Application of time series analysis on molecular dynamics simulations of proteins: a study of different conformational spaces by principal component analysis

The Journal of Chemical Physics
Burak AlakentMehmet C Camurdan

Abstract

Time series analysis is applied on the collective coordinates obtained from principal component analysis of independent molecular dynamics simulations of alpha-amylase inhibitor tendamistat and immunity protein of colicin E7 based on the Calpha coordinates history. Even though the principal component directions obtained for each run are considerably different, the dynamics information obtained from these runs are surprisingly similar in terms of time series models and parameters. There are two main differences in the dynamics of the two proteins: the higher density of low frequencies and the larger step sizes for the interminima motions of colicin E7 than those of alpha-amylase inhibitor, which may be attributed to the higher number of residues of colicin E7 and/or the structural differences of the two proteins. The cumulative density function of the low frequencies in each run conforms to the expectations from the normal mode analysis. When different runs of alpha-amylase inhibitor are projected on the same set of eigenvectors, it is found that principal components obtained from a certain conformational region of a protein has a moderate explanation power in other conformational regions and the local minima are similar to a ce...Continue Reading

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Jul 23, 2004·The Journal of Chemical Physics·Burak AlakentMehmet C Camurdan

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Citations

Jun 20, 2006·Journal of Biomolecular Structure & Dynamics·Pemra DorukerOzge Kurkcuoglu
Jun 21, 2011·Bioinformatics·Andrej J SavolChakra S Chennubhotla
Jun 16, 2005·Nucleic Acids Research·Vlad CojocaruThomas M Jovin
Jan 13, 2016·The Journal of Physical Chemistry. a·Pingying LiuJing Ma
Aug 24, 2010·Journal of Computational Chemistry·Burak AlakentPemra Doruker
Aug 19, 2015·PloS One·Ortal Amber-VitosYossi Tsfadia
Jul 7, 2007·The Journal of Chemical Physics·Alexandros AltisGerhard Stock
Sep 30, 2020·Journal of Biomolecular Structure & Dynamics·Loubna TaidiMohammed Reda Britel
Apr 7, 2009·The Journal of Physical Chemistry. B·Martin G Gotsev, Petko M Ivanov

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