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Biophysical Chemistry

Current research reports and chronological list of recent articles..




The scientific journal Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal.

The publisher is Elsevier. The copyright and publishing rights of specialized products listed below are in this publishing house. This is also responsible for the content shown.

To search this web page for specific words type "Ctrl" + "F" on your keyboard (Command + "F" on a Mac). Then: type the word you are searching for in the window that pops up!

Additional research articles see Current Chemistry Research Articles. Magazines with similar content (biophysical chemistry):

 - Biomacromolecules.

 - Faraday Discussions.

 - Journal of Physical Chemistry B.

 - Physical Chemistry Chemical Physics PCCP.



Biophysical Chemistry - Abstracts



Integration of demand and supply sides in the ATP energy economics of cells

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Sunil Nath

Abstract

The central aspects of the energy economics of living cells revolve around the synthesis and utilization of molecules of adenosine triphosphate (ATP). Current descriptions of cell metabolism and its regulation in most textbooks of biochemistry assume that enzymes and transporters behave in the same way in isolation and in a cell. Calculations of the mechanistic or maximal P/O ratios in oxidative phosphorylation by mammalian cells generally consider only the supply side of the problem without linking to ATP-demand processes. The purpose of this article is to calculate the mechanistic P/O ratio by integration of the supply and demand sides of ATP reactions. The mechanistic stoichiometry calculated from an integrated approach is compared with that obtained from the standard model that considers only ATP supply. After accounting for leaks, slips, and other losses, the actual or operative P/O calculated by the integrated method is found to be in good agreement with the experimental values of the P/O ratio determined in mitochondria for both succinate and NADH-linked respiratory substrates. The thermodynamic consequences of these results and the biological implications are discussed. An integrated model of oxidative phosphorylation that goes beyond the chemiosmotic theory is presented, and a solution to the longstanding fundamental problem of respiratory control is found.

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Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

Author(s): Vivianne Basílio Barbosa, Erik de Oliveira Martins, Gerald Weber

Abstract

Gene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from which we recalculated the nearest-neighbour parameters, reducing the average temperature prediction uncertainty to 1.6 °C. Two experimental sets using temperatures extracted via different methods were used with similar results, with the curve-fitting method achieving a slight advantage in prediction quality over other methods. Additionally, we obtained new parameters for low salt with an average uncertainty of 0.98 °C. We also tested several types of salt correction factors and concluded that it is advisable to use those originally developed for RNA/RNA rather than for DNA/DNA.

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The dynamics of K<sup>+</sup> channel gates as a biological transistor

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Yuval Ben-Abu

Abstract

Potassium channels are pore-forming membrane proteins that open and close in response to changes in a chemical or electrical potential, thereby regulating the flow of potassium ions across biological membranes. Two regions of the same channels are acting in tandem and enable ion flow through the channel pore. I refer to this coupled action as a “gate linker”. To closely examine the role of the gate linker in the channel function, I mutated the amino acids in the cDNA of this region, and used from knowen mutaion, either alone or together with the amino acids of adjacent regions.

I have emphasized the importance of the linker between these two gates - mutations in this region may cause conformational changes that play a fundamental role in mediating the coupling between the voltage sensor, activation gate and selectivity filter elements of Kv channels. I observe that free energy considerations show the significance of the coupling between the activation and inactivation gates. Moreover, a symmetry between the coupling and sensor spring strength leads to the destruction of ion conductivity. I present a thermodynamic framework for the possible study of multiple channel blocks. The arising physical perspective of the gating process gives rise to new research avenues of the coupling mode of potassium channels and may assist in explaining the centrality of the “gate linker” to the channel function.


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Evaluation of heating effects on the morphology and membrane structure of <em>Escherichia coli</em> using electron paramagnetic resonance spectroscopy

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Bade Tonyali, Austin McDaniel, Valentina Trinetta, Umut Yucel

Abstract

Bacterial cell characteristics, such as size, morphology, and membrane integrity, are affected by environmental conditions. Thermal treatment results in related structural changes, extent of which is determined by the microorganism's survival skills and inactivation kinetics. The objective of this study was to characterize changes in cell structure of Escherichia coli during heating using the combined analysis of dynamic light scattering (DLS), electron paramagnetic resonance (EPR) spectroscopy, and transmission electron microscopy (TEM) techniques. The size of E. coli cells increased from 2.3 μm to 3.0 μm with heating up to 50 °C followed by a shrinkage with further heating up to 70 °C. The morphological changes were verified using transmission electron microscopy. Related changes in membrane integrity was quantified via the mobility of 16-doxylstearic acid (16-DSA) spin probe using EPR spectroscopy. Two order parameters S1 and S2 defined on x- and y-axes, respectively, decreased with increasing temperature indicating loss of membrane integrity. The combined techniques as in this study can be used to further understand factors that play role in survival behavior of microorganisms.

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Analyzing protein-ligand and protein-interface interactions using high pressure

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Artem Levin, Süleyman Cinar, Michael Paulus, Julia Nase, Roland Winter, Claus Czeslik

Abstract

All protein function is based on interactions with the environment. Proteins can bind molecules for their transport, their catalytic conversion, or for signal transduction. They can bind to each other, and they adsorb at interfaces, such as lipid membranes or material surfaces. An experimental characterization is needed to understand the underlying mechanisms, but also to make use of proteins in biotechnology or biomedicine. When protein interactions are studied under high pressure, volume changes are revealed that directly describe spatial contributions to these interactions. Moreover, the strength of protein interactions with ligands or interfaces can be tuned in a smooth way by pressure modulation, which can be utilized in the design of drugs and bio-responsive interfaces. In this short review, selected studies of protein-ligand and protein-interface interactions are presented that were carried out under high pressure. Furthermore, a perspective on bio-responsive interfaces is given where protein-ligand binding is applied to create functional interfacial structures.

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How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime?

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Narendra Kumar, Dominik Marx

Abstract

Solvation by water plays an important role in the functional dynamics of biomacromolecules such as proteins or nucleic acids. This suggests that changes in solvation might drastically affect their functionality. Among other solvation stressors such as temperature, cosolvents or crowding agents, applying pressure in the multi-kilobar regime is known to modulate the hydration pattern of solutes, from simple to complex. In this study, we simulated a hairpin ribozyme, being catalytic RNA, using extensive replica-exchange molecular dynamics simulations at ambient and high hydrostatic pressure conditions. By dividing the coordinating water molecules present in the first solvation shell of the ribozyme into two subgroups, namely H-bonding and interstitial water, we discover that the H-bond network remains essentially unaffected even upon compression to 10 kbar compared to the 1 bar reference pressure. In stark contrast, the contribution of interstitial water significantly increases upon compression to 10 kbar, which discloses a differential effect of pressure perturbation on the solvation state of this ribozyme. In simple words: the increased water density due to compressing the aqueous ribozyme solution is locally accommodated by mainly pushing water molecules into the interstitial space offered by the existing H-bonding network of this RNA species. Given the molecularly generic nature of this finding, we expect it to hold true also for other biomacromolecules in aqueous solutions at high hydrostatic pressures, such as DNA or proteins.

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Calcium(II) oscillations to glucose: An astrocyte relation

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Ellen Corcoran, Sheryl Hemkin

Abstract

Astrocytes, the most common type of glial cell, are critical to the health of the central nervous system. Evidence implies that changes in the astrocyte's cytosolic calcium concentration is part of a central mechanism by which information is passed and processed in the cell, and it is linked to both external stimuli impacting the cell as well as downstream events such as metabolism and neurotransmitter release. This work proposes a novel chemical model to further the understanding of how extracellular signals could affect intracellular calcium dynamics and metabolic processes within the cell.

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Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

Author(s): Loana Arns, Jim-Marcel Knop, Satyajit Patra, Christian Anders, Roland Winter

Abstract

In this review we discuss results from temperature and pressure dependent single-molecule Förster resonance energy transfer (smFRET) studies on nucleic acids in the presence of macromolecular crowders and organic osmolytes. As representative examples, we have chosen fragments of both DNAs and RNAs, i.e., a synthetic DNA hairpin, a human telomeric G-quadruplex and the microROSE RNA hairpin. To mimic the effects of intracellular components, our studies include the macromolecular crowding agent Ficoll, a copolymer of sucrose and epichlorohydrin, and the organic osmolytes trimethylamine N-oxide, urea and glycine as well as natural occurring osmolyte mixtures from deep sea organisms. Furthermore, the impact of mutations in an RNA sequence on the conformational dynamics is examined. Different from proteins, the effects of the osmolytes and crowding agents seem to strongly dependent on the structure and chemical make-up of the nucleic acid.

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A simple linearization method unveils hidden enzymatic assay interferences

Publication date: September 2019

Source: Biophysical Chemistry, Volume 252

Author(s): Maria Filipa Pinto, Jorge Ripoll-Rozada, Helena Ramos, Emma E. Watson, Charlotte Franck, Richard J. Payne, Lucília Saraiva, Pedro José Barbosa Pereira, Annalisa Pastore, Fernando Rocha, Pedro M. Martins

Abstract

Enzymes are among the most important drug targets in the pharmaceutical industry. The bioassays used to screen enzyme modulators can be affected by unaccounted interferences such as time-dependent inactivation and inhibition effects. Using procaspase-3, caspase-3, and α-thrombin as model enzymes, we show that some of these effects are not eliminated by merely ignoring the reaction phases that follow initial-rate measurements. We thus propose a linearization method (LM) for detecting spurious changes of enzymatic activity based on the representation of progress curves in modified coordinates. This method is highly sensitive to signal readout distortions, thereby allowing rigorous selection of valid kinetic data. The method allows the detection of assay interferences even when their occurrence is not suspected a priori. By knowing the assets and liabilities of the bioassay, enzymology results can be reported with enhanced reproducibility and accuracy. Critical analysis of full progress curves is expected to help discriminating experimental artifacts from true mechanisms of enzymatic inhibition.

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Quantitative interpretation of isopiestic measurements on aqueous solutions: Urea revisited

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

Author(s): Donald J. Winzor, Peter R. Wills

Abstract

This investigation amends the analysis of isopiestic measurements of solvent thermodynamic activity by taking into account the fact that the solvent activity, traditionally expressed in mole-fraction terms, is a molal parameter because of the constraints (constant temperature and pressure) under which the measurements are made. Application of the revised procedure to published isopiestic measurements on aqueous urea solutions at 25 °C yields a dimerization constant of 0.066 molal−1, which is two-fold larger than an earlier published estimate based on an incorrect definition of the solute activity coefficient. Despite amendments to the quantitative detail, the present study confirms the existence of a large negative entropic contribution that largely counters its enthalpic counterpart arising from the hydrogen bonding responsible for dimer formation. This evidence of enthalpy-entropy compensation is entirely consistent with quantum-mechanical predictions of the adverse effect of water on urea dimerization. Changes in water structure thus contribute significantly to the energetics of urea dimerization in aqueous solution.

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Albumin-bound nanodiscs as delivery vehicle candidates: Development and characterization

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

Author(s): Samar Damiati, Andrea Scheberl, Sonja Zayni, Safa A. Damiati, Bernhard Schuster, Uday B. Kompella

Abstract

Development of synthetic bioarchitectures to improve our understanding of biological systems and produce biosynthetic models with new functions has attracted substantial interest. Synthetic HDL-like phospholipid nanodiscs are a relatively new model of nanoparticles that present a promising carrier for drug delivery and membrane protein investigations. Nanodiscs are soluble nanoscale phospholipid bilayers that are produced based on the self-assembly of phospholipids, membrane scaffold proteins (MSP) and an embedded peptide/protein of interest. To determine the effect of conjugating a protein with a probe, the model protein bovine serum albumin (BSA) with or without FITC conjugation was attached onto 100% 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline (POPC) nanodiscs. The generated discs were analyzed by Fast Protein Liquid Chromatography (FPLC), dynamic light scattering (DLS), and UV-VIS spectroscopy. Empty, BSA- and FITC-BSA-Nanodiscs exhibited different size, charge and elution characteristics as well as different release profiles. Thus, conjugation of proteins to be adsorbed onto nanodiscs surfaces with fluorophores can affect the physical and release properties of nanodiscs, thereby potentially impacting their biophysical, delivery and imaging applications.

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Quantifying length-dependent DNA end-binding by nucleoproteins

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

Author(s): Tam Vo, Amanda V. Albrecht, W. David Wilson, Gregory M.K. Poon

Abstract

The ends of nucleic acids oligomers alter the statistics of interior nonspecific ligand binding and act as binding sites with altered properties. While the former aspect of “end effects” has received much theoretical attention in the literature, the physical nature of end-binding, and hence its potential impact on a wide range of studies with oligomers, remains poorly known. Here, we report for the first time end-binding to DNA using a model helix-turn-helix motif, the DNA-binding domain of ETV6, as a function of DNA sequence length. Spectral analysis of ETV6 intrinsic tryptophan fluorescence by singular value decomposition showed that end-binding to nonspecific fragments was negligible at >0.2 kbp and accumulated to 8% of total binding to 23-bp oligomers. The affinity for end-binding was insensitive to salt but tracked the affinity of interior binding, suggesting translocation from interior sites rather than free solution as its mechanism. As the presence of a cognate site in the 23-bp oligomer suppressed end-binding, neglect of end-binding to the short cognate DNA does not introduce significant error. However, the same applies to nonspecific DNA only if longer fragments (>0.2 kbp) are used.

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Temperature-dependence of the bending elastic constant of DNA and extension of the two-state model. Tests and new insights

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

Author(s): J. Michael Schurr

Abstract

Review and analyses of the experimental data indicate that in nearly all cases bending elastic constants of the effective springs between bp of DNA actually undergo a net increase with increasing T from 278 to 315 K. The exceptions to this rule are bending elastic constants obtained from equilibrium topoisomer distributions of a 2686 bp pUC19 DNA by assuming a fixed T-independent value of the torsion elastic constant. When the same data are analyzed using measured T-dependent values of the torsion elastic constant, which decline with increasing T, a modest increase in bending elastic constant with increasing T is obtained. After revising the torsion elastic constants of the previously formulated two-state cooperative transition model to account for additional data, that model is fitted to the bending elastic constants reckoned from the aforementioned topoisomer distributions to determine the best-fit values for each state. The rather good fit implies a strong negative linear correlation between the inverse bending and inverse torsion elastic constants as T is varied. Predictions of the resulting two-state model, wherein each state has fixed bending and torsion elastic constants, agree surprisingly well with single-molecule relative extension and torque data. The same model also yields good agreement with numerous other experimental data. With increasing T the equilibrium is shifted from the (longer, torsionally stiffer, flexurally softer) b-state toward the (shorter, torsionally softer, flexurally stiffer) a-state. This transition is suggested to be the origin of the so-called broad pre-melting transition exhibited by many, but not all, DNAs.

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Editorial Board

Publication date: August 2019

Source: Biophysical Chemistry, Volume 251

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Prototyping a memristive-based device to analyze neuronal excitability

Publication date: Available online 24 June 2019

Source: Biophysical Chemistry

Author(s): L. Lunelli, C. Collini, A.M. Jimenez-Garduño, A. Roncador, G. Giusti, R. Verucchi, L. Pasquardini, S. Iannotta, P. Macchi, L. Lorenzelli, C. Pederzolli, C. Musio, C. Potrich

Abstract

Many efforts have been spent in the last decade for the development of nanoscale synaptic devices integrated into neuromorphic circuits, trying to emulate the behavior of natural synapses. The study of brain properties with the standard approaches based on biocompatible electrodes coupled to conventional electronics, however, presents strong limitations, which in turn could be overcame by the in-situ growth of neuronal networks coupled to memristive devices. To meet this challenging task, here two different chips were designed and fabricated for culturing neuronal cells and sensing their electrophysiological activity. The first chip was designed to be connected to an external memristor, while the second chip was coated with TiO2 films owning memristive properties. The biocompatibility of chips was preliminary analyzed by culturing the hybrid motor-neuron cell line NSC-34 and by measuring the electrical activity of cells interfacing the chip with a standard patch-clamp setup. Next, neurons were seeded on chips and their activity measured with the same setup. For both cell types total current and voltage responses were evoked and recorded with optimal results with no breakdowns. In addition, an external stimulation was applied to cells through chip electrodes, being effective and causing no damage or pitfalls to the cells. Finally, the whole bio-hybrid system, i.e. the chip interconnected with a commercial memristor, was tested with promising results. Spontaneous electrical activity of neurons grown on the chip was indeed present and this signal was collected and sent to the memristor, changing its state. Taken together, we demonstrated the ability of memristor to work with a synaptic/plastic response together with natural systems, opening the way for the further implementation of basic computing elements able to perform both storage and processing of data, as in natural neurons.


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Cosolvent and pressure effects on enzyme-catalysed hydrolysis reactions

Publication date: Available online 20 June 2019

Source: Biophysical Chemistry

Author(s): Christoph Held, Tanja Stolzke, Michael Knierbein, Michel W. Jaworek, Trung Quan Luong, Roland Winter, Gabriele Sadowski

Abstract

Thermodynamics and kinetics of biochemical reactions depend not only on temperature, but also on pressure and on the presence of cosolvents in the reaction medium. Understanding their effects on biochemical processes is a crucial step towards the design and optimization of industrially relevant enzymatic reactions. Such reactions typically do not take place in pure water. Cosolvents might be present as they are either required as stabilizer, as solubilizer, or in their function to overcome thermodynamic or kinetic limitations. Further, a vast number of enzymes has been found to be piezophilic or at least pressure-tolerant, meaning that nature has adapted them to high-pressure conditions.

In this manuscript, we review existing data and we additionally present some new data on the combined cosolvent and pressure influence on the kinetics of biochemical reactions. In particular, we focus on cosolvent and pressure effects on Michaelis constants and catalytic constants of α-CT-catalysed peptide hydrolysis reactions. Two different substrates were considered in this work, N-succinyl-L-phenylalanine-p-nitroanilide and H-phenylalanine-p-nitroanilide. Urea, trimethyl-N-amine oxide, and dimethyl sulfoxide have been under investigation as these cosolvents are often applied in technical as well as in demonstrator systems. Pressure effects have been studied from ambient pressure up to 2 kbar. The existing literature data and the new data show that pressure and cosolvents must not be treated as independent effects. Non-additive interactions on a molecular level lead to a partially compensatory effect of cosolvents and pressure on the kinetic parameters of the hydrolysis reactions considered.

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Structural and dynamic responses of calcium ion binding loop residues in metallo-proteins

Publication date: Available online 20 June 2019

Source: Biophysical Chemistry

Author(s): Samapan Sikdar, Mahua Ghosh, Arunava Adak, J. Chakrabarti

Abstract

Conformational changes in bio-molecular systems are fundamental to several biological processes. It is important to study changes in responses of underlying microscopic variables, like dihedral angles as conformational change takes place. We perform all-atom simulations and modelling via Langevin equation to illustrate the changes in structural and dynamic responses of dihedral angles of calcium ion binding residues of different proteins in metal ion free (apo) and bound (holo) states. The equilibrium distributions of dihedral angles in apo- and holo-states represent structural response. Our studies show the presence of dihedrals with multiple peaks (isomeric states) separated by barrier heights is more frequent in apo- than in holo-state. The relaxation time-scale of dihedral fluctuations is found to increase linearly with decreasing barrier height due to more frequent barrier re-crossing events. The slow kinetic response of the dihedrals also contributes to slowing down of macro-scale fluctuations, which may be useful to understand kinetics of various bio-molecular processes.

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Cholesterol modulates the pressure response of DMPC membranes

Publication date: Available online 20 June 2019

Source: Biophysical Chemistry

Author(s): Göran Surmeier, Michael Paulus, Paul Salmen, Susanne Dogan, Christian Sternemann, Julia Nase

Abstract

In this work, the effect of cholesterol on the pressure response of solid-supported phospholipid multilayers is analyzed. It is shown that DMPC multilayers become highly pressure-responsive by the incorporation of low amounts of cholesterol, resulting in a strong pressure-induced expansion of the bilayer spacing. This is accompanied by a high tendency of the multilayer system to detach from the substrate. Increasing the cholesterol concentration reduces the pressure-induced expansion and the membrane structure remains largely unchanged upon pressurization, consequently the stability of the multilayers improves. For a determination of the influence of the substrate, the pressure-dependent behavior of multilayers is compared to that of solid-supported bilayers and multi-lamellar vesicles in bulk solution. While single-supported bilayers remain largely unaffected by external pressure independent of their cholesterol content, multi-lamellar vesicles and multilayers behave similarly.

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Category: Current Chemistry Research

Last update: 28.03.2018.






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