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.
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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)
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)
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)
A. Carpinteri, G. Piana, A. Bassani, G. Lacidogna, Terahertz vibrational modes in Na/K-ATPase. J. Biomol. Struct. Dyn. 37, 256–264 (2019)
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
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)
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)
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
E. Castro-Camus, M.B. Johnston, Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy. Chem. Phys. Lett. 455, 289–292 (2008)
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)
F. Tama, Y.H. Sanejouand, Conformational change of proteins arising from normal mode calculations. Protein Eng. 14, 1–6 (2001)
W. Zheng, B.R. Brooks, Normal-mode-based prediction of protein conformational changes guided by distance constraints. Biophys. J. 88, 3109–3117 (2005)
P. Petrone, V.S. Pande, Can conformational change be described by only a few normal modes? Biophys. J. 90, 1583–1593 (2006)
Protein Data Bank. https://www.rcsb.org
W. Humphrey, A. Dalke, K. Schulten, VMD–visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)
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Scaramozzino, D., Lacidogna, G., Carpinteri, A. (2020). Protein Conformational Changes and Low-Frequency Vibrational Modes: A Similarity Analysis. In: Grady, M. (eds) Mechanics of Biological Systems and Materials & Micro-and Nanomechanics, Volume 4. Conference Proceedings of the Society for Experimental Mechanics Series. Springer, Cham. https://doi.org/10.1007/978-3-030-30013-5_2
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DOI: https://doi.org/10.1007/978-3-030-30013-5_2
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