Numerical simulation of nanoindentation and patch clamp experiments on mechanosensitive channels of large conductance in Escherichia coli

Experimental Mechanics

Volumn 49, Issue 1, 2009, Pages 35-46

  Tang, Y ^a   Chen, X ^a   Yoo, J ^b   Yethiraj, A ^b   Cui, Q ^b  

^a Columbia University ^*  (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Finite element simulation; Mechanosensitive channel; Nanoindentation; Patch clamp

Indexed keywords

ALL-ATOM SIMULATIONS; BI LAYERS; CONTINUUM LEVELS; CONTINUUM MODELS; DIPALMITOYLPHOSPHATIDYCHOLINE; E. COLI; ESCHERICHIA COLI (E. COLI); EXTERNAL LOADS; FINITE ELEMENT MODELS; FINITE ELEMENT SIMULATION; GATING MECHANISMS; HIERARCHICAL SIMULATIONS; KEY PARAMETERS; LIPID VESICLES; MATERIAL PROPERTIES; MECHANICAL BEHAVIORS; MECHANICAL RESPONSE; MECHANOSENSITIVE CHANNEL; MOLECULAR-MECHANICS SIMULATIONS; MULTI-SCALE; NUMERICAL SIMULATIONS; PATCH CLAMP; PATCH CLAMP EXPERIMENTS; STRUCTURAL DETAILS; STRUCTURAL TRANSITIONS;

ATOMIC PHYSICS; BIOMECHANICS; CONTINUUM MECHANICS; ESCHERICHIA COLI; EXPERIMENTS; FINITE ELEMENT METHOD; LIPID BILAYERS; MECHANICS; MOLECULAR MECHANICS; NANOINDENTATION;

MECHANISMS;

EID: 58949101606     PISSN: 00144851     EISSN: 17412765     Source Type: Journal    
DOI: 10.1007/s11340-007-9060-x     Document Type: Article

References (28)

1. Hamill OP, Martinac B (2001) Molecular basis of mechanotransduction in living cells. Physiol Rev 81:685-740.
2. Huang H, Kamm RD, Lee RT (2004) Cell mechanics and mechanotransduction: pathways, probes and physiology. Am J Physiol Cell Physiol 287:C1-C11.
3. Martinac B (2004) Mechanosensitive ion channels: Molecules of mechanotransduction. J Cell Sci 117:2449-2460.
4. Sukharev S, Blount P, Martinac B, Kung C (1997) Mechanosensitive channels of Escherichia coli: The MscL gene, protein and activities. Annu Rev Physiol 59:633-657.
5. Sackin H (1995) Mechanosensitive channels. Annu Rev Physiol 57:333-353.
6. Martinac B, Buechner M, Delcour AH, Adler J (1987) Pressure-sensitive ion channel in Escherichia coli. PNAS 84:297-2301.
7. Sukharev S, Sigurdson WJ, Kung C, Sachs F (1999) Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL. J Gen Physiol 113:529-540.
8. Sukharev S, Betanzos M, Chiang CS, Guy HR (2001) The gating mechanism of the large mechanosensitive channel MscL. Nature 409:720-724.
9. Sukharev S, Durell SR, Guy HR (2001) Structural models of the MscL gating mechanism. Biophys J 81:917-936.
10. Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC (1998) Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science 282: 2220-2226.
11. Sukharev S. and Anishkin A. (2004) Mechanosensitive channels: What can we learn from 'simple' model systems? Trends Neurosci 27: 345-351.
12. Perozo E, Cortes DM, Sompornpisut P, Kloda A, Martinac B (2002) Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Nature 418:942-948.
13. Perozo E, Kloda A, Cortes DM, Martinac B (2002) Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating. Nat Struct Biol 9:696-703.
14. Perozo E, Rees DC (2003) Structure and mechanism in prokaryotic mechanosensitive channels. Curr Opin Struct Biol 13:432-442.
15. Levin G, Blount P (2004) Cysteine scanning of MscL transmembrane domains reveals residues critical for mechanosensitive channel gating. Biophys J. 86:2862-2870.
16. Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. PNAS 102:6679-6685.
17. Snow CD, Sorin EJ, Rhee YM, Pande VS (2005) How well can simulation predict protein folding kinetics and thermodynamics? Annu Rev Biophys Biomol Struct 34:43-69.
18. Gullingsrud J, Schulten K (2003) Gating of MscL studied by steered molecular dynamics. Biophys J 85:2087-2099.
19. Kong Y, Shen Y, Warth TE, Ma J (2002) Conformational pathways in the gating of Escherichia coli mechanosensitive channel. PNAS 99:5999-6004.
20. Tang Y, Cao G, Chen X, Yoo J, Yethiraj A, Cui Q (2006) A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J 91:1248-1263.
21. Charras GT, Horton MA (2002) Single cell mechanotransduction and its modulation analyzed by atomic force microscope indentation. Biophys J 82:2970-2981.
22. Choe S, Sun SX (2005) The elasticity of alpha-helices. J Chem Phys 122:244912.
23. Evans E, Rawicz W (1990) Entropy-driven tension and bending elasticity in condensed-fluid membranes. Phys Rev Lett 64:2094-2097.
24. Lindahl E, Edholm O (2000) Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J Chem Phys 113:3882-3893.
25. Hartmann C, Delgado A (2004) Stress and strain in a yeast cell under high hydrostatic pressure. PAMM 4:316-317.
26. Gordon V, Chen X, Hutchinson JW, Bausch AR, Marquez M, Weitz DA (2004) Self-assembled inflated polymer membrane capsules. J Am Chem Soc 126:14117-14122.
27. ABAQUS (2004) ABAQUS 6.4 user's manual. ABAQUS Inc., Providence, RI.
28. Park J, Kahng B, Kamm RD, Hwang W (2006) Atomistic simulation approach to a continuum description of self-assembled β-sheet filaments. Biophys J 90:2510-2524.