Abstract
Understanding the mechanism of mechanobiological processes at the molecular level is an important challenge in modern biophysics. Despite recent advances in experimental and numerical techniques, the intrinsic multiscale nature of mechanobiological processes makes it difficult to meet such challenge in many systems of interest. Recently, a continuum-mechanics based hierarchical modeling and simulation framework has been established and applied to study the mechanical responses and gating behaviors of a prototypical system, the mechanosensitive channel of large conductance (MscL) in bacteria Escherichia coli (E. coli), from which several putative gating mechanisms have been testified and new insights deduced. This article reviews these latest findings and suggests possible improvements for future modeling work. The computationally efficient and versatile continuum-based protocol is expected to make contributions to a variety of mechanobiology problems
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References
Hamill, O.P. and Martinac, B. (2001) Physiological Reviews 81: 685.
Ingber, D.E. (2006) FASEB Journal 20: 811.
Kamm, R.D. and Kaazempur-Mofrad, M.R. (2004) Mechanics and Chemistry of Biosystems 1: 201.
Martinac, B. (2004) Journal of Cell Science 117: 2449.
Chen, X., Cui, Q., Yoo, J., Tang, Y., and Yethiraj, A. (2008) Biophysical Journal 95: 563.
Tang, Y., Cao, G., Chen, X., Yoo, J., Yethiraj, A., and Cui, Q. (2006) Biophysical Journal 91: 1248.
Tang, Y., Yoo, J., Yethiraj, A., Cui, Q., and Chen, X. (2008) Biophysical Journal 95: 581.
Gustin, M.C., Zhou, X.L., Martinac, B., and Kung, C. (1988) Science 242: 762.
Chang, G., Spencer, R.H., Lee, A.T., Barclay, M.T., and Rees, D.C. (1998) Science 282: 2220.
Sukharev, S., Betanzos, M., Chiang, C.S., and Guy, H.R. (2001) Nature 409: 720.
Sukharev, S. and Anishkin, A. (2004) Trends in Neurosciences 27: 345.
Sukharev, S.I., Sigurdson, W.J., Kung, C., and Sachs, F. (1999) Journal of General Physiology 113: 525.
Sukharev, S.I., Blount, P., Martinac, B., Blattner, F.R., and Kung, C. (1994) Nature 368: 265.
Wiggins, P. and Philips, R. (2004) Proceedings of the National Academy of Sciences of the United States of America 101: 4071.
Kloda, A. and Martinac, B. (2001) Cell Biochemistry and Biophysics 34: 321.
Perozo, E., Kloda, A., Cortes, D.M., and Martinac, B. (2002) Nature Structural Biology 9: 696.
Elmore, D.E. and Dougherty, D.A. (2003) Biophysical Journal 85: 1512.
Gullingsrud, J. and Schulten, K. (2004) Biophysical Journal 86: 3496.
Nagle, J.F. and Tristram-Nagle, S. (2000) Biochimica Et Biophysica Acta-Reviews on Biomembranes 1469: 159.
Evans, E. and Hochmuth, R. (1978) Topics in Membrane and Transport 10: 1.
Turner, M.S. and Sens, P. (2004) Physical Review Letters 93: 118103.
Perozo, E. (2006) Nature Reviews Molecular Cell Biology 7: 109.
Kung, C. (2005) Nature 436: 647.
Wiggins, P. and Phillips, R. (2005) Biophysical Journal 88: 880.
Markin, V.S. and Sachs, F. (2004) Biophysical Journal 86: 370A.
Martinac, B., Buechner, M., Delcour, A.H., Adler, J., and Kung, C. (1987) Proceedings of the National Academy of Sciences of the United States of America 84: 2297.
Sukharev, S.I., Blount, P., Martinac, B., and Kung, C. (1997) Annual Review of Physiology 59: 633.
Sukharev, S., Durell, S.R., and Guy, H.R. (2001) Biophysical Journal 81: 917.
Ursell, T., Huang, K.C., Peterson, E., and Phillips, R. (2007) Plos Computational Biology 3: 803.
Gullingsrud, J. and Schulten, K. (2003) Biophysical Journal 85: 2087.
Karplus, M. and McCammon, J.A. (2002) Nature Structural Biology 9: 788.
Gullingsrud, J., Kosztin, D., and Schulten, K. (2001) Biophysical Journal 80: 2074.
Kong, Y.F., Shen, Y.F., Warth, T.E., and Ma, J.P. (2002) Proceedings of the National Academy of Sciences of the United States of America 99: 5999.
Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. (1993) Molecular Simulation 10: 291.
Bilston, L.E. and Mylvaganam, K. (2002) FEBS Letters 512: 185.
Meyer, G.R., Gullingsrud, J., Schulten, K., and Martinac, B. (2006) Biophysical Journal 91: 1630.
Lu, G., Tadmor, E.B., and Kaxiras, E. (2006) Physical Review B 73: 024108.
Yefimov, S., van der Giessen, E., Onck, P.R., and Marrink, S.J. (2008) Biophysical Journal 94: 2994.
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. (1983) Journal of Computational Chemistry 4: 187.
Neria, E., Fischer, S., and Karplus, M. (1996) Journal of Chemical Physics 105: 1902.
Choe, S. and Sun, S.X. (2005) Journal of Chemical Physics 122: 244912.
ABAQUS (2004) Abaqus 6.4 user’s manual. 2004: ABAQUS Inc.
Gu, L.Q., Liu, W.H., and Martinac, B. (1998) Biophysical Journal 74: 2889.
Anishkin, A., Chiang, C.S., and Sukharev, S. (2005) Journal of General Physiology 125: 155.
Anishkin, A. and Kung, C. (2005) Current Opinion in Neurobiology 15: 397.
Ling, C.B. (1948) Journal of Applied Physics 19: 77.
Hartmann, C. and Delgado, A. (2004) PAMM 4: 316.
Gordon, V.D., Chen, X., Hutchinson, J.W., Bausch, A.R., Marquez, M., and Weitz, D.A. (2004) Journal of the American Chemical Society 126: 14117.
Sanner, M. (2008), http://www.scripps.edu/∼sanner/html/msmshome.html.
Bathe, M. (2008) Proteins-Structure Function and Bioinformatics 70: 1595.
Baker, N.A., Sept, D., Joseph, S., Holst, M.J., and McCammon, J.A. (2001) Proceedings of the National Academy of Sciences of the United States of America 98: 10037.
Feig, M. and Brooks, C.L. (2004) Current Opinion in Structural Biology 14: 217.
Zhou, Y.C., Holst, M., and McCammon, J.A. (2008) Journal of Mathematical Analysis and Applications 340: 135.
Akitake, B., Anishkin, A., Liu, N., and Sukharev, S. (2007) Nature Structural & Molecular Biology 14: 1141.
Zwanzig, R. (2001) Non-Equilibrium Statistical Mechanics. New York: Oxford University Press.
Dhaka, A., Viswanath, V., and Patapoutian, A. (2006) Annual Review of Neuroscience 29: 135.
Ramsey, I.S., Delling, M., and Clapham, D.E. (2006) Annual Review of Physiology 68: 619.
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Chen, X., Cui, Q. (2010). Computational Molecular Biomechanics: A Hierarchical Multiscale Framework With Applications to Gating of Mechanosensitive Channels of Large Conductance. In: Dumitrica, T. (eds) Trends in Computational Nanomechanics. Challenges and Advances in Computational Chemistry and Physics, vol 9. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9785-0_18
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