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PubMed Journal Database | Biophysical chemistry RSS

18:51 EDT 15th July 2019 | BioPortfolio

The US National Library of Medicine and National Institutes of Health manage PubMed.gov which comprises of more than 29 million records, papers, reports for biomedical literature, including MEDLINE, life science and medical journals, articles, reviews, reports and  books.

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For example view all recent relevant publications on Epigenetics and associated publications and clincial trials.

Showing PubMed Articles 1–25 of 148 from Biophysical chemistry

Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study.

Peptides can aggregate into ordered structures with different morphologies. The aggregation mechanism and evolving structures are the subject of intense research. In this paper we have used molecular dynamics to examine the sequence-dependence of aggregation kinetics for three short peptides: octaalanine (Ala8), octaasparagine (Asn8), and the heptapeptide GNNQQNY (abbreviated as GNN). First, we compared the aggregation of 20 randomly distributed peptides using the coarse-grained MARTINI force field and the ...

Force dependence of unbinding rate of kinesin motor during its processive movement on microtubule.

Kinesin is a biological molecular motor that can move continuously on microtubule until it unbinds. Here, we studied computationally the force dependence of the unbinding rate of the motor. Our results showed that while the unbinding rate under the forward load has the expected characteristic of "slip bond", with the unbinding rate increasing monotonically with the increase of the forward load, the unbinding rate under the backward load shows counterintuitive characteristic of "slip-catch-slip bond": as the...

Prototyping a memristive-based device to analyze neuronal excitability.

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...

Thermodynamic properties of aqueous osmolyte solutions at high-pressure conditions.

Living organisms can be encountered in nature under extreme conditions. At the seabed, pressure may reach 1000 bar. Yet microorganisms can be found that still function under these conditions. On the one hand, it is known that high pressure even has a positive effect on piezophile enzymes increasing their activity. On the other hand, such microorganisms might contain up to very high concentrations of osmolytes that counteract osmotic stress. To better understand high-pressure influences on biochemical syst...

Structure-based derivation and intramolecular cyclization of peptide inhibitors from PD-1/PD-L1 complex interface as immune checkpoint blockade for breast cancer immunotherapy.

The interaction event between programmed death receptor-1 (PD-1) and its ligand (PD-L1) functions as an essential immune checkpoint against cytotoxic T effector cell activation. Previously, a number of small-molecule inhibitors and antibody drugs have been successfully developed to block the PD1/PDL1 signaling axis for breast cancer immunotherapy. Here, we attempt to directly disrupt the formation of PD-1/PD-L1 complex by using a self-inhibitory peptide (SIP) strategy. In the procedure, the complex crystal ...

Molecular dynamics simulations of membrane properties affected by plasma ROS based on the GROMOS force field.

Cold atmospheric plasma (CAP) has attracted substantial attention in the field of medical disinfection because its main components, reactive oxygen species (ROS), have a strong destructive effect on various cell components. The cell membrane plays an important role in maintaining proper cellular function by blocking harmful substances such as ROS. In this paper, we used molecular dynamics simulations to study the behaviour of different ROS at the membrane-water interface. The results showed that the cell me...

Cholesterol modulates the pressure response of DMPC membranes.

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 struct...

Cosolvent and pressure effects on enzyme-catalysed hydrolysis reactions.

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 ...

The dynamics of K channel gates as a biological transistor.

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 mut...

Calcium(II) oscillations to glucose: An astrocyte relation.

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 signa...

A simple linearization method unveils hidden enzymatic assay interferences.

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 enz...

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

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 revea...

Evaluation of heating effects on the morphology and membrane structure of Escherichia coli using electron paramagnetic resonance spectroscopy.

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 transmi...

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

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 replic...

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

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 elast...

Quantifying length-dependent DNA end-binding by nucleoproteins.

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 funct...

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

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 e...

Delineating the effect of mutations on the conformational dynamics of N-terminal domain of TDP-43.

The structural integrity of N-terminal domain (NTD) of TAR DNA-binding protein-43 (TDP-43) is essential for the biological functions of TDP-43 involved in neurodegenerative diseases. Here, we used all-atom molecular dynamics (MD) simulations to understand the folding, dynamics and conformational stability of four variants of NTD, the wild type (WT) and three mutants (L27A, L28A and V31R). The deleterious and destabilizing nature of NTD mutants were predicted on DynaMut and SAAFEC server. Results show that p...

Mechanism of unfolding and relative stabilities of G-quadruplex and I-motif noncanonical DNA structures analyzed in biased molecular dynamics simulations.

In this work we studied the unfolding processes of the noncanonical telomeric DNA fragments, i.e. G-quadruplex and i-motif. These transitions were analyzed in details by applying biased molecular dynamics simulations. The bias is imposed on the root of mean square displacement of selected atoms from the reference states which are ideal G-quadruplex and i-motif structures. The unfolding is carried out using the telomeric duplex fragment within which these both noncanonical structures are formed in the same p...

Gratitude and acknowledgements: "Marina Diana Mercurio" Award 2018.

Ordering effect of protein surfaces on water dynamics: NMR relaxation study.

Proteins in solution affect the structural and dynamic properties of the bulk water at the protein-water interface, resulting in a contribution to the order of the hydration water. Theoretical and experimental NMR relaxation methods were developed to study the dynamic properties of water molecules in the protein hydration shell. Water non-selective and selective relaxation rates, were shown to be sensitive to contributions from ordered solvent molecules at protein surface. The average rotational correlation...

Elastic compliance as a tool to understand Hofmeister ion specific effect in DMPC liposomes.

Elastic compliance of DMPC liposomes with Hofmeister electrolytes: NaCl, NaSO, NaCO, NaNO, KCl and MgCl studied using Quartz crystal microbalance with dissipation has been correlated with changes in their lamellar spacing from SAXS. The study suggests that hydration water of the different ions has an effect on the overall packing of the lipid bilayer that results as either a dehydrated liposome or where water smears the surface of the liposomes. Ratio of hydrogen bonded carbonyl and phosphate of polar regio...

Hydrodynamic volume of trehalose and its water uptake mechanism.

Trehalose ability to preserve water in biology has spawned research on this special disaccharide and its solutions. Trehalose unlike any other disaccharide, tend to mix with almost any amount of water. In water, Trehalose forms a hydrodynamic volume with bound waters (both coordination water and semicircular heterogeneities), capable of perturbing the very nature of normal bulk water. Switching of the two major conformational forms, defined by their helicities (i, i-HO with lower helicity and ii, ii-HO with...

Single-molecule measurement and bioinformatics analysis suggest a preferred orientation of human coagulation factor VIII on hydrophobic interfaces.

Investigating the adsorption behavior of coagulation proteins on interfaces will contribute to better understating blood clotting and to the development of biocompatible materials. In this work, atomic force microscopy (AFM)-based peakforce quantitative nanomechanical mapping (PF-QNM) was combined with bioinformatics tool to study the adsorption and orientation of coagulation factor VIII (FVIII) on both hydrophilic and hydrophobic interfaces by the height and mechanical measurement of single protein molecul...

Topological effects on the designability and bactericidal potency of antimicrobial peptides.

New ideas and methods are being developed to generate highly designable small functional protein folds beyond the confines of natural structures, from secondary to quaternary level. Highly designable folds can have multiple sequence solutions, which are thermodynamically and kinetically stable. We have previously described how short syndiotactic helices can be exceptionally stable energetically, and how they can be used as a template for designing antibacterial agents. In this work, we have designed four sy...


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