The critical overlap concentration C* is an important concept in polymer solutions and is defined as the boundary between dilute and semidilute regimes. In this study, the chain conformational changes of polystyrene (PS) with both high (Mn = 200,000...
The double-stranded B-form and A-form have long been considered the two most important native forms of DNA, each with its own distinct biological roles and hence the focus of many areas of study, from cellular functions to cancer diagnostics and drug...
The neurotransmitter sodium symporters (NSSs) play critical roles in the neurotransmission of monoamine and amino acid neurotransmitters and are the molecular targets of therapeutic agents in the treatment of several psychiatric disorders. Despite si...
Central among the tools and approaches used for ligand discovery and design are Molecular Dynamics (MD) simulations, which follow the dynamic changes in molecular structure in response to the environmental condition, interactions with other proteins,...
Conformational transitions of double-stranded DNA in different environments have long been studied as vital parts of both in vitro and in vivo processes. In this study, utilizing Fourier transform infrared spectroscopy (FTIR), we provide detailed ana...
The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or ra...
The affinity of amphiphilic compounds for water is important in various processes, e.g., in conformational transitions of biopolymers, protein folding/unfolding, partitioning of drugs in the living systems, and many others. Herein, we study the confo...
The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuat...
High concentrations of Na+ or [Co(NH3)6]3+ can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)4 and (dm5C-dG)4 as models can allow a thermodynamic characterization o...
8 September 2023
Calorimetric (from both isothermal micro-calorimetry and DSC), chiro-optical, viscometric and rheological data on aqueous solutions of pectic acid and low-methoxyl pectin (LMP), published over decades from different laboratories, have been comparativ...
Selenium nanoparticles (SeNPs) are among the emerging selenium supplements because of their high bioactivity and low toxicity. However, bare SeNPs are prone to activity loss caused by aggregation and sedimentation. This study aims to stabilize SeNPs...
Intrinsically disordered proteins exist as highly dynamic conformational ensembles of diverse forms. However, the majority of virtual screening only focuses on proteins with defined structures. This means that computer-aided drug discovery is restric...
Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways an...
Arginine kinase is a key phosphagen kinase in invertebrates that facilitates rapid ATP regeneration by reversibly transferring phosphate groups between phosphoarginine and ADP. Structural studies have shown that the enzyme adopts distinct conformatio...
Post-well conformance assessment requires identifying the realized locations where an as-drilled trajectory changes between its principal inclination regimes; planned breakpoints are targets, not observations. We formulate this task as sparse event l...
Understanding interactions between cations and DNA is essential for elucidating the structural dynamics of this fundamental biomolecule. While B-DNA is well known to dominate in long genomic DNA under physiological ionic conditions, its stability in...
The lowest-energy conformations of four 2-chloroethylnitrososulfamides were determined using the MM+ molecular mechanics method as implemented in Hyperchem 6.0. Some of the calculated structural parameters, angles and bonds lengths were compared with...
Multidrug resistance poses a major challenge to antibiotic therapy. A principal cause of antibiotic resistance is through active export by efflux pumps embedded in the bacterial membrane. Major facilitator superfamily (MFS) efflux pumps constitute a...
In order to elucidate the effect of modification of the hinge region on structural polymorphism associated with conformational transitions, structural studies of hinge-modified oligopeptidase B from Serratia proteamaculans (SpOpBmod) in the crystalli...
Human immunodeficiency virus type-1 (HIV-1) infection is triggered by its envelope (Env) glycoprotein gp120 binding to the host-cell receptor CD4. Although structures of Env/gp120 in the liganded state are known, detailed information about dynamics o...
Two polymorphic forms of a conformationally flexible molecule, 5-[(Diphenylphosphoryl)methyl]-4-(prop-2-en-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, were obtained by crystallization and characterized by X-ray diffraction analysis and differential...
With excellent biocompatibility and biodegradability, silk fibroin has been developed into many protein materials. For producing regenerated silk fibroin (RSF) fibers, the conformation transition of silk fibroin needs to be thoroughly studied during...
It is now well established that most if not all enzymatic proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. A hypothesis is stated that the protein conformational tr...
The quercetin molecule is known to be an effective pharmaceutical compound of a plant origin. Its chemical structure represents two aromatic A and B rings linked through the C ring containing oxygen and five OH hydroxyl groups attached to the 3, 3&pr...
20 November 2015
[FeII(LHiPr)2(NCS)2] (LHiPr = N-2-pyridylmethylene-4-isopropylaniline) showed an abrupt spin-crossover (SCO) at T1/2↓ = 154 K on cooling and at T1/2↑ = 167 K on heating. The thermal hysteresis with a width of 13 K is related with the structural soli...
This article addresses critical challenges in the transition to clean energy sources by highlighting the importance of advanced mathematical modeling and computational techniques in turbine design and operation. Specifically, we extend and generalize...
We employ the recently introduced generalized microcanonical inflection point method for the statistical analysis of phase transitions in flexible and semiflexible polymers and study the impact of the bending stiffness upon the character and order of...
Analysis and design of an ultra-wideband microstrip-to-slotline transition on a low permittivity substrate is presented. Cross-sectional structures along the proposed transition are analyzed using conformal mapping assuming quasi-TEM modes, attaining...
In this paper, by treating the cosmological constant as a thermodynamic pressure, we study the thermodynamics and phase transitions of the dyonic AdS black holes in Gauss-Bonnet-Scalar gravity, where the conformal scalar field is considered. In a mor...
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the las...
Protein homodimers have been classified as three-state or two-state dimers depending on whether a folded monomer forms before association, but the details of the folding–binding mechanisms are poorly understood. Kinetic transition networks of c...
A design of a compact coplanar strip (CPS)-to-microstrip line (MSL) transition using a bended structure on a two-layered substrate is presented. The proposed transition consists of a CPS taper and a bended CPS-to-MSL transition on a two-layered subst...
The glucagon-like peptide-1 receptor (GLP-1R), which belongs to the class B1 G protein-coupled receptor (GPCR) family, is an important target for treatment of metabolic disorders, including type 2 diabetes and obesity. The growing interest in GLP-1R-...
Reliable carbon price forecasts support compliance planning and transition risk management, but multi-source backtests can appear accurate when observations are aligned by calendar date rather than actual availability. We develop a point-in-time fram...
RND family efflux pumps are complex macromolecular machines involved in multidrug resistance by extruding antibiotics from the cell. While structural studies and molecular dynamics simulations have provided insights into the architecture and conforma...
In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydrox...
To study conformational transition occuring upon inferior solvent strength in a brush formed by linear or dendritically branched macromolecules tethered to the inner surface of cylindrical or planar (slit-like) pore, a self-consistent field analytica...
Conformational sampling remains a major challenge in molecular dynamics (MD) simulations of proteins with large-scale functional motions. Here, we use apo Escherichia coli adenylate kinase (AdK) as a benchmark for the open–closed transition and...
A design method for an ultra-wideband coplanar-stripline-based vertical transition that can be used for ultra-high-speed digital interfaces is proposed. A conventional via structure, based on a differential line (DL), inherently possesses performance...
DNA conformational transitions in aqueous environments are strongly influenced by electrostatic interactions with surrounding cations. This review/perspective article summarizes the experimental findings reported during the last decade on the competi...
Two transition metal complexes were synthesized with Ni(II) and Cu(II) using a tetradentate Schiff-base ligand, (R,R) and (S,S)-N,N′-Bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexanediamine. The stereochemical properties of the ligand and the...
A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, an...
Background: The intrinsically disordered, amyloidogenic protein Tau associates with diverse classes of molecules, including proteins, nucleic acids, and lipids. Mounting evidence suggests that fatty acid molecules could play a role in the dysfunction...
Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of...
The mechanism in palladium-catalyzed carboxylation of thiophene and CO2 is investigated using the density functional theory (DFT) calculations, including three consecutive steps of the formation of carbanion through breaking the C–H bond(s) via...
The 1-anilino-8-naphthalenesulfonate (ANS) fluorescent dye is widely used in protein folding studies due to the significant increase in its fluorescence quantum yield upon binding to protein hydrophobic regions that become accessible during protein u...
Hydrogels are attractive materials not only for their tremendous applications but also for theoretical studies as they provide macroscopic monitoring of the conformation change of polymer chains. The pioneering theoretical work of Dusek predicting th...
Polymers in highly confined geometries can display complex morphologies including ordered phases. A basic component of a theoretical analysis of their phase behavior in confined geometries is the knowledge of the number of possible single-chain confo...
The circular dichroism (CD) exciton chirality method (ECM) is a very popular approach for assigning the absolute configuration (AC) of natural products, thanks to its immediacy and ease of application. The sign of an exciton couplet (two electronic C...
Flavin and redox-active disulfide domains of ferredoxin-dependent flavin thioredoxin reductase (FFTR) homodimers should pivot between flavin-oxidizing (FO) and flavin-reducing (FR) conformations during catalysis, but only FR conformations have been d...
of 21