Number Of H-bonds Research Articles

Molecular dynamics simulation on the dissolution process of Kaempferol cluster

Abstract The solid-liquid extraction is an effective method to extract bioactive components from crude medicinal herbs. The dissolution of bioactive molecules is the key to efficient solid-liquid extraction. In this work, a five-nanosecond molecular dynamics simulation was carried out to study the dissolution mechanism of a cluster, including 15 kaempferol molecules in a cubic solvent box of 6 nm. The theoretical and experimental infrared and Raman spectra were taken to confirm the low-energy kaempferol conformers for building the cluster. The effects of ethanol concentration and temperature on the kaempferol dispersion efficiency are investigated. The simulation results show that different concentration of ethanol solution has different dissolution behavior. Because of the intermolecular interaction between kaempferol and solvent, the kaempferol cluster can be decomposed gradually. In order to quantitatively describe the diffusion process of kaempferol cluster, the radial distribution function of the barycenter of the cluster around kaempferol molecules, the number of H-bond between kaempferol molecules, the solvent accessible area of the cluster, the dissolution free energy and the diffusion constant are analyzed. The results show that the optimal dispersion condition is at 80–90% of the ethanol concentration and 323.15 K of the system temperature, which agree with the experiment of extraction. This research provides new insight into the dissolution process of kaempferol on the nanosecond scale. Also, the result of molecular dynamics (MD) can effectively predict the extraction conditions of the actual experiment.

Probing the adsorption and release mechanisms of cytarabine anticancer drug on/from dopamine functionalized graphene oxide as a highly efficient drug delivery system

In this work, the chemical modification of the graphene oxide surface was done via covalent functionalization with dopamine (fGO). The density functional theory (DFT) and molecular dynamics (MD) simulations were applied to study the adsorption of cytarabine (CYT) anticancer drugs on the fGO surface. The DFT calculations demonstrate that the adsorption energy for fGO/CYT complexes is negative which proposes the adsorption process of CYT molecule onto the fGO surface is energetically favorable and the optimized geometries are stable. The electronic and structural properties of cytarabine molecules interacting with fGO were studied using the DFT method. QTAIM calculations confirm the nature of interaction between CYT and fGO nano-sheet is partially covalent and partially electrostatic. It was found in the most stable configuration related to the CYT/fGO interaction, the hydrogen bond (HB) interactions predominate between the CYT molecule and the functional group of fGO. As well as, the MD simulations at various drug concentrations (3, 5, and 10) and in the water solution were examined to assess the dynamics of drug adsorption on the fGO surface. MD simulation results confirm that CYT drugs were strongly adsorbed on the fGO surface by increasing the drug concentration from 3 to 10 molecules, as confirmed by the high number of H-bonds between fGO and CYT and the most negative van der Waals (vdW) and electrostatic interaction energies. Finally, the effect of pH in the adsorption and release of drug molecules from the fGO surface was investigated.

Insight into Speciation and Electrochemistry of Uranyl Ions in Deep Eutectic Solvents.

Understanding the speciation of metal ions in heterogeneous hydrogen-bonded deep eutectic solvents (DES) has immense importance for their wide range of applications in green technology, environmental remediation, and nuclear industry. Unfortunately, the fundamental nature of the interaction between DES and actinide ions is almost completely unknown. In the present work, we outline the speciation, solvation mechanism, and redox chemistry of uranyl ion (UO22+) in DES consisting of choline chloride (ChCl) and urea as the hydrogen-bond donor. Electrochemical and spectroscopic techniques along with molecular dynamics (MD) simulations have provided a microscopic insight into the solvation and speciation of the UO22+ ion in DES and also on associated changes in physical composition of the DES. The hydrogen-bonded structure of DES plays an important role in the redox behavior of the UO22+ ion because of its strong complexation with DES components. X-ray absorption spectroscopy and MD simulations showed strong covalent interactions of uranyl ions with the constituents of DES, which led to rearrangement of the hydrogen-bonding network in it without formation of any clusters or aggregations. This, in turn, stabilizes the most unstable pentavalent uranium (UO2+) in the DES. MD analysis also highlights the fact that the number of H-bonds is reduced in the presence of uranyl nitrate irrespective of the presence of water with respect to pristine reline, which suggests high stability of the formed complexed species. The effect of added water up to 20 v/v % on speciation is insignificant for DES, but the presence of water influences the redox chemistry of UO22+ ions considerably. The fundamental findings of the present work would have far reaching consequences on understanding DES, particularly for application in the field of nuclear fuel reprocessing.

Targeting the microRNA binding domain of argonaute 2: rational inhibitor design and study of mutation effects on protein-ligand interaction

Based on the accumulative evidences during recent decades, miRNAs have been found overexpressed in several human cancer types and also in Down syndrome patients, contributing to the neuropathology of Down syndrome. From this point of view, investigations on the structure and dynamic mechanisms related to the Argonaute 2 miRNAs binding in which silencing of the mRNA occurs, have inspired many clinical researchers to target this complex to inhibit the silencing process. In the current research, we have virtually screened the OTAVA_CNS_library to introduce new inhibitor compounds for the Ago2/miRNA complex. Ten hit compounds were obtained, with just one of them nominated as the best compound. Following the interaction analysis, by utilizing molecular dynamics (MD) simulations, effects of two mutations (Thr526 to isoleucine and Gln545 to alanine) on the dynamic properties of Ago2 in the complex with the best inhibitor compound were investigated. RMSD, RMSF and h-bond number beside other analyses, highlighted the importance of the Thr526 and Gln545 mutations for the stability and flexibility of the (Ago2)/ligand complex.Communicated by Ramaswamy H. Sarma

Understanding the Origin of the Breakdown of the Stokes-Einstein Relation in Supercooled Water at Different Temperature-Pressure Conditions.

A recent experiment has measured the viscosity of water down to approximately 244 K and up to 300 MPa. The correct viscosity and translational diffusivity data at various temperature-pressure (T-P) state points allowed for checking the validity of the Stokes-Einstein (SE) relation, which accounts for the coupling between translational self-diffusion and medium viscosity. The diffusion-viscosity decoupling increases with decreasing temperature, but the increasing pressure reduces the extent of the decoupling. Earlier simulation studies explained the breakdown of the SE relation in terms of the location of the Widom line, emanating from the liquid-liquid critical point (LLCP). Although these studies made a significant contribution to the current understanding of the above phenomena, a detailed molecular picture is still lacking. Recently, our group has explained the diffusion-viscosity decoupling from a jump-diffusion perspective. The jump-diffusion coefficient, emanating from the jump translation of water molecules, is calculated using a quantitative approach for different temperatures at ambient pressure. It has been observed that jump-diffusion is the key factor for diffusion-viscosity decoupling in supercooled water. The same method is adopted in the present work to estimate the jump-diffusion coefficient for different T-P state points and, thereby, explains the role of jump-diffusion for the different extents of the SE relation breakdown at different pressures. The residual diffusion coefficient, the other component of the total diffusion that originates from small step displacement and that is calculated by subtracting the jump-diffusion coefficient from the total diffusion, is seen to be fairly coupled to the viscosity at the entire range of temperature and pressure. Furthermore, we have calculated the average number of H-bonds per water molecule and the tetrahedral order for different T-P state points and investigated an approximate correlation between the average local structure and the contribution of the jump-diffusion to the total diffusion of water. This study, therefore, puts forward a new perspective for explaining the SE relation breakdown in supercooled water under different pressure conditions.

Novel Disassembly Mechanisms of Sigmoid Aβ42 Protofibrils by Introduced Neutral and Charged Drug Molecules.

Alzheimer's disease (AD) is characterized by fibrillar deposits of amyloid-β (Aβ) peptides and neurofibrillary tangles of Tau proteins. Aβ peptides are composed of 37-49 residues, among which the Aβ42 isoform is particularly toxic and aggregation-prone and is enriched in the plaques of AD brains and thus considered central to the development of AD. Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. Here we capture the atomic-level details of the interactions between sigmoid Aβ42 fibril 2MXU or 5KK3 and either natural tanshinone compounds TS1 or TS0 or negatively charged ER, proposing two unprecedented disassembly mechanisms. Natural TS1 or TS0 prefers to insert into the cavity together with part at the surface of the 2MXU to open up the mouth and twist the conformation, destroying the ordered growth of subsequent monomers along the fibril axis. For the more compact two-fold 5KK3 , attachment of TS1 or TS0 at the surface including some inserted in cavity results in the separation of the two folds. In the two sigmoid fibril systems, it is no longer applicable for the routine criteria to assess Aβ42 fibril disassembly by introduction of these drugs, such as either reduced H-bond number, decreased β-sheet contents, or both. ER, like-charged to Aβ42 fibril, is especially exceptional, and departs utterly from the neutral ones to disassemble Aβ42 fibril. Besides the inapplicable routine criteria, positive binding energy between ER and Aβ42 fibril also deviates from the hypotheses of "ligands exhibiting greater affinity for the β-amyloid peptide are effective at altering its aggregation and inhibiting cell toxicity" ( Cairo et al. , Biochemistry 2002 , 41 , 8620 - 8629 ) but results in stronger disassembly effect on the two kinds of sigmoid Aβ42 fibrils than neutral TS0 or TS1. The disassembly power of charged ER molecules derives from its stronger deformation ability to the conformation of Aβ42 fibril than the neutral ones, twisting the one-fold 2MXU into tapered-shape and separating two-fold 5KK3 in two parts further, which is in great agreement with experimental observations ( Irwin et al. Biomacromolecules 2013 , 14 ( 1 ), 264 - 274 ). The unusual disassembly mechanisms fill the gaps and offer an alternative direction in engineering new inhibitors to treat AD.

Substituent dependent selectivity of fluorescent chemosensors derived from coumarin for biologically relevant DNA structures and anions

In this study, we describe facile synthesis of a series of coumarin appended Schiff base chemosensors for the detection of spesific anions such as F−, CN−, AcO−, and H2PO4−. The sensors have been also employed for signaling singlestranded, doublestranded, as well as parallel, anti-parallel and hybrid G-quadruplex DNA structures and increased specificity was detected towards CN− and parallel G-quadruplex structure. The substituents and their positions (ortho, meta, or para) in relation to the OH impacted significantly on the sensing of the anions as well as the acidity of the OH group, in the recognition of the anions. The deprotonation and addition sensing mechanisms of the probes were investigated through UV–vis, fluorimetric, and NMR titration methods. The two signalling mechanisms also have been confirmed using DFT calculations. The bias studies of all the compounds indicated an immediate visible fluorescence change when CN was added to a partial aqueous mixture of DMSO/tap water (6:4, v/v). Furthermore, the chemosensor were studied in neutral and basic mixtures of DMSO/buffer (6:4, v/v) for absorption and emission spectra in the presence and absence of CN−. In the case of DNA structures, up to 5.5-fold fluorescence enhancement was observed in the presence of parallel G-quadruplex as compared with only 1.3-fold in the presence of duplex DNA. Molecular docking studies revealed that, the selectivity is as a result of increased number of H-bonds between DNA and 2b due to modified substituent. In a nutshell, all the fluorophores can be employed in sensing CN− in partial aqueous solution, while 2a, 2b, 2e and 2f showed strong selectivity towards parallel G-quadruplexes over other DNA topologies. Thermal studies of the compounds have shown that the compounds have enough thermal stability properties for application as optic dye.

Thermo-compression of cellulose nanofibrils

All cellulose composites made of 100% cellulose nanofibrils (CNFs) were produced without the use of solvent, binders, chemicals and/or dissolution process. Specimens were produced by thermo-compression and compared with materials made with cellulosic fibers. Different compression conditions such as temperature, time and pressure were tested and their impacts were quantified regarding the mechanical properties of the obtained materials. After determining the optimal compressing conditions, different grades of CNFs were tested and characterized using several characterization methods such as bending properties, Charpy impact strength, water absorption or degree of polymerization. Specimens made of 100% CNFs present improved bending properties, lower Charpy impact strength and lower water sensitivity than samples made with cellulose fibers. CNFs with their smaller size and increased number of possible H-bonds, create samples of lower porosity and allow establishing a solid H-bonding network. However, the particle size of the dry CNF powder influences strongly the self-bonding of the CNFs and the mechanical resistance of the thermo-compressed objects. Objects made of 100% CNFs can now be produced using an environmentally friendly process. Schematic illustration of the study: production of 100% CNF objects by thermo-compression.

Structure-activity relationship study of NPP1 inhibitors based on uracil-N1-(methoxy)ethyl-β-phosphate scaffold

Overexpression of ecto-nucleotide pyrophosphatase-1 (NPP1) is associated with diseases such as calcium pyrophosphate dihydrate deposition disease, calcific aortic valve disease, and type 2 diabetes. In this context, NPP1 inhibitors are potential drug candidates for the treatment of these diseases. The present study focuses on the analysis of the structure-activity relationship of NPP1 inhibitors based on acyclic uracil-nucleotides. For this purpose, we synthesized acyclic uridine-monophosphate analogs, 10-11, uridine-diphosphate analogs, 12–14, and uridine-Pα,α-dithio-triphosphate analogs, 15–17. We evaluated their inhibitory activity and selectivity towards NPP1, -3, NTPDase1, -2, -3, and -8, and P2Y2,4,6 receptors. Analogs 16 and 17 were the most selective and potent NPP1 inhibitors (Ki 0.94 and 0.73 μM, respectively) among the tested molecules. Analogs 10–17 had only minute effect on uracil-nucleotide responding P2Y2,4,6 receptors. Analog 17 (100 μM) displayed 96% inhibition of NPPase activity in osteoarthritic human chondrocytes. Analogs 14–17 displayed weak inhibitory effect on alkaline phosphatase activity at equimolar concentrations in human chondrocytes. All tested analogs showed no toxicity at human chondrocytes. We concluded that ribose-ring to chain transformation, as well as the type of the nucleobase, are parameters of minor significance to NPP1 inhibition, whereas the major parameter is Pα-dithio-substitution. In addition, the length of the phosphate chain also significantly affects inhibition. Overall, the experimental results were well reproduced by molecular docking. A correlation was observed between the activities of the compounds and the number of H-bonds and salt bridges formed between the inhibitors and NPP1 binding site residues. Uracil-N1-(methoxy)ethyl-β-Pα,α-dithio, Pβ,γ-methylene tri-phosphate, 17, was identified as the most potent, selective, and non-toxic NPP1 inhibitor among the tested analogs, and may be used as a lead structure for further drug development.

Identification of RUNX2 variants associated with cleidocranial dysplasia

BackgroundCleidocranial dysplasia (CCD) is a rare autosomal dominant disorder mainly characterized by hypoplastic or absent clavicles, delayed closure of the fontanelles, multiple dental abnormalities, and short stature. Runt-related transcription factor 2 (RUNX2) gene variants can cause CCD, but are not identified in all CCD patients.MethodsIn this study, we detected genetic variants in seven unrelated children with CCD by targeted high-throughput DNA sequencing or Sanger sequencing.ResultsAll patients carried a RUNX2 variant, totally including three novel pathogenic variants (c.722_725delTGTT, p.Leu241Serfs*8; c.231_232delTG, Ala78Glyfs*82; c.909C > G, p.Tyr303*), three reported pathogenic variants (c.577C > T, p.Arg193*; c.574G > A, p.Gly192Arg; c.673 C > T, p.Arg225Trp), one likely pathogenic variant (c.668G > T, p.Gly223Val). The analysis of the variant source showed that all variants were de novo except the two variants (c.909C > G, p.Tyr303*; c.668G > T, p.Gly223Val) inherited from the patient’s father and mother with CCD respectively. Further bioinformatics analysis indicated that these variants could influence the structure of RUNX2 protein by changing the number of H-bonds or amino acids. The experimental result showed that the Gly223Val mutation made RUNX2 protein unable to quantitatively accumulate in the nucleus.ConclusionsThe present study expands the pathogenic variant spectrum of RUNX2 gene, which will contribute to the diagnosis of CCD and better genetic counseling in the future.

Transformation of hydrogen bond network during CO2 clathrate hydrate dissociation

The kinetic process of the solid-liquid first-order phase transition of carbon dioxide CS-I hydrates with various cavity occupation ratios has been investigated in order to understand the framework of the H-bond network and the local structure of each water molecule. This includes the time dependent change in short-range order at temperatures close to the melting point and comparison with the hexagonal ice structure. Using the molecular dynamics method, dependencies of the internal energy of the studied systems on the time of heating were found. Jumps in the internal energy of solids in the range at 275–300K indicate a phase transition. The study of the oxygen‑oxygen radial distribution and hydrogen‑oxygen‑oxygen mutual orientation angles between molecules detached at no >3.2Å led to the determination of the H-bond coordination number for all molecules and the total number of H-bonds and showed instantaneous (<1ns) reorganization of the short-range order of all molecules. Structural analysis of neighbor water molecule pairs showed ~10–15% decrease in the H-bond number after melting whereas all molecules form a single long-range H-bond network. Analysis of the H-bond network showed minor changes in the H-bond interaction energy at the solid-liquid phase transition.

Numerical study on transport properties of the working mixtures for coal supercritical water gasification based power generation systems

Viscosity of H2O/CO2/H2 mixtures or H2O/CO2 mixtures is a vital transport property and required in the design of equipment for coal supercritical water gasification based power generation systems, however, no experimental data and studies have examined these viscosities in supercritical regions of water. In this paper, viscosity of these mixtures in supercritical regions of water is investigated by molecular dynamics method and different theoretical models. Moreover, the self-diffusion coefficient, radial distribution functions and H-bond number are also calculated via molecular dynamics simulations to make a better understanding of the temperature dependences of the viscosity of the mixtures in supercritical regions of water at a molecular level. The breakdown of Stokes–Einstein relation for the H2O/CO2/H2 mixture in supercritical regions of water is found and discussed. The prediction models and data put forth in this paper offer great value for practical application systems involving coal supercritical water gasification.

Pharmacokinetic properties of biomass-extracted substances isolated by green solvents

According to the literature, approximately 41 nutraceutical compounds have been isolated from different types of biomass using green solvents. It is important to collect information on the pharmacokinetic properties of the nutraceutical substances from biomass isolated according to the published papers. The pharmacokinetic properties of the bioactive substances extracted by green solvents, such as the molecular weight, logP, AlogP, H-bond acceptor, H-bond donor, total polar surface area, atom molar refractivity, number of rotatable bonds, number of atoms, rotatable bond count, number of rigid bonds, number of atom rings, and number of H-bonds, were calculated with a drug-likeness tool. In practical terms, the original and most well-known Lipinski’s Rule of Five (Ro5) was applied to 28 substances, namely 3-hydroxytyrosol; apigenin; artemisinin; bergapten; bilobalide; biochanin A; caffeic Acid; caffeoylmalic acid; catechins; cinnamic acid; curcumin; daidzei; daidzin; epicatechin; gallic acid; genistein; ginkgolide A; ginkgolide B; levofloxacin; luteolin; naringenin; p-coumaric acid; protocatechuic acid; psoralen; quercetin; trans-ferulic acid; tyrosol, and vanillin.

Structure and dynamics of atactic Na+-poly(acrylic) acid (PAA) polyelectrolyte in aqueous solution in dilute, semi-dilute and concentrated regimes

ABSTRACTStructural and dynamic properties of aqueous solution of atactic poly(acrylic) acid (PAA) in dilute, semi-dilute and concentrated regimes were studied by fully atomistic molecular dynamics simulations with explicit solvent description, as a function of polymer concentration c (i.e. volume fraction φp) and charge density f. PAA size (Rg, R) decreases with φp in semi-dilute and concentrated regimes, due to increase in counter-ion condensation. For all values of f, in dilute regime (c < c*) chains are expanded and in semi-dilute regime (c*< c < c**) chains are in contact with each other, while for c ≅ c** aggregates comprising of few PAA chains occur (at f = 0.2, 0.4 and 0.7). Number of PAA intrachain h-bonds is greater than PAA–PAA interchain h-bonds at all values of f and φp. The number of h-bonds between carboxylic acid groups and carboxylate groups remain unaffected by φp. The Na+ ion self-diffusion coefficient shows linear decrease with concentration for f < 1 and exponential decrease for f = 1. The PAA self-diffusion coefficient shows power law decrease with concentration for f < 1 and exponential decrease for f = 1. Aggregation of chains is favoured due to PAA–PAA interactions with increase in concentration. Our simulation results are in agreement with experiments and coarse-grained simulations in the literature.

Enhanced water transport through a carbon nanotube controlled by the lateral pressure

The transport of water through carbon nanotubes (CNTs) is now of great importance in bionanotechnology and of considerable interest for potential nanofluidic applications. In this paper, we show by molecular dynamics simulations that the permeation of single-file water molecules through a CNT can be significantly improved by means of tuning the direction of pressure difference, i.e. introducing an additional lateral pressure to the longitudinal one. The water flow exhibits an interesting maximum behavior with the change of lateral pressure, deciphered by the breakdown of single-file water chain inside the CNT. The translocation time decreases monotonously with the increase of lateral pressure and exhibits a clear bifurcation due to the longitudinal pressure, corresponding to the flow enhancement. Therefore, the lateral pressure will increase the difficulty for water entering, while promotes the water conduction inside the CNT, whose competition ultimately leads to the flow maximum behaviors. Along with the water reducing inside the CNT, the CNT switches between the filling and empty states with the unique distributions of water dipole orientation, density and H-bond number. Our results indicate that tuning the direction of pressure difference should be a significant new strategy for enhancing the water permeability, where the key lies in the breakdown of single-file water chain and are thus insightful for future studies.

Ammonium hexafluorosilicates: a new type of anti-caries agents

It is known that dental caries is one of the most common diseases; for children, this pathology ranks first among chronic diseases and has the character of a pandemic. In the modern arsenal of means for the treatment and prevention of caries, fluoride preparations – sodium, potassium fluoride, tin difluoride, sodium monofluoridephosphate, diammine silver fluoride – occupy the leading positions. In recent decades, ammonium hexafluorosilicate and hexafluorosilicates of organic ammonium cations, which have certain advantages over traditional fluoride preparations, have been actively studied as promising anti-caries and hypo-sensitive agents.&#x0D; The aim of this review is to systematize and analyze literature data, reflecting existing experience in the field of synthesis methods, studying the structure, physicochemical properties and biological activity of ammonium hexafluorosilicates as potential anti-caries agents.&#x0D; The general method for the synthesis of ammonium hexafluorosilicates is the interaction of the corresponding base, or its salt, in methanol, ethanol or another solvent with stoichiometric or excess amount of hydrofluoric acid. The structure of ammonium hexafluorosilicates, which are typical supramolecular compounds, is described. Using the example of pyridinium hexafluorosilicates, the relationship between water solubility and structural characteristics of salts was demonstrated. Identification methods have been proposed for the combination of cetylpyridinium hexafluorosilicate. The results of determination of acute toxicity for a number of hexafluorosilicates in animal experiments are given. Studies of the antibacterial activity of hexafluorosilicates are described. It is shown that hexafluorosilicates significantly reduce the number of carious lesions and their depth, and significantly exceed sodium fluoride in all indicators. The feasibility of their use for the prevention of periodontitis is demonstrated. A technological scheme for obtaining a gel containing cetylpyridinium hexafluoro silicate has been proposed.&#x0D; General methods for the synthesis of ammonium hexafluorosilicates include the interaction of an organic base or the corresponding hydrochloride in a solvent medium with an excess of hydrofluoric acid silica. In the crystal structures of hexafluorosilicates, hydrogen bond systems with the participation of fluorine ligands and H-donor fragments of cations perform the main structure-forming and stabilizing function. The solubility of hexafluorosilicates in water varies widely, which is determined by the nature of the ammonium cation and, in the case of pyridinium salts, is antibatically correlated with the number of strong and medium H-bonds in the salt structure. The degree of hydrolysis of hexafluoro silicates in 1×10–4 М aqueous solutions is high and in some cases reaches practically quantitative values. The results of the determination of the acute toxicity of ammonium hexafluorosilicates make it possible to classify these compounds as moderately toxic substances. All studied ammonium hexafluorosilicates exhibit high caries preventive activity, significantly reducing the number and depth of carious lesions, while simultaneously significantly improving the biochemical parameters of dental pulp and periodontal bone tissue. Ammonium hexafluorosilicates can be used as new effective anti-caries and hypo-sensitive agents.

Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase.

Rice grains accumulate starch as their major storage reserve whose biosynthesis is sensitive to heat. ADP-glucose pyrophosphorylase (AGPase) is among the starch biosynthetic enzymes severely affected by heat stress during seed maturation. To increase the heat tolerance of the rice enzyme, we engineered two dominant AGPase subunits expressed in developing endosperm, the large (L2) and small (S2b) subunits of the cytosol-specific AGPase. Bacterial expression of the rice S2b with the rice L2, potato tuber LS (pLS), or with the mosaic rice-potato large subunits, L2-pLS and pLS-L2, produced heat-sensitive recombinant enzymes, which retained less than 10% of their enzyme activities after 5 min incubation at 55°C. However, assembly of the rice L2 with the potato tuber SS (pSS) showed significantly increased heat stability comparable to the heat-stable potato pLS/pSS. The S2b assembled with the mosaic L2-pLS subunit showed 3-fold higher sensitivity to 3-PGA than L2/S2b, whereas the counterpart mosaic pLS-L2/S2b showed 225-fold lower sensitivity. Introduction of a QTC motif into S2b created an N-terminal disulfide linkage that was cleaved by dithiothreitol reduction. The QTC enzyme showed moderate heat stability but was not as stable as the potato AGPase. While the QTC AGPase exhibited approximately fourfold increase in 3-PGA sensitivity, its substrate affinities were largely unchanged. Random mutagenesis of S2bQTC produced six mutant lines with elevated production of glycogen in bacteria. All six lines contained a L379F substitution, which conferred enhanced glycogen production in bacteria and increased heat stability. Modeled structure of this mutant enzyme revealed that this highly conserved leucine residue is located in the enzyme’s regulatory pocket that provides interaction sites for activators and inhibitors. Our molecular dynamic simulation analysis suggests that introduction of the QTC motif and the L379F mutation improves enzyme heat stability by stabilizing their backbone structures possibly due to the increased number of H-bonds between the small subunits and increased intermolecular interactions between the two SSs and two LSs at elevated temperature.

Thermodynamic and transport properties of 1-allyl-3-methylimidazolium bis(trifluromethylsulfonyl)imide + 1-propanol liquid mixtures: A Molecular Dynamics study

In this work, densities, self-diffusion coefficients, viscosities of the mixture 1-allyl-3-methylimidazolium bis(trifluromethylsulfonyl)imide ionic liquid (IL) + 1-propanol are calculated from Molecular Dynamics and compared with measured experimental data. A molecular model of the IL is proposed and corroborated by calculating excess volume and shear viscosity of the mixtures in the whole composition range. Simulation results are in very good agreement to experimental data, showing that the proposed molecular model reproduces adequately the density and viscosity of the binary mixture. The excess molar volume behavior is qualitatively similar to the one calculated from the experimental densities. The difference is due to the differences between calculated densities from Molecular Dynamics and experimental values. Additionally, the number of H-bonds is calculated to explain the intermolecular behavior of the mixture.

Structural and dynamical thermostability of psychrophilic enzyme at various temperatures: Molecular dynamics simulations of tryptophan synthase

Mesophilic enzymes are among the most frequently used biocatalysts, however, psychrophilic enzymes are crucially important for their use in heat-sensitive reactions. How enzymes can work efficiently at various range of temperatures is an interesting subject for researchers, and yet it is very least explored. The structural and dynamical behavior of psychrophilic enzymes and their thermostability at various temperatures can help to understand the mechanism and function at molecular level, and for this purpose the ligand-free α-subunit of Shewanella frigidimarina's tryptophan synthase (Sf-TRPS) in isolated monomeric and in hetero-αβ-dimeric states was subjected to molecular dynamics (MD) simulations study. The simulation sampled a complete open conformation of Loop L6 in α-subunit with and without β-partner, which was further investigated under three temperatures mimicking psychrophilic, mesophilic and thermophilic environment. The results indicated an imperative role of β-subunit in the dynamics of L6 loop as well as in the thermostability of α-subunit by increasing interaction strength at the αβ-interface. An interesting relation was observed between the numbers of H-bonds and residue-pairs forming salt bridges at every temperature, and the combine effect seemed to regulate the balance between protein rigidity and flexibility. The outcome of the study will help to understand the driving forces that lead to the stability of the protein at different temperature, and thereby, assist in enzyme engineering that will be beneficial from industrial point of view.

The effect of electric fields in methane hydrate growth and dissociation: A molecular dynamics simulation

Molecular dynamics simulation was employed to examine the growth and dissociation process of methane hydrate in the presence of static/oscillation electric fields at T = 260 K and P = 100 bars. The intensity of electric field was in range of 1.0–2.0 v/nm, and the frequency of applied e/m field was in range of 2.45 GHz–1.0 THz. Electric field would be a factor controlling the hydrate growth and dissociation because the migration of water molecules may be affected. Total energy of simulation system, final system configurations, hydrate-like methane numbers, radial distribution functions, H-bond numbers with simulation time, and dipole moment were analyzed. There is intensity threshold for e-field to exert an effect on methane hydrate. Static electric fields above the intensity threshold (1.5 v/nm) could push hydrate dissociation by inducing the arrangement of water molecules along the field. Cosine oscillation electric fields could promote both methane hydrate growth and dissociation, and there are different critical field magnitudes for different frequency e-fields to play positive roles in methane hydrate growth or dissociation. In order to promote methane hydrate dissociation, higher the e-field magnitude will need as the e-field frequency is higher.