Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics

Journal of Computational Chemistry
Jae In KimKilho Eom

Abstract

Normal mode analysis (NMA) with coarse-grained model, such as elastic network model (ENM), has allowed the quantitative understanding of protein dynamics. As the protein size is increased, there emerges the expensive computational process to find the dynamically important low-frequency normal modes due to diagonalization of massive Hessian matrix. In this study, we have provided the domain decomposition-based structural condensation method that enables the efficient computations on low-frequency motions. Specifically, our coarse-graining method is established by coupling between model condensation (MC; Eom et al., J Comput Chem 2007, 28, 1400) and component mode synthesis (Kim et al., J Chem Theor Comput 2009, 5, 1931). A protein structure is first decomposed into substructural units, and then each substructural unit is coarse-grained by MC. Once the NMA is implemented to coarse-grained substructural units, normal modes and natural frequencies for each coarse-grained substructural unit are assembled by using geometric constraints to provide the normal modes and natural frequencies for whole protein structure. It is shown that our coarse-graining method enhances the computational efficiency for analysis of large protein complexe...Continue Reading

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Citations

Aug 10, 2011·The Journal of Chemical Physics·Reza SoheilifardGregory J Rodin
Dec 18, 2013·Bioinformatics·Hua Zhang, Lukasz Kurgan
Mar 3, 2015·Physical Chemistry Chemical Physics : PCCP·Jae In KimSungsoo Na

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