Read by QxMD icon Read

Biological thermodynamics

C Binot, C-H Chouard
The existence of an information vector common to very different pathologies is the hypothesis of one of us, the argumentation and discussion of which we present here. It is a mesomorphic state of material called liquid crystal. The liquid-ordered (Lo) phase, made up of membrane rafts mediated by cholesterol, lies at the center of our concept. This mesophase is either preexistent and then modified by the pathogenic process, or initiated by the latter. The most notable disorders involved are Alzheimer's, Parkinson's, Charcot and Creutzfeldt-Jakob diseases, flu-like illnesses and acquired immunodeficiency syndrome (AIDS), although this list may well be extended to include other anisotropic, birefringent amyloid proteinopathies, which have properties compatible with those of liquid crystals...
March 16, 2018: Revue Neurologique
Reza Yekta, Gholamreza Dehghan, Samaneh Rashtbari, Rahim Ghadari, Ali Akbar Moosavi-Movahedi
Farnesiferol C (FC) is a natural sesquiterpene coumarin, which includes a widely range of biological activities. In this work, effects of FC on the structure and catalytic function of bovine liver catalase (BLC) was assessed by various spectroscopic and theoretical methods. Kinetic studies showed that FC has a remarkable inhibitory activity on BLC via mixed-type inhibition. The IC50 value as the inhibitory strength of FC was evaluated 1.5 μM. Fluorescence spectroscopy, synchronous fluorescence, CD spectroscopy and UV-vis absorption studies revealed conformational changes in the tertiary and secondary structure of BLC as well as the position of the heme group in the presence of different concentrations of FC...
March 14, 2018: International Journal of Biological Macromolecules
A R Plastino, E M F Curado, F D Nobre, C Tsallis
Nonlinear Fokker-Planck equations endowed with power-law diffusion terms have proven to be valuable tools for the study of diverse complex systems in physics, biology, and other fields. The nonlinearity appearing in these evolution equations can be interpreted as providing an effective description of a system of particles interacting via short-range forces while performing overdamped motion under the effect of an external confining potential. This point of view has been recently applied to the study of thermodynamical features of interacting vortices in type II superconductors...
February 2018: Physical Review. E
Yanting Wang, Wenxian Lan, Zhenzhen Yan, Jing Gao, Xinlian Liu, Sheng Wang, Xiying Guo, Chunxi Wang, Hu Zhou, Jiuping Ding, Chunyang Cao
Large-conductance Ca2+ - and voltage-dependent K+ (BK) channels display diverse biological functions while their pore-forming α subunit is coded by a single Slo1 gene. The variety of BK channels is correlated with the effects of BKα coexpression with auxiliary β (β1-β4) subunits, as well as newly defined γ subunits. Charybdotoxin (ChTX) blocks BK channel through physically occluding the K+ -conduction pore. Human brain enriched β4 subunit (hβ4) alters the conductance-voltage curve, slows activation and deactivation time courses of BK channels...
March 15, 2018: Scientific Reports
A V Finkelstein
The ability of proteins to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured rates of spontaneous folding of single-domain globular proteins range from microseconds to hours: the difference - 10-11 orders of magnitude - is the same as between the lifespan of a mosquito and the age of the Universe. This review (based on the literature and some personal recollections) describes a winding road to understanding spontaneous folding of protein structure...
January 2018: Biochemistry. Biokhimii︠a︡
Thai M Hoang, Rui Pan, Jonghoon Ahn, Jaehoon Bang, H T Quan, Tongcang Li
Nonequilibrium processes of small systems such as molecular machines are ubiquitous in biology, chemistry, and physics but are often challenging to comprehend. In the past two decades, several exact thermodynamic relations of nonequilibrium processes, collectively known as fluctuation theorems, have been discovered and provided critical insights. These fluctuation theorems are generalizations of the second law and can be unified by a differential fluctuation theorem. Here we perform the first experimental test of the differential fluctuation theorem using an optically levitated nanosphere in both underdamped and overdamped regimes and in both spatial and velocity spaces...
February 23, 2018: Physical Review Letters
Frank Jülicher, Stephan W Grill, Guillaume Salbreux
We review the general hydrodynamic theory of active soft materials that is motivated in partic- ular by biological matter. We present basic concepts of irreversible thermodynamics of spatially extended multicomponent active systems. Starting from the rate of entropy production, we iden- tify conjugate thermodynamic fluxes and forces and present generic constitutive equations of polar active fluids and active gels. We also discuss angular momentum conservation which plays a role in the the physics of active chiral gels...
March 15, 2018: Reports on Progress in Physics
Sneha Munshi, Soundhararajan Gopi, Sandhyaa Subramanian, Luis A Campos, Athi N Naganathan
The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature...
March 10, 2018: Nucleic Acids Research
Negin Sabziparvar, Yosra Saeedi, Mina Nouri, Atefeh Sadat Najafi Bozorgi, Elahe Alizadeh, Farnoosh Attar, Keivan Akhtari, Seyyedeh Elaheh Mousavi, Mojtaba Falahati
NPs have received a great attention in biological and medical applications due to their unique features. However, their induced adverse effects on the biological system are not well explored. Herein, the interaction of silicon dioxide nanoparticle (SiO2 NP) with human hemoglobin (Hb) and lymphocyte cell line was evaluated under physiological conditions by multi spectroscopic (intrinsic and synchronous fluorescence spectroscopy, and circular dichrosim (CD)), molecular docking, and cellular (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide (MTT) and acridine orange/ethidium bromide (AO/EB) staining) methods...
March 14, 2018: Journal of Physical Chemistry. B
Daniel J Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J Andrew McCammon, Ross C Walker
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average...
March 12, 2018: Journal of Computational Chemistry
Hessam Sepasi Tehrani, Ali Akbar Moosavi-Movahedi
Catalase is one of the firsts in every realm of biological sciences. At the same time it also has a number of unusual features. It has one of the highest turnovers numbers of any enzymes. It is essential for neutralizing the noxious hydrogen peroxide both in the nature and the various industries such as dairy, textile and pharmaceutics. It also has the merit of being one of the first protein crystals to be isolated. Ironically its three-dimensional structure was discerned some forty years later. However through the times this senile enzyme has continued to intrigue the scientists by surprising facts and phenomena, such as peculiar interweaving of subunits and remarkable thermal stability...
March 9, 2018: Progress in Biophysics and Molecular Biology
Xiangrong Li, Kaiwei Wang, Yanru Peng
The interaction of nanoparticles (NPs) with proteins is a topic of high relevance for the medical application of nanomaterials. In the study, a comprehensive investigation was performed for the binding properties of silver nanoparticles (AgNPs) to pepsin. The results indicate that the binding of AgNPs to pepsin may be a static quenching mechanism. Thermodynamic analysis reveals that AgNPs binds to pepsin is synergistically driven by enthalpy and entropy, and the major driving forces are hydrophobic and electrostatic interactions...
March 9, 2018: Chemico-biological Interactions
Liora Werber, Yitzhak Mastai
One of the most powerful techniques that are currently available to measure thermodynamic parameters such as enthalpy (ΔH), Gibbs free energy (ΔG), entropy changes (ΔS), and binding affinity in chemical reactions is isothermal titration calorimetry (ITC). Recent advances in instrumentation have facilitated the development of ITC as a very essential analytical tool in biology and chemistry. In this article, we will focus on a review of the literature on the application of ITC for the study of chiral systems and chiral interactions...
March 12, 2018: Chirality
Allan B James, Stuart Sullivan, Hugh G Nimmo
How plants perceive and respond to temperature remains an important question in the plant sciences. Temperature perception and signal transduction may occur through temperature-sensitive intra-molecular folding of primary mRNA transcripts. Recent studies suggested a role for retention of the first intron in the 5'UTR of the clock component LATE ELONGATED HYPOCOTYL (LHY) in response to changes in temperature. Here we identified a set of haplotypes in the LHY 5'UTR, examined their global spatial distribution and obtained evidence that haplotype can affect temperature-dependent splicing of LHY transcripts...
March 8, 2018: Plant, Cell & Environment
Erik W Martin, Tanja Mittag
Liquid-liquid phase separation seems to play critical roles in the compartmentalization of cells through the formation of biomolecular condensates. Many proteins with low-complexity regions are found in these condensates, and they can undergo phase separation in vitro in response to changes in temperature, pH and ion concentration. Low-complexity regions are thus likely important players in mediating compartmentalization in response to stress. However, how the phase behavior is encoded in their amino acid composition and patterning is only poorly understood...
March 8, 2018: Biochemistry
Hong-Liang Bao, Yan Xu
Growing evidence indicates that RNA G-quadruplexes have important roles in various processes such as transcription, translation, regulation of telomere length, and formation of telomeric heterochromatin. Investigation of RNA G-quadruplex structures associated with biological events is therefore essential to understanding the functions of these RNA molecules. We recently demonstrated that the sensitivity and simplicity of19 F NMR can be used to directly observe higher-order telomeric G-quadruplexes of labeled RNA molecules in vitro and in living cells, as well as their interactions with ligands and proteins...
April 2018: Nature Protocols
Pedro Serra, Amber Messmer, Daniel Sanderson, Delano James, Ricardo Flores
Apple hammerhead viroid-like RNA (AHVd RNA) has been reported in different apple cultivars and geographic regions and, considering the presence of hammerhead ribozymes in both polarity strands, suspected to be either a viroid of the family Avsunviroidae or a viroid-like satellite RNA. Here we report that dimeric head-to-tail in vitro transcripts of a 433-nt reference variant of AHVd RNA from cultivar "Pacific Gala" are infectious when mechanically inoculated to apple, thus showing that this RNA is a bona fide viroid for which we have kept the name apple hammerhead viroid (AHVd) until its pathogenicity, if any, is better assessed...
March 3, 2018: Virus Research
Antonio Benedetto, Pietro Ballone
Empirical evidence and conceptual elaboration reveal and rationalise the remarkable affinity of organic ionic liquids for biomembranes. Cations of the so-called room-temperature ionic liquids (RTILs), in particular, are readily absorbed into the lipid fraction of biomembranes, causing a variety of observable biological effects, including generic cytotoxicity, broad anti-bacterial potential, and anti-cancer activity. Chemical-physics analysis of model systems made of phospholipid bilayers, RTIL ions and water confirm and partly explain this evidence, quantifying the mild destabilising effect of RTILs on structural, dynamical and thermodynamic properties of lipids in biomembranes...
March 6, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Rikiya Watanabe, Takaharu Sakuragi, Hiroyuki Noji, Shigekazu Nagata
Transmembrane protein 16F (TMEM16F) is a Ca2+ -dependent phospholipid scramblase that translocates phospholipids bidirectionally between the leaflets of the plasma membrane. Phospholipid scrambling of TMEM16F causes exposure of phosphatidylserine in activated platelets to induce blood clotting and in differentiated osteoblasts to promote bone mineralization. Despite the importance of TMEM16F-mediated phospholipid scrambling in various biological reactions, the fundamental features of the scrambling reaction remain elusive due to technical difficulties in the preparation of a platform for assaying scramblase activity in vitro...
March 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Federico Gnesotto, Federica Mura, Jannes Gladrow, Chase Broedersz
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors...
March 5, 2018: Reports on Progress in Physics
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"