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PubMed2026

Exploring the mechanism of Shengmai San in treating lung adenocarcinoma based on bioinformatics and molecular dynamics simulation.

To investigate the mechanism of Shengmai San (SMS) in the treatment of lung adenocarcinoma (LUAD) based on an integrated strategy combining "network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulation," aiming to provide a precise combination therapy strategy and identify potential bioactive compounds. Differentially expressed genes in LUAD were identified from the Gene Expression Omnibus database using R (originally developed at Bell Laboratories and currently managed by Lucent Technologies). SMS components (ginseng, Ophiopogon japonicus, and Schisandra chinensis) were retrieved from encyclopaedia of traditional Chinese medicine, with Lipinski-compliant compounds selected. Compound targets were predicted via SwissTargetPrediction and Similarity Ensemble Approach. Intersecting targets between differentially expressed genes and compound targets were identified for "herbs-compounds-targets-disease" network construction. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed. Hub targets were identified by analyzing the protein-protein interaction network. High-prognostic relevance targets were screened from The Cancer Genome Atlas. Compounds targeting these were identified through the herbs-compounds-targets-disease network, and absorption, distribution, metabolism, excretion, and toxicity-compliant compounds were selected using SwissADME (a web-based tool provided by the Molecular Modeling Group of the Swiss Institute of Bioinformatics). Core regulatory targets were identified through molecular docking, with complex stability assessed by molecular dynamics simulations. The key bioactive compounds of SMS for treating LUAD were identified as 7-hydroxy-2,5-dimethyl-4H-1-benzopyran-4-one, N-trans-feruloyltyramine, paprazine, and (E)-N-[(2S)-2-hydroxy-2-(4-hydroxyphenyl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide. Hub targets included AURKA, CCNA2, CCNB1, CDK1, CHEK1, KIF11, NEK2, PLK1, TTK, and TYMS. Among these, CDK1, CHEK1, and PLK1 demonstrated both high-prognostic relevance and strong binding affinity with SMS, emerging as core regulatory targets for SMS in LUAD treatment. Mechanistically, SMS exerts its anticancer effects primarily by modulating the tumor necrosis factor, interleukin-17, cell cycle, and Lipid and atherosclerosis signaling pathways. The active components of SMS, such as paprazine, may exert antitumor effects partly through downregulating CDK1, CHEK1, and PLK1 expression. Although the present study did not examine drug-resistance models or combination regimens, our findings raise the possibility that, in patients with high expression of these genes, combining SMS with standard chemotherapy or targeted therapy could potentially enhance chemosensitivity and mitigate the development of resistance. This hypothesis, however, requires formal testing in appropriate preclinical models and functional validation studies.

Molecular Dynamics Simulation↗
PubMed1996

Molecular dynamics simulations of valinomycin and its potassium complex in homogeneous solvents.

Molecular dynamics simulations of kalinomycin (VM) and its potassium complex in water and in a Lennard Jones solvent are reported. In agreement with experimental evidence the structure of K(+)-VM in nonpolar solution is similar to the solid state structure whereas the structure of uncomplexed VM is not. In water uncomplexed VM retains the Lac and HyV faces (which are lost in nonpolar solution) and shows some similarity with the solid-state structure obtained by crystallization from dimethyl sulfoxide (DMSO). However, also in agreement with spectroscopic data a dynamic equilibrium between a set of conformers is established in both solvents. Our model reproduces the experimental dipole moment (3.6 D) of VM in nonpolar solution. We also observed the spontaneous decomplexation of K(+)-VM in water, with the ion passing through the HyV face in preference to the Lac face. Water attack was observed through both faces. The time scale for all conformational transitions is of the order of 100 ps, with structural changes associated with the (de)-complexation reaction controlled by the ring dihedrals in the vicinity of the L-lactic acid residues. Global structural functions, radial distribution functions, and VM ring dihedral analysis are presented, along with an analysis of the decomplexation event.

Algorithms↗
PubMed2006

Molecular dynamics simulations of multilayer films of polyelectrolytes and nanoparticles.

We performed molecular dynamics simulations of multilayer assemblies of flexible polyelectrolytes and nanoparticles. The film was constructed by sequential adsorption of oppositely charged polymers and nanoparticles in layer-by-layer fashion from dilute solutions. We have studied multilayer films assembled from oppositely charged polyelectrolytes, oppositely charged nanoparticles, and mixed films containing both nanoparticles and polyelectrolytes. For all studied systems, the multilayer assembly proceeds through surface overcharging after completion of each deposition step. There is almost linear growth in the surface coverage and film thickness. The multilayer films assembled from nanoparticles show better layer stratification but at the same time have higher film roughness than those assembled from flexible polyelectrolytes.

Journal Article↗
PubMed2005

Molecular dynamics simulation of entropy driven ligand escape process in heme pocket.

Molecular dynamics simulations were performed to investigate the gate effect of protein motion on the escape of O(2) from the heme pocket. The existing geometric entropy in a spherical cavity pushes the ligand toward the cavity surface, and then the ligand escape along the cavity surface is controlled by the gate size and gate modulation, i.e., protein dynamics regulate the gating behavior, which is an inherent feature of proteins such as myoglobin. Our simulation results confirm that the ligand escape process is basically entropy driven.

Journal Article↗
PubMed2006

Molecular dynamics simulation of nanodroplet spreading enhanced by linear surfactants.

We utilize molecular dynamics simulations to probe the surfactant-mediated spreading of a Lennard-Jones liquid droplet on a solid surface. The surfactants are linear hexamers that are insoluble in the liquid and reduce the surface tension of the liquid-vapor interface. We study how the interaction of the surfactant hexamers with the solid substrate influences spreading, as well as the dependence of spreading on surfactant concentration. We find that the spreading speed is strongly influenced by the attraction of the hydrophobic surfactant tail to the solid surface. When this attraction is sufficiently strong, surfactant molecules partition to the liquid-solid interface and facilitate spreading. This partitioning can lead to an inhomogeneous distribution of surfactant over the liquid-vapor interface, which could drive the Marangoni convection. We also observe that the surfactant molecules can assemble into micelles on the solid surface. The repulsion between micelles at the liquid-solid interface can lead to break-off and migration of the micelles from the liquid-solid to the gas-solid interface and spreading is facilitated in this way. Our model system contains features that are believed to underlie superspreading in experimental studies of droplet spreading.

Journal Article↗
PubMed2005

Molecular dynamics simulations of nanoindentation and nanotribology.

We present results of parallel molecular dynamics simulations of nanoindentation and nanotribology experiments. The models we have developed describe both the sample and the indenter atomistically and model the effect of the cantilevers in an atomic force microscope through the use of springs. We show that the simulations are in good qualitative agreement with experiment and help to elucidate many of the mechanisms that take place during these processes. In particular, we illustrate the role that dislocations play both in nanoindentation and also in stick-slip. Further to this we show how real-time visualization and computational steering have been employed in these simulations to capture the dynamical events that take place.

Computer Simulation↗
PubMed2002

Molecular dynamics simulation of polymer helix formation using rigid-link methods.

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under gradual cooling are followed until each reaches a state from which no further change is possible. The interactions are chosen so that the true ground state is a helix, and a high proportion of simulation runs succeed in reaching this state; the fraction that manages to form defect-free helices is a function of both chain length and cooling rate. In order to demonstrate behavior analogous to the formation of protein tertiary structure, additional attractive interactions are introduced into the model, leading to the appearance of aligned, antiparallel helix pairs. The simulations employ a computational approach that deals directly with the internal coordinates in a recursive manner; this representation is able to maintain constant bond lengths and angles without the necessity of treating them as an algebraic constraint problem supplementary to the equations of motion.

Journal Article↗
PubMed2002

Molecular dynamics simulations of crystallization of hard spheres.

We have carried out molecular dynamics simulations of the crystallization of hard spheres modeling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of gravitational forces, polydispersity, and of bounding walls on the phase structure. The simulations employed an extensive exclusive particle grid method and the type and degree of crystalline order was studied in two independent ways: by the structure factor, as in experiments, and through local rotational invariants. We present quantitative comparisons of the nucleation rates of monodisperse and polydisperse hard-sphere systems and benchmark them against experimental results. We show how the presence of bounding walls leads to wall-induced nucleation and rapid crystallization, and discuss the role of gravity on the dynamics of crystallization.

Journal Article↗
PubMed2005

Molecular dynamics simulation of heat conduction in near-critical fluids.

Using molecular dynamics simulations we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity exhibits critical singularity in agreement with the mode-coupling theory in two dimensions. We also calculate distributions of the momentum and heat fluxes at fixed density. They indicate that liquidlike (entropy-poor) clusters move toward the warmer boundary and gaslike (entropy-rich) regions move toward the cooler boundary in a temperature gradient. This counterflow results in critical enhancement of the thermal conductivity.

Journal Article↗
PubMed2000

Orientation dependence in molecular dynamics simulations of shocked single crystals

We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the <100> direction form intersecting stacking faults by slippage along 111 close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the <111> case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the <110> direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation.

Journal Article↗
PubMed2004

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin.

We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, CO, after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the CO motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of CO in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins.

Animals↗
PubMed2006

Why does the intermolecular dynamics of liquid biphenyl so closely resemble that of liquid benzene? Molecular dynamics simulation of the optical-Kerr-effect spectra.

The combination of optical-Kerr-effect (OKE) spectroscopy and molecular dynamics simulations has provided us with a newfound ability to delve into the librational dynamics of liquids, revealing, in the process, some surprising commonalities among aromatic liquids. Benzene and biphenyl, for example, have remarkably similar OKE spectra despite marked differences in their shapes, sizes, and moments of inertia--and even more chemically distinct aromatics tend to have noticeable similarities in their spectra. We explore this universality by using a molecular dynamics simulation to investigate the librational dynamics of molten biphenyl and to predict its OKE spectrum, comparing the results with our previous calculations for liquid benzene. We suggest that the impressive level of quantitative agreement between these two liquids is largely a reflection of the fact that librations in these and other aromatic liquids act as torsional oscillations with oscillator frequencies selected from the liquid's librational bands. Since these bands are centered about the librational Einstein frequencies, the quantitative similarities between the liquids are essentially reflections of the near identities of their Einstein frequencies. Why then are the Einstein frequencies themselves so insensitive to molecular details? We show that, for nearly planar molecules, mean-square torques and moments of inertia tend to scale with molecular dimensions in much the same way. We demonstrate that this near cancellation provides both a quantitative explanation of the close relationship between benzene and biphenyl and a more general perspective on the similarities seen in the ultrafast dynamics of aromatic liquids.

Journal Article↗
PubMed2001

Comment on "Efficient stress relaxation in molecular dynamics simulations of semiflexible n-alkanes".

Contrary to the findings of Mülders, Toxvaerd, and Kneller [Phys. Rev. E 58, 6766 (1998)] (MTK), we are unable to discern any difference in the behavior of long chain alkanes simulated by molecular dynamics at constant pressure using either atomic or molecular scaling schemes. This result confirms our previous study [M. Marchi and P. Procacci, J. Chem. Phys. 109, 5194 (1998)] on hydrated proteins published at the same time as the MTK's paper. This Comment indicates that errors in the calculation of the pressure tensor might be responsible for at least a part of the MTKs results.

Letter↗
PubMed1996

The consistency of large concerted motions in proteins in molecular dynamics simulations.

A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the simulation parameters in each simulation. Parameters studied included temperature, bond constraints, cut-off radius for electrostatic interactions, and initial placement of hydrogen atoms. The essential dynamics technique was used to reveal dynamic differences between the simulations. Similar essential dynamics properties were found for all simulations, indicating that the large concerted motions found in the simulations are not particularly sensitive to small changes in the force field. A thorough investigation into the stability of the essential dynamics properties as derived from a molecular dynamics simulation of a few hundred picoseconds is provided. Although the definition of the essential modes of motion has not fully converged in these short simulations, the subspace in which these modes are confined is found to be reproducible.

Antigens, Bacterial↗
PubMed1988

Molecular dynamics simulations of ribonuclease T1. Effect of solvent on the interaction with 2'GMP.

Molecular dynamics simulations in vacuum and with a water sphere around the active site were performed on the 2'GMP-RNase T1 complex. The presence of water led to the maintenance of the 2'-GMP-RNase T1 interactions as compared to the X-ray structure, including the hydrogen bonds implicated in the enzyme-inhibitor recognition process. The sidechain of His92 in the molecular dynamics water simulation, however, hydrogen bonds directly to the phosphate of 2'GMP in contrast to the X-ray structure but in support of the role of that residue in the enzyme's catalytic mechanism. Fluctuations of active-site residues are not strongly influenced by water, possibly owing to the exclusion of water by the bound 2'GMP, which did show an increase in mobility. Analysis of the 2'GMP-RNase T1 interactions versus time reveal an equilibrium fluctuation in the presence of water, leading to a less favorable 2'GMP-RNase T1 interaction energy, suggesting a possible relationship between picosecond fluctuations and inhibitor dissociation occurring in the millisecond time domain.

Endoribonucleases↗
PubMed2001

Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations.

Folding reaction of goat alpha-lactalbumin has been studied by stopped-flow circular dichroism and molecular dynamics simulations. The effects of four single mutations and a double mutation on the stability of the protein under a native condition were studied. The mutations were introduced into residues located at a hydrophobic core in the alpha-domain of the molecule. Here we show that an amino acid substitution (T29I) increases the native-state stability of goat alpha-lactalbumin against the guanidine hydrochloride-induced unfolding by 3.5 kcal/mol. Kinetic refolding and unfolding of wild-type and mutant goat alpha-lactalbumin measured by stopped-flow circular dichroism showed that the local structure around the Thr29 side chain was not constructed in the transition state of the folding reaction. To characterize the local structural change around the Thr29 side chain to an atomic level of resolution, we performed high-temperature (at 400 K and 600 K) molecular dynamics simulations and studied the structural change at an initial stage of unfolding observed in the simulation trajectories. The Thr29 portion of the molecule experienced structural disruption accompanied with the loss of inter-residue contacts and with the water molecule penetration in the 400-K simulation as well as in four of the six 600-K simulations. Disruption of the N-terminal portion was also observed and was consistent with the results of kinetic refolding/unfolding experiments shown in our previous report.

Animals↗
PubMed1996

Molecular dynamics simulations of isolated transmembrane helices of potassium channels.

In the middle of the S6 helix in voltage-gated potassium channels there is a highly conserved Pro-Val-Pro motif, while the equivalent M2 helix of inward rectifier potassium channels contains a conserved glycine residue in a comparable position. The structural implications of these conserved motifs are of interest given the evidence that S6 and M2 are components of the lining of their respective pores. Multiple sequence alignment and TM helix prediction methods were used to define consensus regions for S6 and M2. Ensembles of 50 structures for each helix were generated by simulated annealing and restrained molecular dynamics. Time-dependent fluctuations of S6 and M2 were investigated by long time scale molecular dynamics simulations on representative members of each ensemble carried out in vacuo in the presence and absence of a hydrophobic potential that mimics a lipid bilayer. The results are discussed in terms of the structural basis of the kink in S6 and M2 and of a putative functional role for flexible helices as "molecular swivels."

Amino Acid Sequence↗
PubMed2002

Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation.

Limited proteolysis by trypsin of monomeric Cu,Zn superoxide dismutase from Escherichia coli induces a specific cleavage of the polypeptide chain at the level of Lys60 located in the S-S subloop of loop 6,5 where, when compared to the eukaryotic enzyme, a seven-residues insertion, completely exposed to the solvent, is observed. This result suggests that this subloop is disordered and flexible, thus enabling binding and adaptation to the active site of the proteolytic enzyme. Indeed, molecular dynamics simulation indicates that the S-S subloop undergoes high fluctuations and that its high flexibility coupled to an high solvent accessibility can explain the specific bond selection of the protease. As a matter of fact, of the possible 14 solvent accessible proteolytic sites only the Lys60 flexible site is cleaved. High flexibility and solvent exposure are confirmed by the short water residence time for the residues corresponding to the cleavage site evaluated by molecular dynamics simulation. These experiments demonstrate that molecular dynamics simulation and limited proteolysis are complementary and unambiguous tools to identify flexible sites in proteins.

Amino Acid Sequence↗