, Chantal Andraud, Marek Samoc, Roberto Improta, Cyrille Monnereau, Katarzyna Matczyszyn
The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. To date, the number of two-photon absorbing fluorogenic dyes with intrinsically large two-photon absorption (TPA) cross-section (σ2) and quantum yield (φf), capable of specific detection of G-motifs over duplex DNAs is still limited. Herein, we report on a NIR two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA...
November 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29142210/millisecond-dynamics-of-btk-reveal-kinome-wide-conformational-plasticity-within-the-apo-kinase-domain
#2
Mohammad M Sultan, Rajiah Aldrin Denny, Ray Unwalla, Frank Lovering, Vijay S Pande
Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK therapeutics would benefit from improved, in-silico structural modeling of the kinase's solution ensemble. However, this remains challenging due to the immense computational cost of sampling events on biological timescales. In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state models (MSMs) to report on the thermodynamics, kinetics, and accessible states of BTK's kinase domain...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133443/the-thermodynamic-efficiency-of-computations-made-in-cells-across-the-range-of-life
#3
Christopher P Kempes, David Wolpert, Zachary Cohen, Juan Pérez-Mercader
Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29131956/site-specific-deuteration-of-polyunsaturated-alkenes
#4
Alexey V Smarun, Milena Petkovic, Mikhail S Shchepinov, Dragoslav Vidovic
Selective deuteration of drugs and biologically relevant molecules is increasingly becoming important in the pharmaceutical industry. Site-selective isotopic reinforcement of polyunsaturated fatty acids (PUFAs) at their bis-allylic sites has been identified as a unique approach in preventing oxidative damage in these molecules, which had been linked to neuronal and retinal diseases, atherosclerosis and aging. Typical methods for preparation of site-selectively deuterated PUFAs require rather long, laborious and expensive syntheses...
November 13, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29131508/an-interactive-computer-lab-of-the-galvanic-cell-for-students-in-biochemistry
#5
Emma Ahlstrand, Antoine Buetti-Dinh, Ran Friedman
We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δr G, Δr H, and Δr S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29128642/the-evolution-of-metabolic-regulation-in-animals
#6
Frank Seebacher
Energy metabolism is determined by a suite of regulatory mechanism, and their increasing complexity over evolutionary time provides the key to understanding the emergence of different metabolic phenotypes. Energy metabolism is at the core of biological processes because all organisms must maintain energy balance against thermodynamic gradients. Energy metabolism is regulated by a bewildering array of interacting molecular mechanisms, and much of what is known about metabolic regulation comes from the medical literature...
November 8, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29126032/human-myeloma-igg4-reveals-relatively-rigid-asymmetric-y-like-structure-with-different-conformational-stability-of-ch2-domains
#7
Vladimir M Tischenko, Zav'yalov Vladimir P, Sergey N Ryazantsev
Human IgG4 (hIgG4) has weak pro-inflammatory activity. The structural basis for this is still unclear. Here a 3D model of myeloma hIgG4 was created at ∼3nm resolution using electron microscopy (EM) with negative staining and single-particle 3D reconstruction. The hIgG4 model reveals relatively rigid asymmetric Y-like structure. The model shows that one Fab subunit is closer to the upper portion of the Fc subunit (CH2 domain) than the other Fab. This is in agreement with X-ray crystallography and X-ray/neutron scattering, recently published by others...
November 7, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29123504/the-minimum-biological-energy-quantum
#8
REVIEW
Volker Müller, Verena Hess
Some anaerobic archaea and bacteria live on substrates that do not allow the synthesis of one mol of ATP per mol of substrate via substrate level phosphorylation (SLP). Energy conservation in these cases is only possible by a chemiosmotic mechanism that involves the generation of an electrochemical ion gradient across the cytoplasmic membrane that then drives ATP synthesis via an ATP synthase. The minimal amount of energy required for ATP synthesis is thus dependent on the magnitude of the electrochemical ion gradient, the phosphorylation potential in the cell and the ion/ATP ratio of the ATP synthase...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29121574/in-vitro-interaction-of-cefotaxime-with-calf-thymus-dna-insights-from-spectroscopic-calorimetric-and-molecular-modelling-studies
#9
Faizan Abul Qais, Iqbal Ahmad
Cefotaxime is third generation antibiotic with known therapeutic efficacy against bacterial infections including cerebral abscesses and bacterial meningitis. The β-lactam group of drugs are considered safest antibiotics. Many antibiotics directly interact with DNA and alter their expression profile. Thus, it is necessary to understand the binding mode and its relevance to drug activity and toxicity. There is considerably a remarkable focus on deciphering the binding mechanism of these therapeutic agents as DNA is one of the major target for wide range of drugs...
October 28, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29119787/cysteine-linkages-accelerate-electron-flow-through-tetra-heme-protein-stc
#10
Xiuyun Jiang, Zdenek Futera, Md Ehesan Ali, Fruzsina Gajdos, Guido F von Rudorff, Antoine Carof, Marian Breuer, Jochen Blumberger
Multi-heme proteins have attracted much attention recently due to their prominent role in mediating extracellular electron transport (ET), but one of their key fundamental properties, the rate constants for ET between the constituent heme groups, have so far evaded experimental determination. Here we report the set of heme-heme theoretical ET rate constants that define electron flow in the tetra-heme protein STC by combining a novel projector-operator diabatization approach for electronic coupling calculation with molecular dynamics simulation of ET free energies...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29119505/parameters-estimation-in-phase-space-landscape-reconstruction-of-cell-fate-a-systems-biology-approach
#11
Sheyla Montero, Reynaldo Martin, Ricardo Mansilla, Germinal Cocho, José Manuel Nieto-Villar
The thermodynamical formalism of irreversible processes offers a theoretical framework appropriate to explain the complexity observed at the macroscopic level of dynamic systems. In this context, together with the theory of complex systems and systems biology, the thermodynamical formalism establishes an appropriate conceptual framework to address the study of biological systems, in particular cancer.The Chapter is organized as follows: In Subheading 1, an integrative view of these disciplines is offered, for the characterization of the emergence and evolution of cancer, seen as a self-organized dynamic system far from the thermodynamic equilibrium...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29108958/novel-physical-chemistry-approaches-in-biophysical-researches-with-advanced-application-of-lasers-detection-and-manipulation
#12
REVIEW
Koichi Iwata, Masahide Terazima, Hiroshi Masuhara
Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29104926/a-demonstration-of-le-chatelier-s-principle-on-the-nanoscale
#13
Wayne Lin, Catherine J Murphy
Photothermal desorption of molecules from plasmonic nanoparticles is an example of a light-triggered molecular release due to heating of the system. However, this phenomenon ought to work only if the molecule-nanoparticle interaction is exothermic in nature. In this study, we compare protein adsorption behavior onto gold nanoparticles for both endothermic and exothermic complexation reactions, and demonstrate that Le Chatelier's principle can be applied to predict protein adsorption or desorption on nanomaterial surfaces...
October 25, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29104308/stereocontrolled-synthesis-of-spiroketals-an-engine-for-chemical-and-biological-discovery
#14
Alyssa L Verano, Derek S Tan
Spiroketals are key structural motifs found in diverse natural products with compelling biological activities. However, stereocontrolled synthetic access to spiroketals, independent of their inherent thermodynamic preferences, is a classical challenge in organic synthesis that has limited in-depth biological exploration of this intriguing class. Herein, we review our laboratory's efforts to advance the glycal epoxide approach to the stereocontrolled synthesis of spiroketals via kinetically controlled spirocyclization reactions...
April 2017: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/29102848/characterization-of-non-covalent-binding-of-6-hydroxyflavone-and-5-7-dihydroxyflavone-with-bovine-hemoglobin-multi-spectroscopic-and-molecular-docking-analyses
#15
Sourav Das, Alka Karn, Rubi Sarmah, Mostofa Ataur Rohman, Sudipta Koley, Pooja Ghosh, Atanu Singha Roy
Flavonoids are biologically imperative compounds used as anti-oxidants, anti-cancer, anti-bacterial agents etc. The current work reports comprehensive binding studies of two important flavonoids, 6-hydroxyflavone and 5,7-dihydroxyflavone (chrysin) with bovine hemoglobin (BHb) at 298K and 308K, in aqueous medium using UV-vis spectroscopy, steady state fluorescence, circular dichroism (CD) measurements, Fourier Transform infrared spectroscopy (FT-IR) and molecular docking studies. Both 6-hydroxyflavone and chrysin can quench the intrinsic fluorescence intensity of BHb via static quenching mechanism...
October 28, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/29101230/glutathione-limits-aquacopper-i-to-sub-femtomolar-concentrations-through-cooperative-assembly-of-a-tetranuclear-cluster
#16
M Thomas Morgan, Lily Anh H Nguyen, Haylie L Hancock, Christoph J Fahrni
The tripeptide glutathione (GSH) is a crucial intracellular reductant and radical scavenger, but may also coordinate the soft Cu(I) cation and thereby yield pro-oxidant species. The GSH-Cu(I) interaction is thus a key consideration for both redox and copper homeostasis in cells. However, even after nearly four decades of investigation, the nature and stability of the GSH-Cu complexes formed under biologically relevant conditions remain controversial. Here, we revealed the unexpected predominance of a tetranuclear [Cu4(GS)6] cluster that is sufficiently stable to limit the effective free aquocopper(I) concentration to the subfemtomolar regime...
November 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29096550/optimization-of-nutraceutical-coenzyme-q10-nanoemulsion-with-improved-skin-permeability-and-anti-wrinkle-efficiency
#17
Eman S El-Leithy, Amna M Makky, Abeer M Khattab, Doaa G Hussein
Coenzyme Q10 (CoQ10) is an insoluble, poorly permeable antioxidant with great biological value which acts as anti-aging and anti-wrinkle agent. To improve its permeability through topical application, the current study aimed at formulating oil/water (o/w) nanoemulsion (NE) as an efficient vehicle for delivering (CoQ10) through the skin barriers. The solubility of (CoQ10) was tested for various oils, surfactants (S), and co-surfactants (CoS). The NE region was determined by constructing pseudoternary phase diagrams...
November 2, 2017: Drug Development and Industrial Pharmacy
https://www.readbyqxmd.com/read/29092677/cooperativity-effect-involving-drug-dna-rna-intermolecular-interaction-a-b3lyp-d3-and-mp2-theoretical-investigation-on-ketoprofen%C3%A2-%C3%A2-%C3%A2-cytosine%C3%A2-%C3%A2-%C3%A2-h2o-system
#18
Jun-Ping Zhen, Xiao-Chun Wei, Wen-Jing Shi, Zhu-Yuan Huang, Bo Jin, Yu-Kun Zhou
In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen∙∙∙cytosine∙∙∙H2O ternary system were investigated by the B3LYP, B3LYP-D3 and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H∙∙∙O, O-H∙∙∙O, O-H∙∙∙N, C-H∙∙∙N, and C-H∙∙∙O H-bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2...
November 1, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29089531/entropy-production-selects-nonequilibrium-states-in-multistable-systems
#19
Robert G Endres
Far-from-equilibrium thermodynamics underpins the emergence of life, but how has been a long-outstanding puzzle. Best candidate theories based on the maximum entropy production principle could not be unequivocally proven, in part due to complicated physics, unintuitive stochastic thermodynamics, and the existence of alternative theories such as the minimum entropy production principle. Here, we use a simple, analytically solvable, one-dimensional bistable chemical system to demonstrate the validity of the maximum entropy production principle...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29078402/abiotic-production-of-sugar-phosphates-and-uridine-ribonucleoside-in-aqueous-microdroplets
#20
Inho Nam, Jae Kyoo Lee, Hong Gil Nam, Richard N Zare
Phosphorylation is an essential chemical reaction for life. This reaction generates fundamental cell components, including building blocks for RNA and DNA, phospholipids for cell walls, and adenosine triphosphate (ATP) for energy storage. However, phosphorylation reactions are thermodynamically unfavorable in solution. Consequently, a long-standing question in prebiotic chemistry is how abiotic phosphorylation occurs in biological compounds. We find that the phosphorylation of various sugars to form sugar-1-phosphates can proceed spontaneously in aqueous microdroplets containing a simple mixture of sugars and phosphoric acid...
October 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
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