A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes

Understanding the molecular flexibility and dynamics is central to the analysis of biomolecular functions. In this work, complex multiscale virtual particle model based elastic network models (CMVP-ENMs) have been proposed for the normal mode analysis of biomolecular complexes or biomolecular assemb...

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Main Authors: Anand, D. Vijay, Meng, Zhenyu, Xia, Kelin
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2021
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Online Access:https://hdl.handle.net/10356/150578
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-1505782021-06-14T07:02:51Z A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes Anand, D. Vijay Meng, Zhenyu Xia, Kelin School of Biological Sciences School of Physical and Mathematical Sciences Engineering::Bioengineering Anisotropic Networks Biomolecular Complexes Understanding the molecular flexibility and dynamics is central to the analysis of biomolecular functions. In this work, complex multiscale virtual particle model based elastic network models (CMVP-ENMs) have been proposed for the normal mode analysis of biomolecular complexes or biomolecular assemblies. The term complex used in our CMVP-ENMs refers to the multi-material or multi-constituent. Different "materials" or constituents contribute differently to the general flexibility and dynamics of complex biomolecular structures. In our CMVP-ENMs, the key idea is to incorporate relative density or weight information of different components into the spring parameter of elastic network models. Two different models, including the CMVP based Gaussian network model (CMVP-GNM) and the CMVP based anisotropic network model (CMVP-ANM), have been proposed. With the consideration of complex component information, our CMVP-GNM, compared with the traditional GNM, can deliver a better accuracy in the B-factor prediction of protein-nucleic acid complexes. Moreover, our CMVP-ANM can be used to remove the "tip effect" by systematically suppressing the extremely-large vectors, in the highly flexible regions, of the normal modes generated by the ANM. In this way, our CMVP-ANM can be used to handle biomolecular structures with large hanging loops or extruding ends, which usually cause an irrationally-large-vector problem in ANM predictions. Finally, we explore the potential applications of our method by the cryo-EM data analysis. We find that by tuning the relative density ratio, we can systematically enhance or suppress the modes in different components, so that it can reveal the dynamics of the special regions that we are interested in. Ministry of Education (MOE) Nanyang Technological University This work was supported in part by the Nanyang Technological University Startup Grant M4081842 and the Singapore Ministry of Education Academic Research Fund Tier 1 RG126/16 and RG31/18, Tier 2 MOE2018-T2-1-033. 2021-06-14T07:02:51Z 2021-06-14T07:02:51Z 2019 Journal Article Anand, D. V., Meng, Z. & Xia, K. (2019). A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes. Physical Chemistry Chemical Physics, 21(8), 4359-4366. https://dx.doi.org/10.1039/c8cp07442a 1463-9076 https://hdl.handle.net/10356/150578 10.1039/c8cp07442a 30724932 2-s2.0-85061863729 8 21 4359 4366 en M4081842 RG126/16 RG31/18 MOE2018-T2-1-033 Physical Chemistry Chemical Physics © 2019 The Owner Societies. All rights reserved.
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Bioengineering
Anisotropic Networks
Biomolecular Complexes
spellingShingle Engineering::Bioengineering
Anisotropic Networks
Biomolecular Complexes
Anand, D. Vijay
Meng, Zhenyu
Xia, Kelin
A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes
description Understanding the molecular flexibility and dynamics is central to the analysis of biomolecular functions. In this work, complex multiscale virtual particle model based elastic network models (CMVP-ENMs) have been proposed for the normal mode analysis of biomolecular complexes or biomolecular assemblies. The term complex used in our CMVP-ENMs refers to the multi-material or multi-constituent. Different "materials" or constituents contribute differently to the general flexibility and dynamics of complex biomolecular structures. In our CMVP-ENMs, the key idea is to incorporate relative density or weight information of different components into the spring parameter of elastic network models. Two different models, including the CMVP based Gaussian network model (CMVP-GNM) and the CMVP based anisotropic network model (CMVP-ANM), have been proposed. With the consideration of complex component information, our CMVP-GNM, compared with the traditional GNM, can deliver a better accuracy in the B-factor prediction of protein-nucleic acid complexes. Moreover, our CMVP-ANM can be used to remove the "tip effect" by systematically suppressing the extremely-large vectors, in the highly flexible regions, of the normal modes generated by the ANM. In this way, our CMVP-ANM can be used to handle biomolecular structures with large hanging loops or extruding ends, which usually cause an irrationally-large-vector problem in ANM predictions. Finally, we explore the potential applications of our method by the cryo-EM data analysis. We find that by tuning the relative density ratio, we can systematically enhance or suppress the modes in different components, so that it can reveal the dynamics of the special regions that we are interested in.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Anand, D. Vijay
Meng, Zhenyu
Xia, Kelin
format Article
author Anand, D. Vijay
Meng, Zhenyu
Xia, Kelin
author_sort Anand, D. Vijay
title A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes
title_short A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes
title_full A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes
title_fullStr A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes
title_full_unstemmed A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes
title_sort complex multiscale virtual particle model based elastic network model (cmvp-enm) for the normal mode analysis of biomolecular complexes
publishDate 2021
url https://hdl.handle.net/10356/150578
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