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Mechanical Mass-Spring Model for Understanding Globular Motion of Proteins

Published online by Cambridge University Press:  25 January 2016

J.-I. Kim ,
K. Eom  and
S. Na
J.-I. Kim
Affiliation:
Department of Mechanical EngineeringKorea UniversitySeoul, Republic of Korea
K. Eom
Affiliation:
College of Sport ScienceSungkyunkwan UniversitySuwon, Republic of Korea
S. Na*
Affiliation:
Department of Mechanical EngineeringKorea UniversitySeoul, Republic of Korea
*
*Corresponding author ([email protected])
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Abstract

The conformational (structural) change of proteins plays an essential role in their functions. Experiments have been conducted to try to understand the conformational change of proteins, but they have not been successful in providing information on the atomic scale. Simulation methods have been developed to understand the conformational change at an atomic scale in detail. Coarse-grained methods have been developed to calculate protein dynamics with computational efficiency when compared with than all-atom models. A structure-based mass-spring model called the elastic network model (ENM) showed excellent performance in various protein studies. Coarse-grained ENM was modified in various ways to improve the computational efficiency, and consequently to reduce required computational cost for studying the large-scale protein structures. Our previous studies report a modified mass-spring model, which was developed based on condensation method applicable to ENM, and show that the model is able to accurately predict the fluctuation behavior of proteins. We applied this modified mass-spring model to analyze the conformational changes in proteins. We consider two model proteins as an example, where these two proteins exhibit different functions and molecular sizes. It is shown that the modified mass-spring model allows for accurately predicting the pathways of conformation changes for proteins. Our model provides structural insights into the conformation change of proteins related to the biological functions of large protein complexes.

Keywords

Mass-spring modelCondensation methodNormal mode analysisConformation change
Type
Research Article
Information
Journal of Mechanics , Volume 32 , Issue 2 , April 2016 , pp. 123 - 129
Copyright
Copyright © The Society of Theoretical and Applied Mechanics, R.O.C. 2016 

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References

1.Bahar, I. and Rader, A. I, “Coarse-Grained Normal Mode Analysis in Structural Biology,” Current Opinion in Structural Biology, 15, pp. 586–592 (2005).CrossRefGoogle ScholarPubMed
2.Atilgan, A. R., et al, “Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model,” Biophysical Journal, 80, pp. 505–515 (2001).CrossRefGoogle ScholarPubMed
3.Bahar, I., et al, “Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability,” Physical Review Letters, 80, p. 2733 (1998).CrossRefGoogle Scholar
4.Haliloglu, T., Bahar, I. and Erman, B., “Gaussian Dynamics of Folded Proteins,” Physical Review Letters, 79, p. 3090 (1997).Google Scholar
5.Kim, J. I., Na, S. and Eom, K., “Domain Decomposition-Based Structural Condensation of Large Protein Structures for Understanding Their Conformational Dynamics,” Journal of Computational Chemistry, 32, pp. 161–169(2011).CrossRefGoogle ScholarPubMed
6.Kim, J.-L, Na, S. and Eom, K., “Large Protein Dynamics Described by Hierarchical-Component Mode Synthesis,” Journal of Chemical Theory and Computation, 5, pp. 1931–1939 (2009).Google Scholar
7.Kim, J. I., et al., “A 3-D Coarser-Grained Computational Model for Simulating Large Protein Dynamics. Computers,” Materials & Continua, 9, pp. 137–152 (2009).Google Scholar
8.Eom, K, et al., “Coarse-Graining of Protein Structures for the Normal Mode Studies,” Journal of Computational Chemistry, 28, pp. 1400–1410 (2007).Google Scholar
9.Eom, K., et al., “Modified Mechanical Mass-Spring Model of Biomolecules for Understanding Dynamics of Proteins,” Journal of Mechanical Science and Technology, 22, pp. 506–513 (2008).Google Scholar
10.Cui, Q. and Bahar, I., Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, Chapman & Hall/CRC, U.K (2006).Google Scholar
11.Tirion, M. M., “Large Amplitude Elastic Motions in Proteins from a Single-Parameter,” Atomic Analysis. Physical Review Letters, 11, p. 1905 (1996).CrossRefGoogle Scholar
12.Maragakis, P. and Karplus, M., “Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase,” Journal of Molecular Biology, 352, pp. 807–822 (2005).Google Scholar
13.Li, G. and Cui, Q., “A Coarse-Grained Normal Mode Approach for Macro molecules: An Efficient Implementation and Application to Ca2+-ATPase,” Biophysical Journal, 83, pp. 2457–2474 (2002).Google Scholar
14.Kim, M. K., Jernigan, R. L. and Chirikjian, G. S., “Efficient Generation of Feasible Pathways for Protein Conformational Transitions,” Biophysical Journal, 83, pp. 1620–1630 (2002).Google Scholar
15.Kantarci-Carsibasi, N, Haliloglu, T. and Doruker, P., “Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes,” Biophysical Journal, 95, pp. 5862–5873 (2008).Google Scholar
16.Yoon, G., et al., “Mechanical Characterization of Amyloid Fibrils Using Coarse-Grained Normal Mode Analysis,” Advanced Functional Materials, 21, pp. 3454–3463 (2011).Google Scholar
17.Ming, D., et al., “Substructure Synthesis Method for Simulating Large Molecular Complexes,” Proceedings of the National Academy of Sciences, 100, pp. 104–109 (2003).CrossRefGoogle ScholarPubMed
18.Xiong, J.-P, et al, “Crystal Structure of the Extra cellular Segment of Integrin Alpha Vbeta 3,” Science, 294, pp. 339–345(2001).CrossRefGoogle Scholar
19.Xiong, J.-P, et al, “Crystal Structure of the Extracellular Segment of Integrin alpha Vbeta 3 in Complex with an Arg-Gly-Asp Ligand,” Science, 296, pp. 151–155(2002).Google Scholar
20.Ranson, N. A., et al, “ATP-Bound States of GroEL Captured by Cryo-Electron Microscopy,” Cell, 107, pp. 869–879 (2001).Google Scholar
21.Tozzini, V, “Coarse-Grained Models for Proteins,“ Current Opinion in Structural Biology, 15, pp. 144–150 (2005).Google Scholar
22.Jang, H., Na, S. and Eom, K, “Multiscale Network Model for Large Protein Dynamics,” The Journal of Chemical Physics, 131, pp. 245106–2451010 (2009).Google Scholar
23.Kim, M. K., Jernigan, R. L. and Chirikjian, G. S., “Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies,“ Biophysical Journal, 89, pp. 43–55 (2005).CrossRefGoogle ScholarPubMed
24.Eom, K., et al, “Robust Reduction Method for Biomolecules Modeling,” CMC-Computers Materials & Continua, 6, pp. 35–42 (2007).Google Scholar