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Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules

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Advance in Structural Bioinformatics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 827))

Abstract

Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

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Authors and Affiliations

  1. Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China

    Zhiyong Zhang

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  1. Zhiyong Zhang
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Correspondence to Zhiyong Zhang .

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Editors and Affiliations

  1. Shanghai JiaoTong University, Shanghai, China

    Dongqing Wei

  2. Shanghai Jiao Tong University, Shanghai, China

    Qin Xu

  3. Shanghai Jiao Tong University, Shanghai, China

    Tangzhen Zhao

  4. Shanghai Jiao Tong University, Shanghai, China

    Hao Dai

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© 2015 Shanghai Jiaotong University Press, Shanghai and Springer Science+Business Media Dordrecht

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Zhang, Z. (2015). Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules. In: Wei, D., Xu, Q., Zhao, T., Dai, H. (eds) Advance in Structural Bioinformatics. Advances in Experimental Medicine and Biology, vol 827. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9245-5_4

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