Molecular dynamics simulations of a fragment of the protein transthyretin and metallic clusters diagnosed by the ultra-fast shape recognition technique, time series segmentation, time series cross correlation analysis and diffusion theory method

• Main Authors: Po-Jen Hsu, 許伯任
• Other Authors: San-Kiong Lai
• Format: Others
• Language: en_US
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/86679394498611521552

博士 === 國立中央大學 === 物理學系 === 102 === Part I--An ultrafast shape-recognition technique was used to analyze the phase transition of finite-size clusters, which, according to our research, has not yet been accomplished. The shape of clusters is the unique property that distinguishes clusters from bulk systems, and is comprehensive and natural for structural analysis. In this study, an isothermal molecular dynamics simulation was performed to generate a structural database for shape recognition of Ag-Cu metallic clusters using empirical many-body potential. The probability contour of the shape similarity exhibits the characteristics of both the specific heat and Lindemann index (bond length fluctuation) of clusters. Moreover, our implementation of the substructure to the probability of shapes provides a detailed observation of the atom/shell-resolved analysis, and the behaviors of the clusters were reconstructed based on the statistical information. The method is efficient, flexible, and applicable in any type of finite-size system, including polymers and nanostructures. Part II--Folded conformations of proteins in thermodynamically stable states have long lifetimes. Between such stable folded conformations the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series clustering. The first procedure measures the differences between statistical distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, the third technique exploits spatial fingerprints of the stable conformations, since strongly correlated atoms in different conformations are different because the bond and steric constraints are different, to map out the sequences of changes preceding the actual folding and unfolding events. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational changes and structural changes associated with rate-limiting precursors translate into brief segments. Guided by these technical procedures, we identify not only the signatures of transitions between α helix and β hairpin for transthyretin fragment TTR(105-115) (the model system chosen in this work for illustration), but also the important role played by weaker correlations in such protein folding dynamics. Part III--Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein, and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C.P. Jaroniec, C.E. MacPhee, N.S. Astrof, C.M. Dobson, and R.G. Griffin, PNAS 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature, and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α-helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.