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Biological thermodynamics

Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
Yue Lu, Javier Ramiro-Garcia, Pieter Vandermeeren, Steffi Herrmann, Danuta Cichocka, Dirk Springael, Siavash Atashgahi, Hauke Smidt
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers...
December 1, 2016: Applied Microbiology and Biotechnology
Rainer G Hanselmann, Cornelius Welter
Cells are open, highly ordered systems that are far away from equilibrium. For this reason, the first function of any cell is to prevent the permanent threat of disintegration that is described by thermodynamic laws and to preserve highly ordered cell characteristics such as structures, the cell cycle, or metabolism. In this context, three basic categories play a central role: energy, information, and matter. Each of these three categories is equally important to the cell and they are reciprocally dependent...
2016: Frontiers in Cell and Developmental Biology
Tao Guo, Yan Lin, Zhi Li, Shan Chen, Guoming Huang, Huirong Lin, Jun Wang, Gang Liu, Huang-Hao Yang
Gold nanorods (GNRs) are emerging as a promising nanoplatform for cancer theranostics because of their unique optical properties. However, they still suffer from many limitations, such as high cytotoxicity, low thermodynamic and biological stability, and a tedious process for integrating other imaging modalities, for further practical biomedical applications. In this work, a strategy by one-step coating of Gd2O2S around GNRs is reported to address these limitations of GNRs. After the coating of the Gd2O2S shell, the as-fabricated Gd2O2S coated GNRs (GNRs@Gd2O2S) show enhanced biocompatibility and photostability, and tunable localized surface plasmon resonance...
December 1, 2016: Nanoscale
Inbar Schlachet, Alejandro Sosnik
Two main hurdles persist towards the more extensive bench-to-bed side translation of non-parenteral polymeric micelles. The first pertains to their thermodynamically-driven disassembly under uncontrolled dilution conditions in the biological milieu and upon interaction with biomacromolecules (e.g., proteins). The second is related to the relatively poor understanding of the pathways by which polymeric micelles improve the bioavailability of the payload by mucosal routes (e.g., intestinal). In this work, a chitosan-g-oligo(N-isopropylacrylamide) (CS-g-oligo(NiPAAm)) copolymer was modified with non-cytotoxic amounts of protoporphyrin IX (PP), a planar molecule of amphiphilic character that undergoes self-aggregation in water by forming π-π stacked supramolecular structures, to induce micellization under disfavored conditions and to serve as a fluorescent tracer for the measurement of the micelle permeability across a model of the intestinal epithelium in vitro...
December 1, 2016: Biomaterials Science
Masanori Shigeno
 Molecular switching is the phenomenon in which a molecular structural change occurs reversibly in response to an external stimulus or energy. It plays an important role in biology, in which it is used for sensing environmental changes. In contrast to well-studied equilibrium molecular switching involving thermodynamically stable states, nonequilibrium molecular switching involving a metastable state is a notable chemical phenomenon and is the theme of this study. Sulfonamido- and aminomethylenehelicene oligomers show a reversible structural change from a double helix to a random coil in dilute solution...
2016: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
Zhen Song, Wen Yuan, Ruitao Zhu, Song Wang, Caifeng Zhang, Binsheng Yang
Curcumin is a widely studied polyphenolic compound which has a variety of biological activity as anti-inflammatory and antitumor drugs. Recent research reported that copper chaperone binding with small molecular may relate to the treatment of cancer. In this work, the interaction between curcumin and CopC has been investigated in detail by means of UV-vis absorption, FTIR, CD, fluorescence spectroscopic and molecular docking methods The results showed that the CopC conformation was altered by curcumin with reduction of β-sheet and increase of random coil...
November 27, 2016: International Journal of Biological Macromolecules
Francesco Tisato, Valentina Peruzzo, Giulia Zanchetta, Sergio Tamburini, Pietro Traldi, Marina Porchia
Tetrahedral [Cu(P)4][BF4]-type complexes (P = tertiary phosphine) are a class of monopositively charged compounds that have shown notable antitumor activity in both in vitro and in vivo tests. This biological property appears to be related to the peculiar physicochemical characteristics of these compounds. Although thermodynamically stable, they are labile at micromolar concentrations. Such a behavior allows the Cu(I) ion in [Cu(P)n](+) assemblies (n < 4) to interact with surrounding molecules, including the rich peptide/protein environment that metal complexes have to face in the physiological milieu on the way to tumor cells...
2016: European Journal of Mass Spectrometry
J Müller, K N Bauer, D Prozeller, J Simon, V Mailänder, F R Wurm, S Winzen, K Landfester
Nanoparticles with long blood circulation time are a prerequisite for targeted drug delivery. To make the nanoparticles invisible for phagocytizing cells, functional moieties on the particle surface are believed to be necessary to attract specific so-called 'stealth' proteins forming a protein 'corona'. Currently, covalent attachment of those moieties represents the only way to achieve that attraction. However, that approach requires a high synthetic effort and is difficult to control. Therefore, we present the coating of model nanoparticles with biodegradable polymeric surfactants as an alternative method...
November 15, 2016: Biomaterials
Tomohiko Hayashi, Masahiro Kinoshita
To elucidate the interactions between aromatic rings, which are believed to play essential roles in a variety of biological processes, we analyze the water-mediated interactions between toluene molecules along face-to-face stacked (FF) and point-to-face T-shaped (TS) paths using a statistical-mechanical theory of liquids combined with a molecular model for water. The theory enables us to decompose each interaction into physically insightful components, revealing detailed hydration effects. The dimers (i.e., molecules in contact with each other) formed in the FF and TS paths, which are referred to as "FF stacking" and "TS contact", respectively, share almost the same stability in vacuum...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
J Ricardo Arias-Gonzalez
Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Stochastic chains are of special significance to molecular biology, where genes are conveyed by linear polymers made up of molecular subunits and transferred from DNA to proteins by specialized molecular motors in the presence of errors. Here, we demonstrate that when memory is introduced, the statistics of the chain depends on the mechanism by which objects or symbols are assembled, even in the slow dynamics limit wherein friction can be neglected...
November 14, 2016: Journal of Chemical Physics
Hamid Dezhampanah, Roghaye Firouzi, Leila Hasani
The interaction of nickel (II) phthalocyanine tetrasulfonic acid tetrasodium salt with bovine serum albumin (BSA) has been investigated by combination of fluorescence, UV-vis absorption, Fourier transform infrared (FT-IR), and circular dichorism (CD) spectroscopies as well as through molecular docking. Fluorescence quenching and absorption spectra were investigated as a mean for estimating the binding parameters. Analysis of fluorescence quenching data at different temperatures was performed in order to specify the thermodynamics parameters for interactions of phthalocyanine complex with BSA...
November 10, 2016: Nucleosides, Nucleotides & Nucleic Acids
Ágnes Blaskó, Zoltán Gazdag, Pál Gróf, Gábor Máté, Szilvia Sárosi, Judit Krisch, Csaba Vágvölgyi, Lilla Makszin, Miklós Pesti
The effects of clary sage (Salvia sclarea L.) oil (CS-oil), and its two main components, linalool (Lol) and linalyl acetate (LA), on cells of the eukaryotic human pathogen yeast Candida albicans were studied. Dynamic and thermodynamic properties of the plasma membrane were investigated by electron paramagnetic resonance (EPR) spectroscopy, with 5-doxylstearic acid (5-SASL) and 16-SASL as spin labels. The monitoring of the head group regions with 5-SASL revealed break-point frequency decrease in a temperature dependent manner of the plasma membrane between 9...
November 8, 2016: Apoptosis: An International Journal on Programmed Cell Death
Ailin Wang, Y Randika Perera, Mackenzie B Davidson, Nicholas C Fitzkee
Gold nanoparticle- (AuNP-) protein conjugates are potentially useful in a broad array of diagnostic and therapeutic applications, but the physical basis of the simultaneous adsorption of multiple proteins onto AuNP surfaces remains poorly understood. Here, we investigate the contribution of electrostatic interactions to protein-AuNP binding by studying the pH-dependent binding behavior of two proteins, GB3 and ubiquitin. For both proteins, binding to 15-nm citrate-coated AuNPs closely tracks with the predicted net charge using standard pKa values, and a dramatic reduction in binding is observed when lysine residues are chemically methylated...
October 27, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Julia H Roberts, Fang Liu, Jaret M Karnuta, Michael C Fitzgerald
Described here is the application of thermodynamic stability measurements to study age-related differences in the protein folding and stability of proteins in a rodent model of ageing. Thermodynamic stability profiles were generated for 809 proteins in brain cell lysates from mice, aged 6- (n=7) and 18-months (n=9) using the Stability of Proteins from Rates of Oxidation (SPROX) technique. The biological variability of the protein stability measurements was low and within the experimental error of SPROX. A total of 83 protein hits was detected with age-related stability differences in the brain samples...
November 2, 2016: Journal of Proteome Research
Jiang Hong, Shangqin Xiong
Trimethylamine N-oxide (TMAO) exemplifies how Nature uses the solute effect as a simple chemical strategy to cope with hydrodynamic pressure or urea stress to maintain proteostasis. It is a gut-microbe-generated metabolite that strongly promotes the development of atherosclerosis. It remains unclear how TMAO exerts its effects. In this study, we experimentally characterized the profile of the preferential interaction potential of TMAO with proteins, a thermodynamic key to understanding the effects of TMAO on protein processes and the distinction of TMAO among osmolytes...
November 1, 2016: Biophysical Journal
Shion A Lim, Kathryn M Hart, Michael J Harms, Susan Marqusee
Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein's folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein's energy landscape is maintained or altered throughout evolution is unclear. To study how a protein's energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
Tadashi Ando, Isseki Yu, Michael Feig, Yuji Sugita
The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell...
October 31, 2016: Journal of Physical Chemistry. B
Rahul L Khade, Yuwei Yang, Yelu Shi, Yong Zhang
HNO plays significant roles in many biological processes. Numerous heme proteins bind HNO, an important step for its biological functions. A systematic computational study was performed to provide the first detailed trends and origins of the effects of iron oxidation state, axial ligand, and protein environment on HNO binding. The results show that HNO binds much weaker with ferric porphyrins than corresponding ferrous systems, offering strong thermodynamic driving force for experimentally observed reductive nitrosylation...
November 21, 2016: Angewandte Chemie
Neal K Broomhead, Mahmoud E Soliman
In the field of medicinal chemistry there is increasing focus on identifying key proteins whose biochemical functions can firmly be linked to serious diseases. Such proteins become targets for drug or inhibitor molecules that could treat or halt the disease through therapeutic action or by blocking the protein function respectively. The protein must be targeted at the relevant biologically active site for drug or inhibitor binding to be effective. As insufficient experimental data is available to confirm the biologically active binding site for novel protein targets, researchers often rely on computational prediction methods to identify binding sites...
October 31, 2016: Cell Biochemistry and Biophysics
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