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Biological thermodynamics

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https://www.readbyqxmd.com/read/28921984/melting-behavior-of-a-dna-four-way-junction-using-spectroscopic-and-calorimetric-techniques
#1
Carolyn E Carr, Luis A Marky
Intramolecular four-way junctions are structures present during homologous recombination, repair of double stranded DNA breaks and integron recombination, in addition to many others. Because of the wide range of biological processes four-way junctions are involved in, understanding how and under what conditions these structures form is critical. In this work, we used a combination of spectroscopic and calorimetric techniques to present a complete thermodynamic description of the unfolding of a DNA four-way junction (FWJ) and its appropriate control stem-loop motifs (Dumbbell, GAAATT-Hp, CTATC-Hp, GTGC-Hp, and GCGC-Hp)...
September 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28915267/cooling-induces-phase-separation-in-membranes-derived-from-isolated-cns-myelin
#2
Julio M Pusterla, Emanuel Schneck, Sérgio S Funari, Bruno Démé, Motomu Tanaka, Rafael G Oliveira
Purified myelin membranes (PMMs) are the starting material for biochemical analyses such as the isolation of detergent-insoluble glycosphingolipid-rich domains (DIGs), which are believed to be representatives of functional lipid rafts. The normal DIGs isolation protocol involves the extraction of lipids under moderate cooling. Here, we thus address the influence of cooling on the structure of PMMs and its sub-fractions. Thermodynamic and structural aspects of periodic, multilamellar PMMs are examined between 4°C and 45°C and in various biologically relevant aqueous solutions...
2017: PloS One
https://www.readbyqxmd.com/read/28913524/reassessing-sers-enhancement-factors-using-thermodynamics-to-drive-substrate-design
#3
J A Guicheteau, A Tripathi, E D Emmons, S D Christesen, Augustus W Fountain
Over the past 40 years fundamental and application research into Surface-Enhanced Raman Scattering (SERS) has been explored by academia, industry, and government laboratories. To date however, SERS has achieved little commercial success as an analytical technique. Researchers are tackling a variety of paths to help break through the commercial barrier by addressing the reproducibility in both the SERS substrates and SERS signals as well as continuing to explore the underlying mechanisms. To this end, investigators use a variety of methodologies, typically studying strongly binding analytes such as aromatic thiols and azarenes, and report SERS enhancement factor calculations...
September 15, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28912575/thermodynamics-of-nanodisc-formation-mediated-by-styrene-maleic-acid-2-1-copolymer
#4
Anne Grethen, Abraham Olusegun Oluwole, Bartholomäus Danielczak, Carolyn Vargas, Sandro Keller
Styrene/maleic acid copolymers (SMA) have recently attracted great interest for in vitro studies of membrane proteins, as they self-insert into and fragment biological membranes to form polymer-bounded nanodiscs that provide a native-like lipid-bilayer environment. SMA copolymers are available in different styrene/maleic acid ratios and chain lengths and, thus, possess different charge densities, hydrophobicities, and solubilisation properties. Here, we studied the equilibrium solubilisation properties of the most commonly used copolymer, SMA(2:1), by monitoring the formation of nanodiscs from phospholipid vesicles using (31)P nuclear magnetic resonance spectroscopy, dynamic light scattering, and differential scanning calorimetry...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28885748/extensive-study-on-physicochemical-properties-of-polychlorinated-biphenyls-in-a-commercial-ion-trap-mass-spectrometer-relevance-in-analytical-and-environmental-chemistry
#5
R Narizzano, F Risso, A Magherini, G Cordone, M Ottonelli, E Smirnova, S Nadotti, L Rivara, R La Rocca, E Magi, S Lottici, S Maggiolo, C E Pepe, M Garbarino
Polychlorinated biphenyls (PCBs) exist as 209 congeners, consisting of biphenyl molecules, where the number and substitution positions of halogen atoms are known to affect industrial uses, environmental transport mechanisms, distribution, fate, and toxicity. The complexity of the problem requires accurate physicochemical studies of an increasing number of congeners in order to understand the environmental and biological processes at play. This work presents a systematic study on the thermodynamic and kinetic properties of PCBs by quadrupole ion trap mass spectrometry...
September 8, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28876055/supramolecular-assembly-of-peptide-amphiphiles
#6
Mark P Hendricks, Kohei Sato, Liam C Palmer, Samuel I Stupp
Peptide amphiphiles (PAs) are small molecules that contain hydrophobic components covalently conjugated to peptides. In this Account, we describe recent advances involving PAs that consist of a short peptide sequence linked to an aliphatic tail. The peptide sequence can be designed to form β-sheets among the amino acids near the alkyl tail, while the residues farthest from the tail are charged to promote solubility and in some cases contain a bioactive sequence. In water, β-sheet formation and hydrophobic collapse of the aliphatic tails induce assembly of the molecules into supramolecular one-dimensional nanostructures, commonly high-aspect-ratio cylindrical or ribbonlike nanofibers...
September 6, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28876046/electron-bifurcation-thermodynamics-and-kinetics-of-two-electron-brokering-in-biological-redox-chemistry
#7
Peng Zhang, Jonathon L Yuly, Carolyn E Lubner, David W Mulder, Paul W King, John W Peters, David N Beratan
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently...
September 6, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28874584/a-classical-view-on-nonclassical-nucleation
#8
Paul J M Smeets, Aaron R Finney, Wouter J E M Habraken, Fabio Nudelman, Heiner Friedrich, Jozua Laven, James J De Yoreo, P Mark Rodger, Nico A J M Sommerdijk
Understanding and controlling nucleation is important for many crystallization applications. Calcium carbonate (CaCO3) is often used as a model system to investigate nucleation mechanisms. Despite its great importance in geology, biology, and many industrial applications, CaCO3 nucleation is still a topic of intense discussion, with new pathways for its growth from ions in solution proposed in recent years. These new pathways include the so-called nonclassical nucleation mechanism via the assembly of thermodynamically stable prenucleation clusters, as well as the formation of a dense liquid precursor phase via liquid-liquid phase separation...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28869862/bmp-2-and-bmp-9-binding-specificities-with-alk-3-in-aqueous-solution-with-dynamics
#9
Orkid Coskuner, Vladimir N Uversky
Signal ligands of the transforming growth factor-β (TGF-β) superfamily include the bone morphogenetic proteins (BMPs). BMPs bind to type I and type II serine-threonine kinase receptors and trigger the transphosphorylation cascade, wherein the active type II receptor phosphorylates the inactive type I receptor. This process further activates the cytoplasmic effectors of the pathway, such as SMAD proteins, which are homologs of both the Drosophila protein MAD (mothers against decapentaplegic) and the Caenorhabditis elegans protein SMA (small body size)...
August 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28858496/characterization-of-the-fleeting-hydroxoiron-iii-complex-of-the-pentadentate-tmc-py-ligand
#10
Wei-Min Ching, Ang Zhou, Johannes E M N Klein, Ruixi Fan, Gerald Knizia, Christopher J Cramer, Yisong Guo, Lawrence Que
Nonheme mononuclear hydroxoiron(III) species are important intermediates in biological oxidations, but well-characterized examples of synthetic complexes are scarce due to their instability or tendency to form μ-oxodiiron(III) complexes, which are the thermodynamic sink for such chemistry. Herein, we report the successful stabilization and characterization of a mononuclear hydroxoiron(III) complex, [Fe(III)(OH)(TMC-py)](2+) (3; TMC-py = 1-(pyridyl-2'-methyl)-4,8,11-trimethyl-1,4,8,11-tetrazacyclotetradecane), which is directly generated from the reaction of [Fe(IV)(O)(TMC-py)](2+) (2) with 1,4-cyclohexadiene at -40 °C by H-atom abstraction...
August 31, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28830066/partitioning-of-hydrophobic-organic-contaminants-between-polymer-and-lipids-for-two-silicones-and-low-density-polyethylene
#11
Foppe Smedes, Tatsiana P Rusina, Henry Beeltje, Philipp Mayer
Polymers are increasingly used for passive sampling of neutral hydrophobic organic substances (HOC) in environmental media including water, air, soil, sediment and even biological tissue. The equilibrium concentration of HOC in the polymer can be measured and then converted into equilibrium concentrations in other (defined) media, which however requires appropriate polymer to media partition coefficients. We determined thus polymer-lipid partition coefficients (KPL) of various PCB, PAH and organochlorine pesticides by equilibration of two silicones and low density polyethylene (LDPE) with fish oil and Triolein at 4 °C and 20 °C...
November 2017: Chemosphere
https://www.readbyqxmd.com/read/28828732/coding-of-class-i-and-ii-aminoacyl-trna-synthetases
#12
Charles W Carter
The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene...
August 22, 2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28810057/crowders-and-cosolvents-major-contributors-to-the-cellular-milieu-and-efficient-means-to-counteract-environmental-stresses
#13
Roland Hermann Alfons Winter, Mimi Gao, Christoph Held, Satyajit Patra, Loana Arns, Gabriele Sadowski
The free energy and conformational landscape of biomolecular systems as well as biochemical reactions depend not only on temperature and pressure, but also only the particular solution conditions. Such conditions include the effects of cosolvents (for example osmolytes) and macromolecular crowding, which are crucial components to understand the energetics and kinetics of biological processes in living system. Such conditions are also important for the understanding of many debilitating diseases, such as those where misfolding and amyloid formation of proteins are involved...
August 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28809537/confined-water-structure-dynamics-and-thermodynamics
#14
Sudip Chakraborty, Hemant Kumar, Chandan Dasgupta, Prabal K Maiti
Understanding the properties of strongly confined water is important for a variety of applications such as fast flow and desalination devices, voltage generation, flow sensing, and nanofluidics. Confined water also plays an important role in many biological processes such as flow through ion channels. Water in the bulk exhibits many unusual properties that arise primarily from the presence of a network of hydrogen bonds. Strong confinement in structures such as carbon nanotubes (CNTs) substantially modifies the structural, thermodynamic, and dynamic (both translational and orientational) properties of water by changing the structure of the hydrogen bond network...
August 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28809494/on-protein-assembly-and-building-blocks-beyond-the-limits-of-the-lego-bricks-metaphor
#15
Yaakov Levy
Proteins, similarly to other biomolecules, have a modular and hierarchical structure. Various building blocks serve to construct proteins of high structural complexity and diverse functionality. In multi-domain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO bricks metaphor is justified as a means of simplifying the complexity of 3-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talks that are essential to protein function...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28808810/interactions-of-cisplatin-analogues-with-lysozyme-a-comparative-analysis
#16
Giarita Ferraro, Ilaria De Benedictis, Annamaria Malfitano, Giancarlo Morelli, Ettore Novellino, Daniela Marasco
The biophysical characterization of drug binding to proteins plays a key role in structural biology and in the discovery and optimization of drug discovery processes. The search for optimal combinations of biophysical techniques that can correctly and efficiently identify and quantify binding of metal-based drugs to their final target is challenging, due to the physicochemical properties of these agents. Different cisplatin derivatives have shown different citotoxicities in most common cancer lines, suggesting that they exert their biological activity via different mechanisms of action...
August 14, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28808343/structure-formation-during-translocon-unassisted-co-translational-membrane-protein-folding
#17
Nicola J Harris, Eamonn Reading, Kenichi Ataka, Lucjan Grzegorzewski, Kalypso Charalambous, Xia Liu, Ramona Schlesinger, Joachim Heberle, Paula J Booth
Correctly folded membrane proteins underlie a plethora of cellular processes, but little is known about how they fold. Knowledge of folding mechanisms centres on reversible folding of chemically denatured membrane proteins. However, this cannot replicate the unidirectional elongation of the protein chain during co-translational folding in the cell, where insertion is assisted by translocase apparatus. We show that a lipid membrane (devoid of translocase components) is sufficient for successful co-translational folding of two bacterial α-helical membrane proteins, DsbB and GlpG...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808132/defining-electron-bifurcation-in-the-electron-transferring-flavoprotein-family
#18
Amaya M Garcia Costas, Saroj Poudel, Anne-Frances Miller, Gerrit J Schut, Rhesa N Ledbetter, Kathryn R Fixen, Lance C Seefeldt, Michael W W Adams, Caroline S Harwood, Eric S Boyd, John W Peters
Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low and high potential electrons. It is the third recognized form of energy conservation in biology and has recently been described in select electron transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via ETF quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer as well as a non-redox active adenosine monophosphate (AMP)...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28806872/di-and-trivalent-metal-ion-solution-studies-with-the-phosphinate-containing-heterocycle-deda-po
#19
David M Weekes, Maria de Guadalupe Jaraquemada-Peláez, Thomas I Kostelnik, Brian O Patrick, Chris Orvig
A 7-membered triprotic heterocycle, DEDA-(PO), was synthesized, characterized, and tested for its solution properties with three trivalent lanthanides (La(3+), Gd(3+), and Lu(3+)) and three biologically relevant divalent metal ions (Ca(2+), Zn(2+), and Cu(2+)). The ligand synthesis has been reported once before; however, the characterization results were previously misinterpreted to correspond to a larger, 14-membered heterocycle, TETA-(PO)2. This manuscript serves to correct the original paper. Potentiometric titrations were carried out with each of the metal ions, and the thermodynamic stability values in terms of log β and log KML were calculated showing a 1:1 metal-to-ligand ratio preference for the divalent metal ions and a 1:2 ratio for the lanthanides...
August 15, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28806680/sequestration-of-aluminium-iii-by-different-natural-and-synthetic-organic-and-inorganic-ligands-in-aqueous-solution
#20
Paola Cardiano, Rosalia Maria Cigala, Francesco Crea, Fausta Giacobello, Ottavia Giuffrè, Anna Irto, Gabriele Lando, Silvio Sammartano
The speciation of Al(3+) in aqueous solutions containing organic and inorganic ligands important from a biological (citrate (Cit(3-)), gluconate (Gluc(-)), lactate (Lac(-)), silicate (H2SiO4(2-)), carbonate (CO3(2-)), fluoride (F(-))) and industrial (Gantrez(®); polymethyl-vinyl-ether-co-maleic acids; GTZ S95 and GTZ AN169) point of view is reported. The stability constants of Al(3+)/L(z-) complexes (L(z-) = ligand with z(-) charge) were determined by potentiometry at T = 298.15 K and 0.10 ≤ I/M ≤ 1...
November 2017: Chemosphere
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