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Protein Conformational Changes and Low-Frequency Vibrational Modes: A Similarity Analysis

  • Domenico ScaramozzinoEmail author
  • Giuseppe Lacidogna
  • Alberto Carpinteri
Conference paper
Part of the Conference Proceedings of the Society for Experimental Mechanics Series book series (CPSEMS)

Abstract

The study of protein vibration and dynamics is receiving increasing attention among researchers, both from a numerical and experimental perspective. By using terahertz spectroscopy techniques, it has been shown that conformational changes, crucial for protein biological function, are strictly related to low-frequency vibrational modes. These motions generally occur in the terahertz range (~0.1–2 THz) involving large portions of the protein. The present contribution aims at investigating the role of terahertz (expansion-contraction) vibrational modes to protein conformational change from a numerical viewpoint. Modal analysis is performed by using Cα-only coarse-grained mechanical models: the obtained mode shapes are compared, by means of three similarity indexes, to the displacement field of protein conformational change. In particular, lysine-arginine-ornithine (LAO) binding protein is selected as a case study.

Keywords

Conformational change THz vibrational modes Modal analysis Similarity indexes LAO binding protein 

References

  1. 1.
    S.E. Lee, R.D. Kamm, M.R.K. Mofrad, A molecular perspective on mechanotransduction in focal adhesion, in Cellular mechanotransduction: diverse perspectives from molecules to tissues, ed. by M. R. K. Mofrad, R. D. Kamm, (Cambridge University Press, Cambridge, 2009)Google Scholar
  2. 2.
    S. Mahajan, Y.H. Sanejouand, On the relationship between low-frequency normal modes and large-scale conformational changes of proteins. Arch. Biochem. Biophys. 567, 59–65 (2015)CrossRefGoogle Scholar
  3. 3.
    A. Carpinteri, G. Lacidogna, G. Piana, A. Bassani, Terahertz mechanical vibrations in lysozyme: Raman spectroscopy vs modal analysis. J. Mol. Struct. 1139, 222–230 (2017)CrossRefGoogle Scholar
  4. 4.
    A. Carpinteri, G. Piana, A. Bassani, G. Lacidogna, Terahertz vibrational modes in Na/K-ATPase. J. Biomol. Struct. Dyn. 37, 256–264 (2019)CrossRefGoogle Scholar
  5. 5.
    G. Lacidogna, D. Scaramozzino, G. Piana, A. Carpinteri, Terahertz protein vibrations: The usefulness of coarse-grained numerical models. in: M.E. Grady (ed.), Mechanics of Biological Systems and Materials & Micro- and Nanomechanics, Volume 4, Conference Proceedings of the Society for Experimental Mechanics Series.  https://doi.org/10.1007/978-3-030-30013-5_1
  6. 6.
    K.G. Brown, S.C. Erfurth, E.W. Small, W.L. Peticolas, Conformationally dependent low-frequency motions of proteins by laser Raman spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 69, 1467–1469 (1972)CrossRefGoogle Scholar
  7. 7.
    G. Lacidogna, G. Piana, A. Bassani, A. Carpinteri, Raman spectroscopy of Na/K-ATPase with special focus on low-frequency vibrations. Vib. Spectrosc. 92, 298–301 (2017)CrossRefGoogle Scholar
  8. 8.
    D.A. Turton, H.M. Senn, T. Harwood, A.J. Lapthorn, E.M. Ellis, K. Wynne, Terahertz underdamped vibrational motion governs protein-ligand binding in solution. Nat. Commun. (2014).  https://doi.org/10.1038/ncomms4999
  9. 9.
    E. Castro-Camus, M.B. Johnston, Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy. Chem. Phys. Lett. 455, 289–292 (2008)CrossRefGoogle Scholar
  10. 10.
    H. Chen, G.Y. Chen, S.Q. Li, L. Wang, Reversible conformational changes of PsbO protein detected by terahertz time-domain spectroscopy. Chin. Phys. Lett. 26, 084204 (2009)CrossRefGoogle Scholar
  11. 11.
    F. Tama, Y.H. Sanejouand, Conformational change of proteins arising from normal mode calculations. Protein Eng. 14, 1–6 (2001)CrossRefGoogle Scholar
  12. 12.
    W. Zheng, B.R. Brooks, Normal-mode-based prediction of protein conformational changes guided by distance constraints. Biophys. J. 88, 3109–3117 (2005)CrossRefGoogle Scholar
  13. 13.
    P. Petrone, V.S. Pande, Can conformational change be described by only a few normal modes? Biophys. J. 90, 1583–1593 (2006)CrossRefGoogle Scholar
  14. 14.
    Protein Data Bank. https://www.rcsb.org
  15. 15.
    W. Humphrey, A. Dalke, K. Schulten, VMD–visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)CrossRefGoogle Scholar

Copyright information

© Society for Experimental Mechanics, Inc. 2020

Authors and Affiliations

  • Domenico Scaramozzino
    • 1
    Email author
  • Giuseppe Lacidogna
    • 1
  • Alberto Carpinteri
    • 1
  1. 1.Politecnico di Torino, Department of Structural, Geotechnical and Building EngineeringTorinoItaly

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