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Biological thermodynamics

Wonseok Hwang, Changbong Hyeon
An efficient molecular motor would deliver cargos to the target site at a high speed and in a punctual manner while consuming a minimal amount of energy. According to a recently formulated thermodynamic principle, referred to as the thermodynamic uncertainty relation, the travel distance of a motor and its variance are, however, constrained by the free energy being consumed. Here we use the principle underlying the uncertainty relation to quantify the transport efficiency of molecular motors for varying ATP concentration ([ATP]) and applied load (f)...
January 12, 2018: Journal of Physical Chemistry Letters
Alan J Situ, So-Min Kang, Benjamin B Frey, Woojin An, Chungho Kim, Tobias S Ulmer
The function of membrane proteins relies on a defined orientation of protein relative to lipid. In apparent correlation to protein anchoring, tryptophan residues are enriched in the lipid headgroup region. To characterize the thermodynamic and structural basis of this relationship in α-helical membrane proteins, we examined the role of three conserved tryptophans in the folding of the heterodimeric integrin αIIbβ3 transmembrane (TM) complex in phospholipid bicelles and mammalian membranes. In the homogenous lipid environment of bicelles, tryptophan was replaceable by residues of distinct polarities...
January 11, 2018: Journal of Physical Chemistry. B
Huan-Xiang Zhou, Xiaodong Pang
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions...
January 10, 2018: Chemical Reviews
Cheng-Cheng Zhang, Jin-Song Guo, You-Peng Chen, Fang-Ying Ji, Jing Wang, Peng Yan, Yun Bai
The removal of antibiotics in biological wastewater treatment plants has attracted an ever-increasing interest. Extracellular polymeric substances (EPS) play a crucial role in antibiotics bio-adsorption using activated sludge, but the interaction mechanism between antibiotics and EPS remains unclear. In this study, the thermodynamics of interactions between extracellular polymeric substances (EPS) and antibiotics (acetaminophen (ACT) and sulfamethazine (SMZ)) were investigated via isothermal titration calorimetry (ITC)...
January 10, 2018: Environmental Technology
Hossein Nikoofard, Mohsen Sargolzaei, Farnosh Faridbod
A computational study at the density functional theory (DFT) as well as electrochemical methods, was carried out on the structural and physico-chemical properties of a series of sulfonamide derivatives (SAs) as WHO essential medications in the treatment of basic health system. The B3LYP/6-311++G(d,p) level of theory carried out on sulfadiazine (SDZ), sulfathiazole (STZ), sulfaquinoxaline (SQX), sulfacetamide (SAA), and the reference unsubstituted sulfonamide (SA) was discussed and rationalized in term of the N1-sulfonamide substituent...
December 2017: Acta Chimica Slovenica
Lela Lackey, Aaztli Coria, Chanin Woods, Evonne McArthur, Alain Laederach
The precise impact of inherited and somatic mutations on messenger RNA (mRNA) structure remains poorly understood. Recent technological advances that leverage next generation sequencing to obtain experimental structure data, such as SHAPE-MaP (Selective 2' Hydroxyl Acylation by Primer Extension and Mutational Profiling), can reveal structural effects of mutations especially when this data is rigorously incorporated in RNA structural modeling. Here we analyze the ability of SHAPE-MaP to detect the relatively subtle structural changes caused by single nucleotide mutations...
January 9, 2018: RNA
Andres Fernandez-Reche, Eva S Cobos, Irene Luque, Javier Ruiz-Sanz, Jose C Martinez
In 1972 Christian B. Anfinsen received the Nobel Prize in Chemistry for "…his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation." The understanding of this principle is crucial for physical biochemistry students, since protein folding studies, bio-computing sciences and protein design approaches are founded on such a well-demonstrated connection. Herein, we describe a detailed and easy-to-follow experiment to reproduce the most relevant assays carried out at Anfinsen's laboratory in the 60s...
January 4, 2018: Biochemistry and Molecular Biology Education
Joel Berry, Cliff Brangwynne, Mikko P Haataja
Exciting recent developments suggest that phase transitions represent an important and ubiquitous mechanism underlying intracellular organization. We describe key experimental findings in this area of study, as well as the application of classical theoretical approaches for quantitatively understanding these data. We also discuss the way in which equilibrium thermodynamic driving forces may interface with the fundamentally out-of-equilibrium nature of living cells. In particular, time and/or space-dependent concentration profiles may modulate the phase behavior of biomolecules in living cells...
January 9, 2018: Reports on Progress in Physics
Hongze Gang, Celine Galvagnion, Georg Meisl, Thomas Müller, Alexander K Buell, Aviad Levin, Christopher M Dobson, Bo-Zhong Mu, Tuomas P J Knowles
Elucidation of the fundamental interactions of proteins with biological membranes under native conditions is crucial for understanding the molecular basis of their biological function and malfunction. Notably, the large surface to volume ratio of living cells provides a molecular landscape for significant interactions of cellular components with membranes modulating their function. However, such interactions can be challenging to probe using conventional biophysical methods due to the heterogeneity of the species and processes involved...
January 9, 2018: Analytical Chemistry
Kun Zhang, Jin Wang
Cell cycle is an indispensable process in the proliferation and development. Despite significant efforts, global quantification and physical understanding are still challenging. In this study, we explored the mechanisms of Xenopus laevis embryonic cell cycle by quantifying the underlying landscape and flux. We uncovered the Mexican hat landscape of the Xenopus laevis embryonic cell cycle with several local basins and barriers on the oscillation path. The local basins characterize the different phases of Xenopus laevis embryonic cell cycle and the local barriers represent the checkpoints...
January 8, 2018: Journal of Physical Chemistry. B
Dibyendu Mandal, Katherine Klymko, Michael R DeWeese
Active biological systems reside far from equilibrium, dissipating heat even in their steady state, thus requiring an extension of conventional equilibrium thermodynamics and statistical mechanics. In this Letter, we have extended the emerging framework of stochastic thermodynamics to active matter. In particular, for the active Ornstein-Uhlenbeck model, we have provided consistent definitions of thermodynamic quantities such as work, energy, heat, entropy, and entropy production at the level of single, stochastic trajectories and derived related fluctuation relations...
December 22, 2017: Physical Review Letters
M Muthukumar
From the beginning of life with the information-containing polymers until the present era of a plethora of water-based materials in health care industry and biotechnology, polyelectrolytes are ubiquitous with a broad range of structural and functional properties. The main attribute of polyelectrolyte solutions is that all molecules are strongly correlated both topologically and electrostatically in their neutralizing background of charged ions in highly polarizable solvent. These strong correlations and the necessary use of numerous variables in experiments on polyelectrolytes have presented immense challenges toward fundamental understanding of the various behaviors of charged polymeric systems...
December 26, 2017: Macromolecules
Robert C Jennings, Erica Belgio, Giuseppe Zucchelli
It is often suggested that Life may lay outside the normal laws of Physics and particularly of Thermodynamics, though this point of view is refuted by many. As the Living State may be thought of as an open system, often far from equilibrium, most attempts at placing Life under the umbrella of the laws of Physics have been based, particularly in recent years, on non-equilibrium Thermodynamics and particularly the Maximum Entropy Production Principle. In this view it is the dissipation of entropy (heat) which permits the ever increasing complexity of Living Systems in biological evolution and the maintenance of this complexity...
December 19, 2017: Biophysical Chemistry
Patrick D Mathews, Ana Carolina Monge Fernandes Patta, Joao Vitor Gonçalves, Gabriella Dos Santos Gama, Irene Teresinha Santos Garcia, Omar Mertins
Biomaterials conceived for vectorization of bioactives are currently considered for biomedical, biological and environmental applications. We have produced a pH sensitive biomaterial composed of natural source alginate and chitosan polysaccharides for application as drug delivery system via oral administration. The composite particles preparation was in situ monitored by means of isothermal titration calorimetry. The strong interaction established between the macromolecules during particles assembling lead to 0...
December 28, 2017: Biomacromolecules
Min-Chul Kim, Sang-Yup Lee
Carbonic anhydrase (CA) is a ubiquitous metalloenzyme with a Zn cofactor coordinated with trigonal histidine imidazole moieties in a tetrahedral geometry. Removal of the Zn cofactor in CA and subsequent binding of Ir afforded CA[Ir]. Under mild and neutral conditions (30 °C, pH 7), CA[Ir] exhibited water-oxidizing activity with a turnover frequency (TOF) of 39.8 min-1, comparable to those of other Ir-based molecular catalysts. Coordination of Ir to the apoprotein of CA is thermodynamically preferred and is associated with an exothermic energy change (ΔH) of -10...
December 28, 2017: Chemistry, An Asian Journal
Gaetano Campi, Michael Di Gioacchino, Nicola Poccia, Alessandro Ricci, Manfred Burghammer, Gabriele Ciasca, Antonio Bianconi
Ultrastructural fluctuations at nanoscale are fundamental to assess properties and functionalities of advanced out-of-equilibrium materials. We have taken myelin as a model of supramolecular assembly in out-of-equilibrium living matter. Myelin sheath is a simple stable multi-lamellar structure of high relevance and impact in biomedicine. Although it is known that myelin has a quasi-crystalline ultrastructure there is no information on its fluctuations at nanoscale in different states due to limitations of the available standard techniques...
December 27, 2017: ACS Nano
Pallavi Banerjee, Sudip Roy, Nitish Nair
We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intra-polymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations...
December 26, 2017: Journal of Physical Chemistry. B
S Thirupathi Reddy, Sandeep Shrivastava, Amitabha Chattopadhyay
The molecular mechanism underlying the action of local anesthetics is still elusive. Phenylethanol (PEtOH) is an ingredient of essential oils with a rose-like odor and has been used as a local anesthetic. In this work, we have explored the effect of PEtOH on thermotropic behavior and organization of dipalmitoylphosphatidylcholine (DPPC) membranes utilizing differential scanning calorimetry (DSC) and small angle X-ray scattering (SAXS). Our results indicate that the phase transition temperature of DPPC exhibited decrease with increasing PEtOH concentration...
December 21, 2017: Chemistry and Physics of Lipids
Rudolf Rigler, Jerker Widengren
In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later...
December 19, 2017: European Biophysics Journal: EBJ
Xiao Cong, Yang Liu, Wen Liu, Xiaowen Liang, Arthur Laganowsky
The diverse lipid environment of the biological membrane can modulate the structure and function of membrane proteins. However, little is known about the role that lipids play in modulating protein-protein interactions. Here we employed native mass spectrometry (MS) to determine how individual lipid-binding events to the ammonia channel (AmtB) modulate its interaction with the regulatory protein, GlnK. The thermodynamic signature of AmtB-GlnK in the absence of lipids indicates conformational dynamics. A small number of lipids bound to AmtB is sufficient to modulate the interaction with GlnK, and lipids with different headgroups display a range of allosteric modulation...
December 19, 2017: Nature Communications
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