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Computer Simulation of Protein Materials at Multiple Length Scales: From Single Proteins to Protein Assemblies

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Abstract

Computer simulation of protein materials and their dynamic or mechanical behavior is of high significance, as proteins perform their functions through their structural changes in response to a force (or stimulus). The computer simulation enables the detailed insight into the structure and behavior of proteins at atomistic resolution, which is inaccessible with experimental toolkits such as single-molecule experiments. With the advancement of computing resources, the computer simulation has recently played a vital role as a virtual microscopy in understanding and characterizing the structure and behaviors of protein materials at atomistic resolution. For examples, computer simulations allow for gaining insight into how some protein domains can exhibit the remarkable mechanical properties and functions. In this article, we would like to address the current state-of-arts of computer simulations that have been employed for studying the structure and properties (or behaviors) of proteins at multiple length scales ranging from single proteins to protein assemblies. Specifically, we summarize various computational modeling techniques, ranging from atomistic models to coarse-grained models and continuum models, applicable for modeling protein structures at multiple length scales from single proteins to protein assemblies. This paper discusses how such various computational modeling/simulation techniques can be employed for studying the structure and properties of protein materials at multiple length scales. This paper sheds light on computer simulations, which are able to unveil the hidden, complex mechanisms related to the structure and properties of protein materials at multiple length scales.

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Fig. 1

Figure is adopted with permission from Ref. [4]. Copyright (1997) The American Association for the Advancement of Science

Fig. 2
Fig. 3

Figures are adopted from Ref. [92] under Creative Commons Attribution License

Fig. 4

Figures are adopted with permission from Ref. [104]. Copyright (2012) AIP Publishing

Fig. 5

Figures are adopted with permission from Ref. [110]. Copyright (2005) National Academy of Sciences, U.S.A (color figure online)

Fig. 6

Figures are adopted from Ref. [132] under Creative Commons Attribution License

Fig. 7

Figures are adopted with permission from Ref. [137]. Copyright (2018) Royal Society of Chemistry

Fig. 8

Figures are adopted with permission from Ref. [139]. Copyright (2007) The American Association for the Advancement of Science

Fig. 9

Figures are adopted from Ref. [136] under Creative Commons Attribution License

Fig. 10

Figures are adopted with permission from Ref. [25]. Copyright (2010) Springer Nature

Fig. 11

Figures are adopted with permission from Ref. [150]. Copyright (2005) Elsevier

Fig. 12

Figures are adopted with permission from Ref. [156]. Copyright (2010) Elsevier

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Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF) under Grant no. NRF-2015R1A2A2A04002453.

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    Kilho Eom

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Eom, K. Computer Simulation of Protein Materials at Multiple Length Scales: From Single Proteins to Protein Assemblies. Multiscale Sci. Eng. 1, 1–25 (2019). https://doi.org/10.1007/s42493-018-00009-7

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