Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and proteins. However, the underlying bases for interactions are not well understood. The crystal structure of Boc-l-4-thiolphenylalanine tert-butyl ester revealed organization centered on interaction thiol S-H ring an adjacent molecule, a through-space Hthiol···Caromatic distance 2.71 Å, below 2.90 Å sum van der Waals radii H C. nature this was further examined by DFT calculations, IR...

Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure surface tension effects, experiments invoke porelike configurations during the solute transfer process into vesicles cells. The initiation formation pores are associated nontrivial free-energy cost, thus necessitating consideration pore attendant free energies. Because experimental...

Phosphorylation and dephosphorylation of proteins by kinases phosphatases are central to cellular responses function. The structural effects serine threonine phosphorylation were examined in peptides proteins, circular dichroism, NMR spectroscopy, bioinformatics analysis the PDB, small-molecule X-ray crystallography, computational investigations. both residues induces substantial conformational restriction their physiologically more important dianionic forms. Threonine exhibits a...

In the vicinity of a tipping point, critical transitions occur when small changes in an input condition cause sudden, large, and often irreversible state system. Many natural systems ranging from ecosystems to molecular biosystems are known exhibit their response stochastic perturbations. diseases, early prediction upcoming healthy disease by using early-warning signals is prime interest due potential application forecasting onset. Here, we analyze cell-fate between different phenotypes...

Electrohydrodynamics of a leaky dielectric suspended drop subjected to the combined influence uniform electric field and linear velocity is analysed analytically numerically. In limit small charge convection shape deformation, an analytical solution obtained for deformed when imposed flow uniaxial extensional type with component aligned in direction field. This perturbation approach then applied towards obtaining effect on effective rheology dilute emulsion. Key results indicate that...

Objectives: Recently introduced competency-based medical education (CBME) curriculum necessitates a heavy presence of ably trained educators. Contrarily, Phase I subjects are facing severe shortage faculty, piloting double setback to the system in form stress and burnout among faculty along with curtailed implementation much-needed CBME curriculum. Methods: A cross-sectional, observational electronically distributed questionnaire-based study was conducted analyze perceptions undergraduate...

The Cdc2-cyclin B/Wee1 kinase system exhibits bistability between alternative steady states, which emerges due to the mutual inhibition B and Wee1 kinases. Alternative states are {\em M...

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in hydration is the thickness layer (i.e., distance from surface up which water influenced by protein). Estimation crucial understand better properties "biological water" and role it plays guiding protein's function. We have performed an atomistic molecular simulation aqueous solution villin headpiece subdomain or HP-36 estimate its In particular, several dynamical different...

Structural mechanisms and underlying thermodynamic determinants of efficient internalization charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, their variants, into cells, cellular constructs, model membrane/lipid bilayers (large giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center endocytotic nonendocytotic (diffusive) processes. Espousing view a purely diffusive...

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in hydration layer protein villin headpiece subdomain or HP-36. attempt is made explore how heterogeneous rigidity layers different segments (three α helices) protein, strength protein−water hydrogen bonds, and their differential relaxation behavior influence distribution density states layers. The calculations revealed that compared bulk these...

Formation of protein–DNA complex is an important step in regulation genes living organisms. One issue this problem the role played by water mediating interactions. In work, we have carried out atomistic molecular dynamics simulations to explore heterogeneous molecules present different regions around a formed between DNA binding domain human TRF1 protein and telomeric DNA. It demonstrated that such motions are correlated with relaxation time scales hydrogen bonds those The calculations...

Water present near the surface of a protein exhibits dynamic properties different from that water in pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation an aqueous solution hen egg-white lysozyme. Attempts been made to explore correlation between local heterogeneous mobility around segments and rigidity hydration layers with microscopic hydrogen bonds formed by molecules residues. The kinetics breaking reformation involving calculated. It is found...

We have performed an atomistic molecular dynamics simulation of aqueous solution hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses been carried out to explore the differential flexibility secondary structural segments protein and structure ordering around them. It is found that overall molecule primarily controlled by few large-amplitude bistable motions exhibited two coils; one connecting α-helical in domain-1 other a 310 helix β-sheet domain-2...

Atomistic molecular dynamics simulation of an aqueous solution the small protein HP-36 has been carried out with explicit solvent at room temperature. Efforts have made to explore influence on relative packing and ordering water molecules around its secondary structures, namely, three α-helices. The calculations reveal that inhomogeneous density distributions helices are correlated their hydrophobicity. Importantly, we identified existence a narrow relatively dehydrated region containing...

COVID-19 outbreak has been declared as a public health emergency of international concern, and later pandemic. In most countries, the incidence curve rises sharply in short period, suggesting transition from disease-free (or low-burden disease) equilibrium state to sustained infected high-burden state. Such is often known exhibit characteristics `critical slowing down'. Critical down can be, general, successfully detected using many statistical measures such variance, lag-1 autocorrelation,...

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore question similarity thermodynamic structural predictions obtained molecular dynamics simulations using all-atom Martini coarse-grain force fields. Specifically, estimate potentials mean associated with standard (CHARMM36 lipid) polarizable nonpolarizable fields, as well a series modified Martini-based parameter sets. We find...

We study a metacommunity model of consumer-resource populations coupled via dispersal under an environment-dependent framework, and we explore the occurrence multistability critical transition. By emphasizing two magnitudes acting on dynamic environment at temporal spatial scales, system with simple diffusive coupling nonlinear environmental enables various interesting complex dynamics such as bistability, multistability, transitions. Using basin stability measure, find probability attaining...

COVID-19 outbreak has been declared as a public health emergency of international concern, and later pandemic. In most countries, the incidence curve rises sharply in short period, suggesting transition from disease-free (or low-burden disease) equilibrium state to sustained infected high-burden state. Such is often known exhibit characteristics ‘critical slowing down’. Critical down can be, general, successfully detected using many statistical measures such variance, lag-1 autocorrelation,...

Alzheimer's disease is caused due to aggregation of amyloid beta (Aβ) peptide into soluble oligomers and insoluble fibrils in the brain. In this study, we have performed room temperature molecular dynamics simulations probe size-dependent conformational features thermodynamic stabilities five Aβ17-42 protofilaments, namely, O5 (pentamer), O8 (octamer), O10 (decamer), O12 (dodecamer), O14 (tetradecamer). Analysis free energy profiles aggregates showed that higher order protofilaments (O10,...

Recreational fishing is a highly socioecological process. Although recreational fisheries are self-regulating and resilient, changing anthropogenic pressure drives these to overharvest collapse. Here, we evaluate the effect of demographic environmental stochasticity for social-ecological two-species fish model. In presence noise, find that an increase in harvesting rate critical transition from high-yield--low-price low-yield--high-price fisheries. To calculate stochastic trajectories derive...

Protein–DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue this problem how protein recognizes DNA and identifies its target base sequences. Water molecules present around are also expected to play role mediating recognition controlling structure complex. We have performed atomistic molecular dynamics simulations aqueous solution protein–DNA complex formed between domain human TRF1 a telomeric DNA....

Nearly identical cells can exhibit substantially different responses to the same stimulus that causes phenotype diversity. Such interplay between diversity and architecture of regulatory circuits is crucial since it determines state a biological cell. Here, we theoretically analyze how circuit blueprints NF-κB in cellular environments are formed their role determining cells' metabolic state. The collective name for developmental conserved family five transcription factors form homodimers or...

Electrophoresis of charged particles has important applications in biochemical separation processes. The mobility these depends on the surrounding electric double layer (EDL), which is impacted by solvent restructuring because hydration interactions. Nevertheless, most theoretical estimates ignore such interactions during computation electrophoretic mobility. Here, we employ a complementary blend mean-field analysis and molecular dynamics simulations performed for peptide–G-quadruplex...

Controlled microscale transport is at the core of many scientific and technological advancements, including medical diagnostics, separation biomolecules, etc., often involves complex fluids. One challenges in this regard to actuate flows small scales an energy efficient manner, given strong viscous forces opposing fluid motion. We try address issue here by probing a combined time-periodic pressure electrokinetically driven flow viscoelastic obeying simplified linear Phan-Thien-Tanner model,...