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Biological thermodynamics

Sabine Peres, Mario Jolicœur, Cécile Moulin, Philippe Dague, Stefan Schuster
We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of elementary flux modes (EFMs) by a factor of two. Declaring in advance some reactions as irreversible, based on reliable biochemical expertise, can in general reduce the number of EFMs by a greater factor...
2017: PloS One
Sayeed Ashique Ahmed, Banibrata Maity, Soma Seth Duley, Debabrata Seth
The modulation of photophysical behaviour of small organic molecules in the presence of macrocycles is one of the most interesting areas of research. In this work we reported the interaction of two biologically active molecules 3-hydroxyflavone and 7-hydroxyflavone with macrocyclic host cucurbit [7]uril in aqueous medium. To investigate the change of photophysical properties of these two flavones, we have used steady state absorption, fluorescence, time resolved fluorescence emission spectroscopy and isothermal titration calorimetric technique...
February 9, 2017: Journal of Photochemistry and Photobiology. B, Biology
Wouter Engelen, Lenny H H Meijer, Bram Somers, Tom F A de Greef, Maarten Merkx
DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically...
February 17, 2017: Nature Communications
Alexander B Boyd, Dibyendu Mandal, James P Crutchfield
Information engines can use structured environments as a resource to generate work by randomizing ordered inputs and leveraging the increased Shannon entropy to transfer energy from a thermal reservoir to a work reservoir. We give a broadly applicable expression for the work production of an information engine, generally modeled as a memoryful channel that communicates inputs to outputs as it interacts with an evolving environment. The expression establishes that an information engine must have more than one memory state in order to leverage input environment correlations...
January 2017: Physical Review. E
Imad Younus Hasan, Adam Mechler
Partitioning of lipid molecules in biomimetic membranes is a model system for the study of naturally occurring domains, such as rafts, in biological membranes. The existence of nanometer scale membrane domains in binary lipid mixtures has been shown with microscopy methods; however, the nature of these domains has not been established unequivocally. A common notion is to ascribe domain separation to thermodynamic phase equilibria. However, characterizing thermodynamic phases of single bilayer membranes has not been possible due to their extreme dimensions: the size of the domains falls to the order of tens to hundreds of nanometers whereas the membrane thickness is only a few nanometers...
February 7, 2017: Analytical Chemistry
David J Scott
Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations from ideal behaviour which is manifested as thermodynamic non-ideality. The range of concentrations at which this behaviour typically is exhibited is as low as 1-2 mg/ml, well within the range of concentrations used for their analysis by techniques such as small-angle scattering...
December 2016: Biophysical Reviews
Franco O Tzul, Daniel Vasilchuk, George I Makhatadze
Theoretical and experimental studies have firmly established that protein folding can be described by a funneled energy landscape. This funneled energy landscape is the result of foldable protein sequences evolving following the principle of minimal frustration, which allows proteins to rapidly fold to their native biologically functional conformations. For a protein family with a given functional fold, the principle of minimal frustration suggests that, independent of sequence, all proteins within this family should fold with similar rates...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
Jonasz Słomka, Jörn Dunkel
Classical turbulence theory assumes that energy transport in a 3D turbulent flow proceeds through a Richardson cascade whereby larger vortices successively decay into smaller ones. By contrast, an additional inverse cascade characterized by vortex growth exists in 2D fluids and gases, with profound implications for meteorological flows and fluid mixing. The possibility of a helicity-driven inverse cascade in 3D fluids had been rejected in the 1970s based on equilibrium-thermodynamic arguments. Recently, however, it was proposed that certain symmetry-breaking processes could potentially trigger a 3D inverse cascade, but no physical system exhibiting this phenomenon has been identified to date...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
Marcello Berto, Stefano Casalini, Michele Di Lauro, Simone L Marasso, Matteo Cocuzza, Denis Perrone, Marcello Pinti, Andrea Cossarizza, Candido F Pirri, Daniel T Simon, Magnus Berggren, Francesco Zerbetto, Carlo A Bortolotti, Fabio Biscarini
Biorecognition is a central event in biological processes in the living systems that is also widely exploited in technological and health applications. We demonstrate that the Electrolyte Gated Organic Field Effect Transistor (EGOFET) is an ultrasensitive and specific device that allows us to quantitatively assess the thermodynamics of biomolecular recognition between a human antibody and its antigen, namely, the inflammatory cytokine TNFα at the solid/liquid interface. The EGOFET biosensor exhibits a superexponential response at TNFα concentration below 1 nM with a minimum detection level of 100 pM...
December 20, 2016: Analytical Chemistry
Ferdinand Greiss, Franziska Kriegel, Dieter Braun
The formation of supramolecular complexes is found in many natural systems and is the basis for cooperative behavior. Here, we report on the development of a high-throughput platform to measure the complex binding behavior in 500 nL volumes and 1 536-well plates. The platform enabled us to elucidate the thermodynamic properties of a heterotrimeric DNA complex that portrays the structure of a biological relevant three-way junction. In a complementing set of cooperative networks, binding constants from ∼0...
January 31, 2017: Analytical Chemistry
Alexei V Finkelstein, Azat J Badretdin, Oxana V Galzitskaya, Dmitry N Ivankov, Natalya S Bogatyreva, Sergiy O Garbuzynskiy
The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured folding times of single-domain globular proteins range from microseconds to hours: the difference (10-11 orders of magnitude) is the same as that between the life span of a mosquito and the age of the universe. This review describes physical theories of rates of overcoming the free-energy barrier separating the natively folded (N) and unfolded (U) states of protein chains in both directions: "U-to-N" and "N-to-U"...
January 27, 2017: Physics of Life Reviews
Vytautas Gapsys, Bert L de Groot
With the increase of available computational power and improvements in simulation algorithms, the alchemical molecular dynamics based free energy calculations have developed into routine usage in the field of computational structural biology. To further facilitate the usability of the alchemical methods for the amino acid mutations, we have developed a web based infrastructure for obtaining hybrid protein structures and topologies. The presented webserver allows amino acid mutation selection in five contemporary molecular mechanics force fields...
February 9, 2017: Journal of Chemical Information and Modeling
Calvin R Chen, George I Makhatadze
Hydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms (for example, piezophiles). Increase in hydrostatic pressure, much like increase in temperature, perturbs the thermodynamic equilibrium between native and unfolded states of proteins. Experimentally, it has been observed that increase in hydrostatic pressure can both increase and decrease protein stability. These observations suggest that volume changes upon protein unfolding can be both positive and negative...
February 7, 2017: Nature Communications
Arne Biesiekierski, Dehai Ping, Yuncang Li, Jixing Lin, Khurram S Munir, Yoko Yamabe-Mitarai, Cuie Wen
: While titanium alloys represent the current state-of-the-art for orthopedic biomaterials, concerns still remain over their modulus. Circumventing this via increased porosity requires high elastic admissible strains, yet also limits traditional thermomechanical strengthening techniques. To this end, a novel β-type Ti-Zr-Ta alloy system, comprised of Ti-45Zr-10Ta, Ti-40Zr-14Ta, Ti-35Zr-18Ta and Ti-30Zr-22Ta, was designed and characterized mechanically and microstructurally. As-cast, this system displayed extremely high yield strengths and elastic admissible strains, up to 1...
February 2, 2017: Acta Biomaterialia
Fan Zhang, Runsheng Liu, Jie Zheng
BACKGROUND: Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a Cytoscape plugin that is able to simulate time-course gene expression data given the user-defined external stimuli to the signaling pathways. METHODS: A generalized logical model is used in modeling the upstream signaling pathways. Then a Boolean model and a thermodynamics-based model are employed to predict the downstream changes in gene expression based on the simulated dynamics of transcription factors in signaling pathways...
December 23, 2016: BMC Systems Biology
A B Gurung, A Bhattacharjee, M Ajmal Ali, F Al-Hemaid, Joongku Lee
Protein-protein interaction is a vital process which drives many important physiological processes in the cell and has also been implicated in several diseases. Though the protein-protein interaction network is quite complex but understanding its interacting partners using both in silico as well as molecular biology techniques can provide better insights for targeting such interactions. Targeting protein-protein interaction with small molecules is a challenging task because of druggability issues. Nevertheless, several studies on the kinetics as well as thermodynamic properties of protein-protein interactions have immensely contributed toward better understanding of the affinity of these complexes...
February 2017: Saudi Journal of Biological Sciences
Jonathan Rittle, Jonas C Peters
Fe-mediated biological nitrogen fixation is thought to proceed via either a sequence of proton and electron transfer steps, concerted H atom transfer steps, or some combination thereof. Regardless of the specifics and whether the intimate mechanism for N2-to-NH3 conversion involves a distal pathway, an alternating pathway, or some hybrid of these limiting scenarios, Fe-NxHy intermediates are implicated that feature reactive N-H bonds. Thermodynamic knowledge of the N-H bond strengths of such species is scant, and is especially difficult to obtain for the most reactive early stage candidate intermediates (e...
February 17, 2017: Journal of the American Chemical Society
Rintaro Iwata Hara, Yusuke Maeda, Taiichi Sakamoto, Takeshi Wada
Novel double-stranded RNA (dsRNA)-binding molecules were developed for the effective thermodynamic and biological stabilization of nucleic acids including short interfering RNAs (siRNAs). β-(1→4)-Linked-2,6-diamino-2,6-dideoxy-d-galactopyranose oligomers (ODAGals) were synthesized for this purpose, and their binding ability with dsRNAs was evaluated. Fluorescence anisotropy measurements showed the 3mer and 4mer of ODAGals to be strongly bound (Kd < 0.02 μM). The UV melting experiments demonstrated that the binding of ODAGals to dsRNAs proceeded with significant thermodynamic stabilization of the duplexes...
January 31, 2017: Organic & Biomolecular Chemistry
Yuqing Qiu, Nathan Odendahl, Arpa Hudait, Ryan Mason, Allan K Bertram, Francesco Paesani, Paul J DeMott, Valeria Molinero
Heterogeneous nucleation of ice induced by organic materials is of fundamental importance for climate, biology, and industry. Among organic ice-nucleating surfaces, monolayers of long chain alcohols are particularly effective, while monolayers of fatty acids are significantly less so. As these monolayers expose to water hydroxyl groups with an order that resembles the one in the basal plane of ice, it was proposed that lattice matching between ice and the surface controls their ice-nucleating efficiency. Organic monolayers are soft materials and display significant fluctuations...
February 14, 2017: Journal of the American Chemical Society
Jun Dai, Chunlei Wang, Sarah C Traeger, Lorell Discenza, Mary T Obermeier, Adrienne A Tymiak, Yingru Zhang
Atropisomers are stereoisomers resulting from hindered bond rotation. From synthesis of pure atropisomers, characterization of their interconversion thermodynamics to investigation of biological stereoselectivity, the evaluation of drug candidates subject to atropisomerism creates special challenges and can be complicated in both early drug discovery and later drug development. In this paper, we demonstrate an array of analytical techniques and systematic approaches to study the atropisomerism of drug molecules to meet these challenges...
March 3, 2017: Journal of Chromatography. A
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