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Biological thermodynamics

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https://www.readbyqxmd.com/read/28345702/the-role-of-conformational-heterogeneity-in-regulating-the-apoptotic-activity-of-bax-protein
#1
Te-Yu Kao, Chia-Jung Tsai, Yu-Jing Lan, Yun-Wei Chiang
While activation of BAX is required for initiating mitochondria-mediated apoptosis, the underlying mechanisms remain unsettled. We studied conformations of BAX protein using pressure- and temperature-resolved ESR techniques and obtained the thermodynamic properties of the conformations. We show that inactive BAX is structurally heterogeneous and exists in equilibrium between two major populations of the conformations, UM and UM', of which the former is thermodynamically favored at room temperature. An increase in the population of UM', induced by either pressure or point mutations of BAX, renders BAX susceptible to oligomerization, which leads to cell death...
March 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28335682/effect-of-lipophilicity-of-amylamine-and-amylglycine-ligands-on-biological-activity-of-new-anticancer-cisplatin-analog
#2
Fatemeh Safa Shams Abyaneh, Mahboube Eslami Moghadam, Moayyed Hoseini Sadr, Adeleh Divsalar
Investigation of side effects and solubility of anticancer drugs is a major challenge in chemotherapy science. Thus, design and synthesis of cisplatin analogs with higher lipophilicity as novel water-soluble anticancer drugs is valuable. In this work, two new Pt (II) complexes were synthesized with formula cis-[Pt (NH3)2(amylgly)] NO3 and cis-[Pt (amylamine)2(amylgly)]NO3; where gly is penthyl glycine as an amino acid. The new compounds were synthesized and extensively characterized using analytical techniques; spectroscopic methods and conductivity measurement...
March 23, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28334744/stabilization-of-rna-hairpins-using-non-nucleotide-linkers-and-circularization
#3
Agnieszka Kiliszek, Leszek Blaszczyk, Ryszard Kierzek, Wojciech Rypniewski
An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28330071/unexpected-formation-of-n-phenyl-thiophosphorohydrazidic-acid-o-s-dimethyl-ester-from-acephate-chemical-biotechnical-and-computational-study
#4
Vijay Kumar, Sukhmanpreet Kaur, Simranjeet Singh, Niraj Upadhyay
By the nucleophilic attack of phenylhydrazine on acephate in aqueous medium, a stable product N'-phenyl-thiophosphorohydrazidic acid O,S-dimethyl ester (1) was obtained and characterized by elemental, spectral and thermal analysis. Thermodynamic parameters, Ea, ΔH°, ΔS° and ΔG°, have found to be 62.15, -67.95, -0.068 and -20.05 kJ mol(-1) according to the Coats-Redfern equation. Analysis of interaction of 1 with BSA protein was done by using the UV-Vis and FTIR spectroscopic methods. The observed binding constants was 1...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328200/fluorescence-resonance-energy-transfer-based-dna-tetrahedron-nano-tweezer-for-highly-reliable-detection-of-tumor-related-mrna-in-living-cells
#5
Lei He, Dan-Qing Lu, Hao Liang, Sitao Xie, Can Luo, Miaomiao Hu, Liujun Xu, Xiaobing Zhang, Weihong Tan
Accurate detection and imaging of tumor-related mRNA in living cells hold great promise for early cancer detection. However, currently, most probes designed to image intracellular mRNA confront intrinsic interferences arising from complex biological matrices and resulting in inevitable false-positive signals. To circumvent this problem, a new class of intracellular DNA nanoprobe, termed DNA tetrahedron nano-tweezer (DTNT), was developed to reliably image tumor-related mRNA in living cells based on the FRET (fluorescence resonance energy transfer) "off" to "on" signal readout mode...
March 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28322561/accuracy-of-substrate-selection-by-enzymes-is-controlled-by-kinetic-discrimination
#6
Kinshuk Banerjee, Anatoly B Kolomeisky, Oleg A Igoshin
Enzymes have the remarkable ability to select the correct substrate from the pool of chemically similar molecules. The accuracy of such a selection is determined by differences in the free energy profiles for the right and wrong reaction pathways. Here, we investigate what features of the free energy landscape govern the variation and minimization of selectivity error. It is generally believed that minimal error is affected by both kinetic (activation barrier heights) and thermodynamic (binding stability) factors...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28318906/analysis-of-molecular-mechanisms-of-atp-synthesis-from-the-standpoint-of-the-principle-of-electrical-neutrality
#7
REVIEW
Sunil Nath
Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis...
March 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28318252/molecular-dynamics-in-mixed-solvents-reveals-protein-ligand-interactions-improves-docking-and-allows-accurate-binding-free-energy-predictions
#8
Juan Pablo Arcon, Lucas A Alfredo Defelipe, Carlos Pablo Modenutti, Elias Daniel Lopez, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Due to its low cost relative to its experimental sibling, Molecular Dynamics (MD) simulations in the presence of different solvent probes mimicking specific type of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28317184/self-assembled-multivalent-samul-polyanion-binding-impact-of-hydrophobic-modifications-in-the-micellar-core-on-dna-and-heparin-binding-at-the-peripheral-cationic-ligands
#9
Buthaina Albanyan, Erik Laurini, Paola Posocco, Sabrina Pricl, David K Smith
This paper reports a small family of cationic surfactants designed to bind polyanions such as DNA and heparin. Each molecule has the same hydrophilic cationic ligand, and a hydrophobic aliphatic group with eighteen carbon atoms with either one, two or three alkene groups within the hydrophobic chain (C18-1, C18-2 and C18-3). Dynamic light scattering indicates that more alkenes lead to geometric distortion, giving rise to larger self-assembled multivalent (SAMul) nanostructures. Mallard Blue and Ethidium Bromide dye displacement assays demonstrate that heparin and DNA have markedly different binding preferences, with heparin binding most effectively to C18-1, and DNA to C18-3, even though the molecular structural differences of these SAMul systems are buried in the hydrophobic core...
March 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28300202/thermoalign-a-genome-aware-primer-design-tool-for-tiled-amplicon-resequencing
#10
Felix Francis, Michael D Dumas, Randall J Wisser
Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28298489/mechanisms-of-kinetic-stabilization-by-the-drugs-paclitaxel-and-vinblastine
#11
Brian T Castle, Seth McCubbin, Louis S Prahl, Jordan N Bernens, David Sept, David J Odde
Microtubule-targeting agents (MTAs), widely used as biological probes and chemotherapeutic drugs, bind directly to tubulin subunits and "kinetically stabilize" microtubules, suppressing the characteristic self-assembly process of dynamic instability. However, the molecular-level mechanisms of kinetic stabilization are still unclear, and the fundamental thermodynamic and kinetic requirements for dynamic instability and its elimination by MTAs have yet to be defined. Here we integrate a computational model for microtubule assembly with nanometer-scale fluorescence microscopy measurements to identify the kinetic and thermodynamic basis of kinetic stabilization by the MTAs paclitaxel, an assembly promoter, and vinblastine, a disassembly promoter...
March 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28286146/altered-gene-expression-in-late-onset-alzheimer-s-disease-due-to-snps-within-3-utr-microrna-response-elements
#12
Jyoti Roy, Bibekanand Mallick
Late-onset Alzheimer's disease (LOAD) is a progressive and fatal neurodegenerative disease found in people older than 65years of age. Disease etiology is complex, as susceptibility has been linked to multiple gene variants conferred by single nucleotide polymorphisms (SNPs). However, the molecular mechanisms by which SNPs contribute to LOAD pathogenesis have not been extensively studied, particularly for SNPs within the 3' untranslated regions (3'UTRs), the hubs for microRNA binding. Therefore, we screened for SNPs within the 3'UTRs of LOAD-associated genes that may create or destroy microRNA response elements (MREs) and thus alter gene expression...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28284158/synthesis-spectroscopic-dft-and-in-vitro-biological-studies-of-vanadium-iii-complexes-of-aryldithiocarbonates
#13
Savit Andotra, Sandeep Kumar, Mandeep Kour, Vikas, Chayawan, Vishal Sharma, Sundeep Jaglan, Sushil K Pandey
Vanadium(III) tris(dithiocarbonates), [(ROCS2)3V] (R=o-, m-, p-CH3C6H4 and 4-Cl-3-CH3C6H3) and donor stabilized addition complexes [(ROCS2)2V(Cl)·L] [L=NC5H5 or P(C6H5)3] were synthesized and characterized by elemental analyses, IR, mass, TGA/DTA, SEM magnetic susceptibility and heteronuclear NMR ((1)H, (13)C and (31)P) spectroscopic studies. The cytotoxicity of the complexes was measured in vitro using the cultivated human cell lines. In addition, the antioxidant activities of the ligands and its vanadium complexes were also investigated through their scavenging effect on DPPH radicals...
March 6, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28283210/osmolyte-depletion-viewed-in-terms-of-the-dividing-membrane-and-its-work-of-expansion-against-osmotic-pressure
#14
Seishi Shimizu, Nobuyuki Matubayasi
How osmolytes enhance the folding, binding, and self-assembly of biological macromolecules at a microscopic scale has long been a matter of debate. Ambiguities persist on the key interpretive concepts, such as the "effective membrane" (which marks the boundary of the volume from which osmolytes are excluded) and the "free energy of exclusion" of osmolytes from biomolecular surfaces. In this paper, we formulate these elusive concepts based upon chemical thermodynamics and rigorous statistical thermodynamics (the Kirkwood-Buff theory)...
February 27, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28278762/evaluation-of-dna-bsa-binding-and-antimicrobial-activity-of-new-synthesized-neodymium-complex-containing-29-dimethyl-110-phenanthroline
#15
Zohreh Moradi, Mozhgan Khorasani-Motlagh, Ali Reza Rezvani, Meissam Noroozifar
In order to evaluate biological potential of a novel synthesized complex [Nd(dmp)2Cl3.OH2] where dmp is 29-dimethyl 110-phenanthroline, the DNA-binding, cleavage, BSA binding, and antimicrobial activity properties of the complex are investigated by multispectroscopic techniques study in physiological buffer (pH 7.2).The intrinsic binding constant (Kb) for interaction of Nd(III) complex and FS-DNA is calculated by UV-Vis (Kb = 2.7 ± 0.07 × 10(5)) and fluorescence spectroscopy (Kb = 1.13 ± 0.03 × 10(5))...
February 21, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28275729/radar-interferometry-offers-new-insights-into-threats-to-the-angkor-site
#16
Fulong Chen, Huadong Guo, Peifeng Ma, Hui Lin, Cheng Wang, Natarajan Ishwaran, Peou Hang
The conservation of World Heritage is critical to the cultural and social sustainability of regions and nations. Risk monitoring and preventive diagnosis of threats to heritage sites in any given ecosystem are a complex and challenging task. Taking advantage of the performance of Earth Observation technologies, we measured the impacts of hitherto imperceptible and poorly understood factors of groundwater and temperature variations on the monuments in the Angkor World Heritage site (400 km(2)). We developed a two-scale synthetic aperture radar interferometry (InSAR) approach...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28272886/first-principles-models-for-van-der-waals-interactions-in-molecules-and-materials-concepts-theory-and-applications
#17
Jan Hermann, Robert A DiStasio, Alexandre Tkatchenko
Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches)...
March 8, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28268605/parameter-estimation-for-gene-regulatory-networks-a-two-stage-mcmc-bayesian-approach
#18
Niannan Xue, Wei Pan, Yike Guo
Genetic regulatory networks have emerged as a useful way to elucidate the biochemical pathways for biological functions. Yet, determination of the exact parametric forms for these models remain a major challenge. In this paper, we present a novel computational approach implemented in C++ to solve this inverse problem. This takes the form of an optimization stage first after which Bayesian filtering takes place. The key advantage of such a flexible, general and robust approach is that it provides us with a joint probability distribution of the model parameters instead of single estimates, which we can propagate to final predictions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28267566/aging-and-efficiency-in-living-systems-complexity-adaptation-and-self-organization
#19
Atanu Chatterjee, Georgi Georgiev, Germano Iannacchione
Living systems are open, out-of-equilibrium thermodynamic entities, that maintain order by locally reducing their entropy. Aging is a process by which these systems gradually lose their ability to maintain their out-of-equilibrium state, as measured by their free-energy rate density, and hence, their order. Thus, the process of aging reduces the efficiency of those systems, making them fragile and less adaptive to the environmental fluctuations, gradually driving them towards the state of thermodynamic equilibrium...
March 3, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28262684/conserved-intergenic-sequences-revealed-by-ctag-profiling-in-salmonella-thermodynamic-modeling-for-function-prediction
#20
Le Tang, Songling Zhu, Emilio Mastriani, Xin Fang, Yu-Jie Zhou, Yong-Guo Li, Randal N Johnston, Zheng Guo, Gui-Rong Liu, Shu-Lin Liu
Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure...
March 6, 2017: Scientific Reports
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