Home  About us  Contact
 

Dynamics Trajectories (dynamics + trajectory)

Distribution by Scientific Domains
Chemistry85%

Kinds of Dynamics Trajectories

  • molecular dynamics trajectory
    		•

    Selected Abstracts

    Molecular dynamics simulations of solvated UDP,glucose in interaction with Mg2+ cations

    FEBS JOURNAL, Issue 20 2001
    Pavla Petrová
    ,Glycosyltransferases are key enzymes involved in biosynthesis of oligosaccharides. Nucleotide-sugars, the glycosyltransferase substrates, serve as activated donors of sugar residues during the enzymatic reaction Although very little is known about the catalytic mechanism of these enzymes, it appears that the catalytic activity in most glycosyltransferases is dependent upon the presence of a divalent cation, for example Mn2+ or Mg2+. It is not known whether the ion is bound to the enzyme before its interaction with the substrate, or if it binds the substrate before the enzymatic reaction to modify its conformation to fit better the active site of the enzyme. We have inspected the latter possibility by running four 2-ns molecular dynamics trajectories on fully solvated UDP-glucose in the presence of Mg2+ ions. Our results indicate that the divalent cation interacts strongly with the nucleotide-sugar in solution, and that it can alter its conformational behavior. It is also shown that a conformation of the pyrophosphate moiety that results in an eclipsed or almost eclipsed orientation of two of the oxygen atoms, and which is found in protein interacting with a nucleotide di- or tri-phosphate X-ray data, is energetically favored. The results are also discussed in light of existing NMR data, and are found to be in a good agreement with them. [source]

    Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor

    JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2008
    Michel Masella
    Abstract The dynamic coupling between a polarizable protein force field and a particle-based implicit solvent model is described. The polarizable force field, TCPEp, developed recently to simulate protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in efficiency for an equal chemical accuracy. The Polarizable Pseudo-Particle (PPP) solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard-Jones pseudo-particles. The solvent-induced dipoles are sensitive to the solute electric field, but not to each other, so that the computational cost of solvent,solvent interactions is basically negligible. The solute and solvent induced dipoles are determined self-consistently and the equations of motion are solved using an efficient iterative multiple time step procedure. The solvation cost with respect to vacuum simulations is shown to decrease with solute size: the estimated multiplicative factor is 2.5 for a protein containing about 1000 atoms, and as low as 1.15 for 8000 atoms. The model is tested for six 20 ns molecular dynamics trajectories of a traditional benchmark system: the hydrated Bovine Pancreatic Trypsin Inhibitor (BPTI). Even though the TCPEp parameters have not been refined to be used with the solvent PPP model, we observe a good conservation of the BPTI structure along the trajectories. Moreover, our approach is able to provide a description of the protein solvation thermodynamic at the same accuracy as the standard Poisson-Boltzman continuum methods. It provides in addition a good description of the microscopic structural aspects concerning the solute/solvent interaction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

    Information theoretical measures to analyze trajectories in rational molecular design

    JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2007
    K. Hamacher
    Abstract We develop a new methodology to analyze molecular dynamics trajectories and other time series data from simulation runs. This methodology is based on an information measure of the difference between distributions of various data extract from such simulations. The method is fast as it only involves the numerical integration/summation of the distributions in one dimension while avoiding sampling issues at the same time. The method is most suitable for applications in which different scenarios are to be compared, e.g. to guide rational molecular design. We show the power of the proposed method in an application of rational drug design by reduced model computations on the BH3 motif in the apoptosis inducing BCL2 protein family. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source]

    Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains

    PROTEIN SCIENCE, Issue 5 2002
    Michal Otyepka
    Abstract One-nanosecond molecular dynamics trajectories of three haloalkane dehalogenases (DhlA, LinB, and DhaA) are compared. The main domain was rigid in all three dehalogenases, whereas the substrate specificity-modulating cap domains showed considerably higher mobility. The functionally relevant motions were spread over the entire cap domain in DhlA, whereas they were more localized in LinB and DhaA. The highest amplitude of essential motions of DhlA was noted in the ,4,-helix-loop-,4-helix region, formerly proposed to participate in the large conformation change needed for product release. The highest amplitude of essential motions of LinB and DhaA was observed in the random coil before helix 4, linking two domains of these proteins. This flexibility is the consequence of the modular composition of haloalkane dehalogenases. Two members of the catalytic triad, that is, the nucleophile and the base, showed a very high level of rigidity in all three dehalogenases. This rigidity is essential for their function. One of the halide-stabilizing residues, important for the catalysis, shows significantly higher flexibility in DhlA compared with LinB and DhaA. Enhanced flexibility may be required for destabilization of the electrostatic interactions during the release of the halide ion from the deeply buried active site of DhlA. The exchange of water molecules between the enzyme active site and bulk solvent was very different among the three dehalogenases. The differences could be related to the flexibility of the cap domains and to the number of entrance tunnels. [source]

    Ever since Clements: from succession to vegetation dynamics and understanding to intervention

    APPLIED VEGETATION SCIENCE, Issue 1 2009
    S.T.A. Pickett
    Abstract Introduction: This paper surveys a framework for vegetation dynamics to provide conceptual background for a series of papers addressing the role of vegetation dynamics in restoration. Richness of the foundation: Classical succession theory provides key ingredients for contemporary process studies of vegetation dynamics. The contemporary framework incorporates processes identified by Gleason and other critics of Clements' theory. Multiple causality: The Clementsian causes, when expanded to include interaction and to clarify net effects, accommodate those now recognized in vegetation dynamics. A mature successional framework: A hierarchical framework has emerged to evaluate the causes of vegetation dynamics. The framework identifies the general causes as site availability, species availability, and species performance. Differentials as drivers: Differentials in any of the three general causes can drive change in plant communities. Each general cause consists of specific mechanisms. A model template: To predict vegetation dynamics trajectories, models are required. A model template is presented to operationalize the hierarchical framework. Outcomes are contingent on species pools and environmental contexts and may be progressive or retrogressive. Relationships of frameworks: Other contemporary frameworks in biology relate to vegetation dynamics. Application to restoration: The vegetation dynamics framework is relevant to restoration through linkages with landscape ecology, disturbance ecology, competition, invasion ecology, and community assembly. The differentials of site availability, species availability, and species performance suggest the processes and strategies available for restoration. Conclusions: A synthetic framework of vegetation brings together the mechanisms required for successful restoration. [source]

    Structure and hydration of the amylopectin trisaccharide building blocks,Synthesis, NMR, and molecular dynamics

    BIOPOLYMERS, Issue 12 2008
    Peter I. Hansen
    Abstract To gain insight into the molecular details and hydration of amylopectin, the five constituting trisaccharides have been chemically synthesized as their methyl ,-glycosides. All five trisaccharides were subjected to 950 MHz NMR spectroscopy for complete assignment and nanosecond molecular dynamics trajectories were calculated to study the structure and dynamics of the trisaccharides in aqueous solution. Systematic analysis of the simulation data revealed several examples of bridging water molecules playing an important role in the stabilization of specific amylopectin conformations, which was also supported by the experimental NMR data such as interresidue NOE's and heteronuclear scalar couplings between nuclei from neighboring residues. Although ,-maltotriose, ,-iso-maltotriose, ,-panose and ,-isopanose are relatively well characterized structures, the study also includes one less characterized trisaccharide with the structure ,Glcp(1,4),Glcp(1,6),Glcp. This trisaccharide, tentatively labelled ,-forkose, is located at the branch point of amylopectin, forking the amylopectin into two strands that align into double-helical segments. The results show that the conformation of ,-forkose takes a natural bend form which fits well into the structure of the double-helical segment of amylopectin. As the only trisaccharide in this study the structure of ,-forkose is not significantly influenced by the hydration. In contrast, ,-isopanose takes a restricted, but rather extended form due to an exceptionally strong localized water density. The two homo-linkage oligomers, ,-maltotriose and ,-iso-maltotriose, showed to be the most extended and the most flexible trimers, respectively, providing regular structure for crystalline domains and maximum linker flexibility for amorphous domains. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1179,1193, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]

    Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulations

    PROTEIN SCIENCE, Issue 1 2000
    David A. Horita
    Abstract Molecular dynamics calculations provide a method by which the dynamic properties of molecules can be explored over timescales and at a level of detail that cannot be obtained experimentally from NMR or X-ray analyses. Recent work (Philippopoulos M, Mandel AM, Palmer AG III, Lim C, 1997, Proteins 28:481,493) has indicated that the accuracy of these simulations is high, as measured by the correspondence of parameters extracted from these calculations to those determined through experimental means. Here, we investigate the dynamic behavior of the Src homology 3 (SH3) domain of hematopoietic cell kinase (Hck) via 15N backbone relaxation NMR studies and a set of four independent 4 ns solvated molecular dynamics calculations. We also find that molecular dynamics simulations accurately reproduce fast motion dynamics as estimated from generalized order parameter (S2) analysis for regions of the protein that have experimentally well-defined coordinates (i.e., stable secondary structural elements). However, for regions where the coordinates are not well defined, as indicated by high local root-mean-square deviations among NMR-determined structural family members or high B -factors/low electron density in X-ray crystallography determined structures, the parameters calculated from a short to moderate length (less than 5,10 ns) molecular dynamics trajectory are dependent on the particular coordinates chosen as a starting point for the simulation. [source]