In Silico Study on the Interaction of Thiazolidinediones and β-Lactoglobulin by Molecular Dynamics and Docking Approach

Thiazolidinediones are widely used in the treatment of diabetes mellitus type 2. An investigation of their interaction with a transport protein, such as β-lactoglobulin (BLG), at the atomic level could be a valuable factor in controlling their transport to biological sites. The interaction of troglitazone, pioglitazone, and rosiglitazone, as representative thiazolidinediones, and BLG, as a transport protein, was investigated using molecular docking and molecular dynamics (MD) simulation methods. The molecular docking results showed that these thiazolidinediones bind to the internal cavity of BLG and the BLG affinity for binding the thiazolidinediones decreases in the following order: troglitazone > pioglitazone > rosiglitazone. The analysis of MD simulation trajectories showed that the BLG and BLG-thiazolidinedione complexes became stable at approximately 2500 ps and that there was little conformational change in the BLG-thiazolidinedione complexes over a 10 ns timescale. In addition, the profiles of atomic fluctuations showed the rigidity of the ligand-binding site during the simulation time.     

Computational Studies on the Interaction of Arctiin and Liquiritin With β-lactoglobulin

The study of the interaction of drugs purified from natural sources and a transport protein, such as β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to study the interaction of arctiin and liquiritin as natural drugs and BLG as the transport protein. The molecular docking results indicated that these drugs bind in the internal cavity of BLG and the BLG affinity for binding the liquiritin is greater than arctiin. The docking results also indicated that the hydrogen bond interactions have a dominant role in the BLG-drug complex stability. The analysis of MD simulation trajectories showed that the root mean square deviation (RMSD) of BLG-liquiritin, unliganded BLG, and BLG-arctiin reached equilibrium and fluctuated around the mean value at about 1000, 3500, and 4000 ps, respectively. The time evolution of the radius of gyration and total solvent accessible surface of the protein showed that BLG-arctiin and BLG-liquiritin complexes became stable around 2500 and 5000 ps, respectively. Also, the profiles of atomic fluctuations during the simulation showed the rigidity of the ligand binding sites.     

Molecular Dynamics Simulation of Myoglobin Collision with Low Energy Ions

Collisions of a low energy heavy ion with a myoglobin in water are simulated by molecular dynamics model. The increase of total energy is very small. The mean squared fluctuation decreases at 300 K and increases at 250K. This is an important novel cooling effect that protects the protein from ion damage. The possible collision side effect is the change of tertiary structure that blocks the normal functions of the myoglobin.     

Dynamics of α-Tocopherol Acetate: Proton Relaxation Studies Supported by Molecular Dynamics Simulations

Dynamical properties of α-tocopherol acetate (commonly known as vitamin E) have been investigated in a broad temperature range (below and above the glass transition) by means of proton spin–lattice relaxation. Two distinct relaxation processes have been detected in the studied temperature range. One of them, present in the solid phase, has been attributed to reorientation of methyl groups. In order to identify the motional process leading to the proton relaxation above the glass transition temperature (T _g), molecular dynamics (MD) simulations have been performed, which provided time correlation functions for several internuclear vectors in the molecule. The high-temperature relaxation process is primarily due to dynamics of the aromatic rings of the tocopherol molecule; however, a considerable contribution of diffusion of the aliphatic chain cannot be excluded. Comparing the nuclear magnetic resonance (NMR) results with MD and relaxation data of dielectric spectroscopy (DS) available in the literature (K. Kamiński, S. Maślanka, J. Zioło, M. Paluch, K.J. McGrath, C.M. Roland, Phys Rev E 75:011903-7, 2007; E. Szwajczak, J. Świergiel, R. Stagraczyński, J. Jadżyn, Phys Chem Liq 47:460–466, 2009), the motional process observed in NMR relaxation studies above T _g has been identified with the δ process observed in DS.     

Structural and Dynamic Properties of Amorphous Silicon： Tight-Binding Molecular Dynamics Simulation

The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Q1 are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak.     

Molecular Dynamics Simulation of Elongation of Copper–Platinum Nanocontacts

Journal of Experimental and Theoretical Physics - The formation of nanocontacts consisting of copper (Cu) and platinum (Pt) atoms at various temperatures (0–300 K), relative concentrations of...     

Molecular Dynamics Simulation of Water Confined in Carbon Nanotubes

Molecular dynamics simulations are performed for water confined in carbon nanotubes with various diameters （11.0-13.8 A ）. The simulations under an isobaric pressure （one atmosphere） by lowering temperatures from 300 K to 190K are carried out. Water molecules within variously sized tubes tend to transform from disorder to order with different configurations （four-water-molecule ring, six-water-molecule ring and seven-water-molecule ring） at phase transition temperatures, which may be lowered by the increasing tube radius. It is also found that the configurations of water in （10, 10） tube are not unique （seven-molecule ring and seven-molecule ring plus water chain）.     

Studies on the Interaction of Tricyclazole with β-cyclodextrin and human Serum Albumin by Spectroscopy

The interaction of tricyclazole (TCZ) with β-cyclodextrin (β-CD) and human serum albumin (HSA) were studied by fluorescence spectrum, UV-visible spectrum and second-order scattering technology. It was shown that TCZ has quite a strong ability to quench the fluorescence launching from HSA by reacting with it and forming a certain kind of new compound. The quenching and the energy transfer mechanisms were discussed, respectively. The binding constants and thermodynamic parameters at four different temperatures, the binding locality, and the binding power were obtained. The conformation of HSA was discussed by synchronous and three-dimensional fluorescence techniques. The inclusion reaction between β-CD and TCZ was explored by scattering method, the inclusion constants and the thermodynamic parameters at 297 K and 311 K were figured out, respectively. The mechanism of inclusion reaction was speculated and linkage among the toxicity of TCZ, the exterior environment and its concentration was attempted to explain on molecule level.     

Simulation of Ab Initio Molecular Dynamics of Shock Wave on Copper

The relation between particle velocity Up, up to 4 km/s, and shock wave velocity Us in copper has been simulated with ab initio molecular dynamics. The simulated relationship without considering the correction of zero-point and finite temperature effects is Us = 4.23 1.53Up. After considering the correction the relation becomes Us = 4.08 1.53Up, which is consistent with the experimental result.     

Molecular Dynamics Simulation of the Structure I Empty Gas Hydrate

The 368 water molecule structure I empty gas hydrates with three possible hydrogen orientations are calculated using TIP4P potential molecular dynamical simulations.The thermodynamic properties and hydrogen bonding are compared with ice Ih.The density of states is analysed based on experimental measurements.The empty gas hydrate at low temperature is stable without gas molecules encaged.     

Spectroscopic,Viscositic and Molecular Modeling Studies on the Interaction of 3′-Azido-Daunorubicin Thiosemicarbazone with DNA

A new daunorubicin has been synthesized and structurally characterized. The interaction of native calf thymus DNA (ctDNA) with 3′-azido-daunorubicin thiosemicarbazone (ADNRT) was investigated under simulated physiological conditions by multi-spectroscopic techniques, viscometric measurements and molecular modeling study. It concluded that ADNRT could intercalate into the base pairs of ctDNA, and the fluorescence quenching by ctDNA was static quenching type. Thermodynamic parameters calculated suggested that the binding of ADNRT to ctDNA was mainly driven by hydrophobic interactions. The relative viscosity of ctDNA increased with the addition of ADNRT, which confirmed the intercalation mode. Furthermore, molecular modeling studies corroborate the above experimental results.     

Simulation of Helium Behaviour in Titanium Crystals Using Molecular Dynamics

The behaviour of helium in Ti crystals at 300 K has been investigated by means of the molecular dynamics. The study is focused on the influences of He-Ti interaction on the aggregation of helium atoms in the substrate. When a Born-Mayer potential is used to describe the He-Ti interaction, the He atoms are unable to cluster with each other due to the weak bridge barrier that cannot trap the helium atoms, Whereas using a He-Ti potential that is constructed by fitting the ab initio pairwise He-Ti potential, the clustering of He atoms can be observed. The results indicate that suitable He-Ti potential plays an important role in the formation of He clusters in metals. Moreover, it is noted that the shape of the formed He cluster is irregular, and the produced defect prefers to congregating on one side of the He cluster rather than spreading symmetrically around it.     

Molecular Dynamics Simulation of Cage Effect in the Glass Transition of Argon

The glass transition process of argon is studied by molecular dynamics simulations with Lennard-Jones potential. The cage effect appears at about 24K. The Lindemann length of argon is found to be 0.55A. Two relaxation processes are clearly observed near the glass transition temperature, which is in agreement with the mode-coupling theory.     

Molecular Dynamics Simulation on Charge Transfer Relaxation between Myoglobin and Water

Dynamical processes of myoglobin after photon-excited charge transfer between Fe ion and surrounding water anion are simulated by a molecular dynamics model. The roles of Coulomb interaction effect and water effect in the relaxation process are discussed. It is found that the relaxations before and after charge transfer are similar. Strong Coulomb interactions and less water mobility decrease Coulomb energy fluctuations. An extra transferred charge of Fe ion has impact on water packing with a distance up to 0.86nm.     

The changing of the guard: Molecular diversity and rapid evolution of β-defensins

Summary Defensins are small cationic peptides involved in innate immunity and are components of the first line of defence against invading pathogens. β-defensins are a subgroup of the defensin family that display a particular cysteine spacing and pattern of intramolecular bonding. These molecules are produced mostly by epithelia lining exposed surfaces and appear to have both antimicrobial and cell signalling functions. The unusually high degree of sequence variation in the mature peptide produced by the paralogous and in some cases orthologous genes implies extensive specialisation and species specific adaptation. Here we review recent functional data that are an important addition to our knowledge of the innate immune response and novel antibiotic design. We also consider the organisation and evolution of the genomic loci harbouring these genes where radical and rapid changes in β-defensin sequences have been shown to result from the interplay of both positive and negative selection. Consequently these genes provide some unusually clear glimpses of the processes of duplication and specialisation that have shaped the mammalian genome.     

Excimer Emission in Norepinephrine and Epinephrine Drugs with α- and β-Cyclodextrins: Spectral and Molecular Modeling Studies

The inclusion complexation behavior of norepinephrine (NORE) and epinephrine (EPIN) with native cyclodextrins (α-CD and β-CD) were investigated by UV-visible, fluorimetry, time-resolved fluorescence, SEM, TEM, FT-IR, ¹H NMR, DSC, powder XRD and PM3 methods. Single emission was observed in aqueous solution where as dual emission (excimer) noticed in the CD solutions. Both drugs form 1:1 drug-CD complexes in lower CD concentrations and 1:2 CD-drug₂ complexes in the higher CD concentrations. Time-resolved fluorescence studies indicated that both drugs showed single exponential decay in water and biexponential decay in CD. Nano-sized self-aggregated particles of drug-CD were found by TEM studies. Molecular modeling studies indicated that aliphatic chain part of the drug was entrapped in the CD cavity. Thermodynamic parameters and binding affinity of complex formation of the CD were determined according to PM3 method. The PM3 results were in good agreement with the experimental results.     

Encapsulation of Labetalol, Pseudoephedrine in β-cyclodextrin Cavity: Spectral and Molecular Modeling Studies

The absorption and fluorescence spectra of labetalol and pseudoephedrine have been studied in different polarities of solvents and β-cyclodextrin (β-CD). The inclusion complexation with β-CD is investigated by UV-visible, steady state and time resolved fluorescence spectra and PM3 method. In protic solvents, the normal emission originates from a locally excited state and the longer wavelength emission is due to intramolecular charge transfer (TICT). Labetalol forms a 1:2 complex and pseudoephedrine forms 1:1 complex with β-CD. Nanosecond time-resolved studies indicated that both molecules show triexponential decay. Thermodynamic parameters (ΔG, ΔH, ΔS) and HOMO, LUMO orbital investigations confirm the stability of the inclusion complex. The geometry of the most stable complex shows that the aromatic ring is deeply self included inside the β-CD cavity and intermolecular hydrogen bonds were established between host and guest molecules. This suggests that hydrophobic effect and hydrogen bond play an important role in the inclusion process.     

Dynamical Transition of Myoglobin and Cu／Zn Superoxide Dismutase Revealed by Molecular Dynamics Simulation

We have carried out parallel moecular dynamics simulations of solvated and non-solvated myoglobin and solvated Cu/Zn superoxide dismutase at different temperatures.By analysis of several methods,the simulati8ons reproduce the quasielastic neutron scattering experimental reults.Below 200K these two proteins behave as harmonic solids with essentially only vibrational motion,while above this temperature,there is a striking dynamic transition into anharmonic motion.Moreover,the simulations further show that water molecules play an important role for this dynamical transition.There is no such sharp dynamical transition in non-solvated proteins and the higher the solvate density is ,the steeper at transition point the curve of mean square displacement versus temperature will be.The simulations also display that the dynamical transition is a general propoerty for globular protein and this transition temperature is a demarcation of enzyme activity.     

Molecular Dynamics Simulation of Glass Transition of the Supercooled Zr–Nb Melt

Journal of Experimental and Theoretical Physics - The glass transition of the supercooled Zr–Nb melt has been investigated by molecular dynamics simulation. The dependence of the critical...     

Thermodynamic Studies on the Interaction of Dioxopromethazine to β-Cyclodextrin and Bovine Serum Albumin

The interaction of dioxopromethazine (DOPM) with beta-cyclodextrin (beta-CD) and bovine serum albumin (BSA) were investigated by fluorescence quenching method. It was shown that DOPM has quite a strong ability to quench the fluorescence launching from BSA by reacting with it and forming a certain kind of new compound. The quenching and the energy transfer mechanisms were discussed, respectively. The binding constants and thermodynamic parameters at four different temperatures, the binding locality, and the binding power were obtained. The conformation of BSA was discussed by synchronous and three-dimensional fluorescence techniques. The inclusion reaction between beta-CD and DOPM was explored by both Lineweaver-Burk equation and Benesi-Hildebrand equation. The inclusion constants and the thermodynamic parameters at 297 and 307 K were figured out, respectively. The mechanism of inclusion reaction was speculated and the slow release characteristics of beta-CD to DOPM was attempted to explain at molecule level.