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...
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...
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...
Protein packing within crystal lattices plays a critical role in determining molecular flexibility; therefore, the observed conformation and flexibility of protein side chains can vary depending on the crystal space group. Protein crystal dehydration...
The Mad2 protein, with two distinct conformations of open- and closed-states, is a key player in the spindle checkpoint. The closed Mad2 state is more active than the open one. We carried out conventional and targeted molecular dynamics simulations f...
We measured the changes in the higher-order structure of DNA molecules (λ phage DNA, 48 kbp) at different concentrations of 1- and 2-propanol through single-molecular observation. It is known that 2-propanol is usually adapted for the procedur...
Sialidases are increasingly used in the production of sialyloligosaccharides, a significant component of human milk oligosaccharides. Elucidating the catalytic mechanism of sialidases is critical for the rational design of better biocatalysts, thereb...
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,...
Maintaining iron homeostasis is fundamental for almost all living beings, and its deregulation correlates with severe and debilitating pathologies. The process is made more complicated by the omnipresence of iron and by its role as a fundamental comp...
Morphological control of nanostructures that are composed of amphiphilic di- or tri-block molecules by external stimuli broadens their applications for molecular containers, nanoreactors, and controlled release materials. In this study, triblock amph...
In this work, the conformational behaviors of ring polyelectrolyte in tetravalent salt solutions are discussed in detail through molecular dynamics simulation. For simplification, here we have neglected the effect of the twisting interaction, althoug...
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...
Guanidinyl tryptophan derivatives TGN1, TGN2, TGN3, and TGN4 were synthesized, and these compounds were shown to possess in vitro inhibitory activity for amyloid aggregation in a previous study. Nevertheless, the influence of the TGN series of compou...
Human adenylate kinase 1 (hAK1) plays a vital role in the energetic and metabolic regulation of cell life, and impaired functions of hAK1 are closely associated with many diseases. In the presence of Mg2+ ions, hAK1 in vivo can catalyze two ADP molec...
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...
trans-3,4-Dihydroxyselenolane (DHS), a water-soluble cyclic selenide, exhibits selenoenzyme-like unique redox activities through reversible oxidation to the corresponding selenoxide. Previously, we demonstrated that DHS can be applied as an antioxida...
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...
Oligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a...
The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent no...
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...
The four most important and well-studied phenomena of mirror symmetry breaking of molecules were analyzed for the first time in terms of available common features and regularities. Mirror symmetry breaking of the primary origin of biological homochir...
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...
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...
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...
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...
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...
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...
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...
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...
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