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Biological thermodynamics

Kunihiko Kaneko, Chikara Furusawa
We present a macroscopic theory to characterize the plasticity, robustness, and evolvability of biological responses and their fluctuations. First, linear approximation in intracellular reaction dynamics is used to demonstrate proportional changes in the expression of all cellular components in response to a given environmental stress, with the proportion coefficient determined by the change in growth rate as a consequence of the steady growth of cells. We further demonstrate that this relationship is supported through adaptation experiments of bacteria, perhaps too well as this proportionality is held even across cultures of different types of conditions...
May 20, 2018: Annual Review of Biophysics
Joseph Fernandez-Moure, Nuzhat Maisha, Erin B Lavik, Jeremy Cannon
With the development of new biologics and bioconjugates, storage and preservation have become more critical than ever before. Lyophilization is a method of cell and protein preservation by removing a solvent such as water from a substance followed by freezing. This technique has been used in the past and still holds promise for overcoming logistic challenges in safety net hospitals with limited blood banking resources, austere environments such as combat, and in mass casualty situations where existing resources may be outstripped...
May 23, 2018: Bioconjugate Chemistry
Charles A Lewis, Richard Wolfenden
S-Adenosylmethionine (SAM+) serves as the prin-cipal methylating agent in biological systems, but the thermodynamic basis of its reactivity does not appear to have been established. Here, we show that methionine, methanol and H+ combine to form S-methylmethionine (SMM+) with a temperature-independent equilibrium constant of 9.9 M-2. The corresponding group transfer potential of SMM+, i. e. its free energy of hydrolysis at pH 7, is -8.2 kcal/mol. The "energy-rich" nature of sulfonium ions is related to the extreme acidity (pKa -5...
May 22, 2018: Biochemistry
Artem O Surov, Andrei V Churakov, Alexey N Proshin, Xia-Lin Dai, Tongbu Lu, German L Perlovich
Three distinct solid forms, namely anhydrous cocrystals with 2 : 1 and 1 : 1 drug/acid ratios ([TDZ : GA] (2 : 1), [TDZ : GA] (1 : 1)), and a hydrated one having 1 : 1 : 1 drug/acid/water stoichiometry ([TDZ : GA : H2O] (1 : 1 : 1)), have been formed by cocrystallization of the biologically active 1,2,4-thiadiazole derivative (TDZ) with gallic acid (GA). The thermodynamic stability relationships between the cocrystals were rationalized in terms of Gibbs energies of the formation reactions and further verified by performing a set of competitive and exchange mechanochemical reactions...
May 22, 2018: Physical Chemistry Chemical Physics: PCCP
Zhirui Niu, Shaokang Zhang, Lin Zhu
Mn-Zn ferrite (Mn1 - x Zn x Fe2 O4 , x = 0.2, 0.4, 0.6, and 0.8) nanomaterials were prepared by bioleaching and hydrothermal synthesis from waste Zn-Mn batteries. The materials were characterized by XRD, SEM, BET, VSM, CEC, and isoelectric point. It turned out when x = 0.4, synthesized Mn-Zn ferrite had best performance which was nanoferrite crystal structure with a specific surface area that reached 37.77 m2 /g, the saturation magnetization was 62.85 emu/g, and isoelectric point and the CEC value were 7...
May 21, 2018: Environmental Science and Pollution Research International
Agnese Carino, Christian Ludwig, Antonio Cervellino, Elisabeth Müller, Andrea Testino
The experimental data on calcium phosphates formation were collected in dilute solution at constant pH (7.40) and temperature (37.0 °C) at different levels of ionic strength (IS). The evolution of the solid phase formation is described in detail using a thermodynamic-kinetic model. The thermodynamic model takes into account all relevant chemical species as well as Posner's clusters; the kinetic model, based on the discretized population balance approach, accounts for the solid formation from solution. The experimental data are consistent with an initial formation of dicalcium phosphate dihydrate (DCPD, brushite), which dominates the nucleation rate, and its rapid transformation into octacalcium phosphate (OCP) or hydroxyapatite (HA), which dominates the growth rate...
May 17, 2018: Acta Biomaterialia
Jiao Guan, Xin Yan, Yajing Zhao, Yinhe Sun, Xin Peng
The antimicrobial triclocarban (TCC) is frequently found in various personal care products (PCPs), and recent studies have demonstrated that it shows a high unintended biological activity on humans and wildlife. To evaluate the toxicity of TCC at the protein level, the effect of TCC on bovine serum albumin (BSA) has been investigated using various spectroscopic methods in combination with molecular modeling. Analysis of fluorescence quenching data of BSA revealed the formation of a ground state BSA-TCC complex with a binding constant of 2...
May 9, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Rahul Dev Mukhopadhyay, Gourab Das, Ayyappanpillai Ajayaghosh
Precise control of host-guest interaction as seen in biological processes is difficult to achieve with artificial systems. Herein we have exploited the thermodynamic benefits of a system in equilibrium to achieve controlled stepwise release and capture of cyclodextrin (guest) using a coordination polymer (Mg-CP) as the host and temperature as the stimulus. Since temperature is not a precision stimulus for artificial host-guest interaction, the present system is a distinct prototype that manifests temperature-controlled natural host-guest interaction...
May 18, 2018: Nature Communications
Tobias Baumann, Franz-Josef Schmitt, Almut Pelzer, Vivian Jeanette Spiering, Georg Johannes Freiherr von Sass, Thomas Friedrich, Nediljko Budisa
Fluorescent proteins are fundamental tools for the life sciences, in particular for fluorescence microscopy of living cells. While wild-type and engineered variants of the green fluorescent protein from Aequorea victoria (avGFP) as well as homologs from other species already cover large parts of the optical spectrum, a spectral gap remains in the near-infrared region, for which avGFP-based fluorophores are not available. Red-shifted fluorescent protein (FP) variants would substantially expand the toolkit for spectral unmixing of multiple molecular species, but the naturally occurring red-shifted FPs derived from corals or sea anemones have lower fluorescence quantum yield and inferior photo-stability compared to the avGFP variants...
April 27, 2018: Journal of Visualized Experiments: JoVE
Asma Yangui, Manef Abderrabba
Activated carbon coated with milk proteins was used for the removal and recovery of phenolic compounds from actual olive mill wastewater (OMW). The extraction of polyphenols using the new adsorbent based on natural coating agent has significant potential compared with traditional extraction methods, as it significantly increases the extraction yield (80%) and overall efficiencies of the process for total phenols (75.4%) and hydroxytyrosol (90.6%) which is the most valuable compound. Complete discussions on the adsorption isotherms, kinetic and thermodynamic were performed and the optimum adsorption variables were investigated using the response surface methodology and the central composite experimental design...
October 1, 2018: Food Chemistry
Dawei Xu, Damien S K Samways, He Dong
Effective strategies to fabricate finite organic nanoparticles and understanding their structure-dependent cell interaction is highly important for the development of long circulating nanocarriers in cancer therapy. In this contribution, we will capitalize on our recent development of finite supramolecular nanofibers based on the self-assembly of modularly designed cationic multidomain peptides (MDPs) and use them as a model system to investigate structure-dependent cell penetrating activity. MDPs self-assembled into nanofibers with high density of cationic charges at the fiber-solvent interface to interact with the cell membrane...
December 2017: Bioactive Materials
Sabine Peres, Stefan Schuster, Philippe Dague
Metabolic pathway analysis is a key method to study metabolism and the elementary flux modes (EFMs) is one major concept allowing one to analyze the network in terms of minimal pathways. Their practical use has been hampered by the combinatorial explosion of their number in large systems. The EFMs give the possible pathways at steady state, but the real pathways are limited by biological constraints. In this review, we display three different methods that integrate thermodynamic constraints in terms of Gibbs free energy in the EFMs computation...
May 9, 2018: Biochemical Society Transactions
Elise Rosati, Morgan Madec, Jean-Baptiste Kammerer, Luc Hébrard, Christophe Lallement, Jacques Haiech
We recently demonstrated the possibility to model and to simulate biological functions using hardware description languages (HDLs) and associated simulators traditionally used for microelectronics. Nevertheless, those languages are not suitable to model and simulate space-dependent systems described by partial differential equations. However, in more and more applications space- and time-dependent models are unavoidable. For this purpose, we investigated a new modeling approach to simulate molecular diffusion on a mesoscopic scale still based on HDL...
May 9, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Vladimir Potapov, Jennifer L Ong, Bradley W Langhorst, Katharina Bilotti, Dan Cahoon, Barry Canton, Thomas F Knight, Thomas C Evans, Gregory Js Lohman
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction...
May 8, 2018: Nucleic Acids Research
Jordan T White, Jing Li, Emily Grasso, James O Wrabl, Vincent J Hilser
Allostery is an important regulatory phenomenon enabling precise control of biological function. Initial understanding of allostery was gained from seminal work on conformational changes exhibited by structured proteins. Within the last decade, protein allostery has also been demonstrated to occur within intrinsically disordered proteins. This emerging concept of disorder-mediated allostery can be usefully understood in the context of a thermodynamic ensemble. The advantage of this ensemble allosteric model is that it unifies the explanations of allostery occurring within both structured and disordered proteins...
June 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Maude Reggane, Johannes Wiest, Marco Saedtler, Cornelius Harlacher, Marcus Gutmann, Sven H Zottnick, Philippe Piechon, Ina Dix, Klaus Müller-Buschbaum, Ulrike Holzgrabe, Lorenz Meinel, Bruno Galli
Realizing the full potential of co-crystals enhanced kinetic solubility demands a comprehensive understanding of the mechanisms of dissolution, phase conversion, nucleation and crystal growth, and of the complex interplay between the active pharmaceutical ingredient (API), the coformer and co-existing forms in aqueous media. One blueprint provided by nature to keep poorly water-soluble bases in solution is the complexation with phenolic acids. Consequently, we followed a bioinspired strategy for the engineering of co-crystals of a poorly water-soluble molecule - Imatinib - with a phenolic acid, syringic acid (SYA)...
May 4, 2018: European Journal of Pharmaceutics and Biopharmaceutics
Tolutola Oyetunde, Forrest Sheng Bao, Jiung-Wen Chen, Hector Garcia Martin, Yinjie J Tang
Genome scale modeling (GSM) predicts the performance of microbial workhorses and helps identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and thermodynamics have shown remarkable progress in both elucidating complex cellular phenomena and computational strain design (CSD). Nonetheless, these models still show high uncertainty due to a poor understanding of innate pathway regulations, metabolic burdens, and other factors (such as stress tolerance and metabolite channeling)...
May 2, 2018: Biotechnology Advances
Chiara Cardelli, Alessandro Barducci, Piero Procacci
In this report we have tested a parallel implementation for the simulation of lipid bilayers at the atomistic level, based on a generalized ensemble protocol where only the torsional degrees of freedom of the alkyl chains of the lipids are heated. The results in terms of configurational sampling enhancement have been compared with a conventional simulation produced with a widespread molecular dynamics code. Results show that the proposed thermodynamic-based multiple trajectories parallel protocol for membrane simulations allows for an efficient use of CPU resources with respect to the conventional single trajectory, providing accurate results for area and volume per lipid, membrane thickness, undulation spectra and boosting significantly diffusion and mixing in lipid bilayers due to the sampling enhancement of gauche/trans ratios of the alkyl chain dihedral angles...
April 30, 2018: Biochimica et Biophysica Acta
Monique J Kauke, Alison W Tisdale, Ryan L Kelly, Christian J Braun, Michael T Hemann, K Dane Wittrup
Mutated in approximately 30% of human cancers, Ras GTPases are the most common drivers of oncogenesis and render tumors unresponsive to many standard therapies. Despite decades of research, no drugs directly targeting Ras are currently available. We have previously characterized a small protein antagonist of K-Ras, R11.1.6, and demonstrated its direct competition with Raf for Ras binding. Here we evaluate the effects of R11.1.6 on Ras signaling and cellular proliferation in a panel of human cancer cell lines...
May 2, 2018: Molecular Cancer Therapeutics
S Sevim, A Sorrenti, C Franco, S Furukawa, S Pané, A J deMello, J Puigmartí-Luis
Self-assembly is a crucial component in the bottom-up fabrication of hierarchical supramolecular structures and advanced functional materials. Control has traditionally relied on the use of encoded building blocks bearing suitable moieties for recognition and interaction, with targeting of the thermodynamic equilibrium state. On the other hand, nature leverages the control of reaction-diffusion processes to create hierarchically organized materials with surprisingly complex biological functions. Indeed, under non-equilibrium conditions (kinetic control), the spatio-temporal command of chemical gradients and reactant mixing during self-assembly (the creation of non-uniform chemical environments for example) can strongly affect the outcome of the self-assembly process...
May 1, 2018: Chemical Society Reviews
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