Mechanical unfolding of titin I27 domain: Nanoscale simulation of mechanical properties based on virial theorem via steered molecular dynamics technique

Scientia Iranica - Tập 19 - Trang 1526-1533 - 2012
M.H. Abolbashari1, S. Ameli1
1Department of Mechanical Engineering, Lean Production Engineering Research Center, Ferdowsi University of Mashhad, Mashhad, P.O. Box 91775-1111, Iran

Tài liệu tham khảo

in‘t Veld, 2008, Simulation of the mechanical strength of a single collagen molecule, Biophys. J., 95, 33, 10.1529/biophysj.107.120659 Li, 2005, Mechanical unfolding intermediates observed by single-molecule force spectroscopy in a fibronectin type III module, J. Mol. Biol., 345, 817, 10.1016/j.jmb.2004.11.021 Anderson, 2010, The effects of PKCα phosphorylation on the extensibility of titin’s PEVK element, J. Struct. Biol., 170, 270, 10.1016/j.jsb.2010.02.002 Gao, 2001, Simulated refolding of stretched titin immunoglobulin domains, Biophys. J., 81, 2268, 10.1016/S0006-3495(01)75874-2 Zhang, 2009, Mechanical properties of double-stranded DNA biolayers immobilized on microcantilever under axial compression, J. Biomech., 42, 1483, 10.1016/j.jbiomech.2009.03.050 Grützner, 2009, Modulation of titin-based stiffness by disulfide bonding in the cardiac titin N2-B unique sequence, Biophys. J., 97, 825, 10.1016/j.bpj.2009.05.037 Sulkowska, 2007, Mechanical stretching of proteins: a theoretical survey of the protein data bank, J. Phys.: Condens. Matter, 19, 283201, 10.1088/0953-8984/19/28/283201 Duff, 2006, Stretching the immunoglobulin 27 domain of the titin protein: the dynamic energy landscape, Biophys. J., 91, 3446, 10.1529/biophysj.105.074278 Li, 2006, Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions, PNAS, 103, 93, 10.1073/pnas.0503758103 LeWinter, 2007, Cardiac titin: structure, functions and role in disease, Clin. Chim. Acta, 375, 1, 10.1016/j.cca.2006.06.035 Li, 2007, Secondary structure, mechanical stability and location of transition state of proteins, Biophys. J., 93, 2644, 10.1529/biophysj.107.106138 Gabovich, 2009, Mechanical stability of proteins, J. Chem. Phys., 131, 024121, 10.1063/1.3170940 Kawakami, 2006, Viscoelastic study of the mechanical unfolding of a protein by AFM, Biophys. J., 91, L16, 10.1529/biophysj.106.085019 Kellermayer, 2001, Mechanical fatigue in repetitively stretched single molecules of titin, Biophys. J., 80, 852, 10.1016/S0006-3495(01)76064-X Toofanny, 2006, Simulations of multi-directional forced unfolding of titin I27, J. Mol. Graphics Modell., 24, 396, 10.1016/j.jmgm.2005.09.005 Taniguchi, 2008, The effect of temperature on mechanical resistance of the native and intermediate states of I27, Biophys. J., 95, 5296, 10.1529/biophysj.108.141275 Li, 2003, Mechanical design of the first proximal Ig domain of human cardiac titin revealed by single molecule force spectroscopy, J. Mol. Biol., 334, 75, 10.1016/j.jmb.2003.09.036 Wang, 2001, Single molecule measurements of titin elasticity, Prog. Biophys. Mol. Biol., 77, 1, 10.1016/S0079-6107(01)00009-8 Tsai, 1979, The virial theorem and stress calculation in molecular dynamics, J. Chem. Phys., 70, 1375, 10.1063/1.437577 Cheung, 1991, Atomic-level stress in an inhomogeneous system, J. Appl. Phys., 70, 5688, 10.1063/1.350186 Lutsko, 1988, Stress and elastic constants in anisotropic solids: molecular dynamics techniques, J. Appl. Phys., 64, 1152, 10.1063/1.341877 Cormier, 2001, Stress calculation in atomistic simulations of perfect and imperfect solids, J. Appl. Phys., 89, 99, 10.1063/1.1328406 Zhou, 2003, A new look at the atomic level virial stress: on continuum-molecular system equivalence, Proc. R. Soc. Lond. Ser. A, 459, 2347, 10.1098/rspa.2003.1127 Zimmerman, 2004, Calculation of stress in atomistic simulation, Modell. Simul. Mater. Sci. Eng., 12, 319, 10.1088/0965-0393/12/4/S03 Andia, 2006, A classical mechanics approach to the determination of the stress & strain response of particle systems, Modell. Simul. Mater. Sci. Eng., 14, 741, 10.1088/0965-0393/14/4/015 Sun, 2006, On stress calculations in atomistic simulations, Modell. Simul. Mater. Sci. Eng., 14, 423, 10.1088/0965-0393/14/3/006 Subramaniyan, 2008, Continuum interpretation of virial stress in molecular simulations, Int. J. Solids Struct., 45, 4340, 10.1016/j.ijsolstr.2008.03.016 Izrailev, 1998 MacKerell, 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B, 102, 3586, 10.1021/jp973084f Improta, 1996, Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity, Structure, 4, 323, 10.1016/S0969-2126(96)00036-6 Phillips, 2005, Scalable molecular dynamics with NAMD, J. Comput. Chem., 26, 1781, 10.1002/jcc.20289 Humphrey, 1996, VMD—visual molecular dynamics, J. Mol. Graphics Modell., 14, 33, 10.1016/0263-7855(96)00018-5 Swenson, 1983, Comments on virial theorems for bounded systems, Amer. J. Phys., 51, 940, 10.1119/1.13390 Yu, 2007, A descent nonlinear conjugate gradient method for large-scale unconstrained optimization, Appl. Math. Comput., 187, 636, 10.1016/j.amc.2006.08.087 Schlick, 2010 Martyna, 1994, Constant pressure molecular dynamics algorithms, J. Chem. Phys., 101, 4177, 10.1063/1.467468 Tachibana, 2004, Effect of intracrystalline water on longitudinal sound velocity in tetragonal hen-egg-white lysozyme crystals, Phys. Rev., 69, 921 Ikai, 2007, Pulling and pushing protein molecules by AFM, Curr. Nanosci., 3, 17, 10.2174/157341307779940535 Afrin, 2005, Pretransition and progressive softening of bovine carbonic anhydrase II as probed by single molecule atomic force microscopy, Protein Sci., 14, 1447, 10.1110/ps.041282305 Dubey, 2009, Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen–hydroxyapatite biomaterials, J. Mech. Phys. Solids, 57, 1702, 10.1016/j.jmps.2009.07.002 Zeiger, 2008, Molecular modeling of the axial and circumferential elastic moduli of tubulin, Biophys. J., 95, 3606, 10.1529/biophysj.108.131359 Parra, 2007, Nanomechanical properties of globular proteins: lactate oxidase, Langmuir, 23, 2747, 10.1021/la062864p Caylor, 2001, Measuring the elastic properties of protein crystals by Brillouin scattering, J. Cryst. Growth, 232, 498, 10.1016/S0022-0248(01)01092-2 Yoon, 2009, Mesoscopic model for mechanical characterization of biological protein materials, J. Comput. Chem., 30, 873, 10.1002/jcc.21107 Labeit, 1995, Titins: giant proteins in charge of muscle ultrastructure and elasticity, Science, 270, 293, 10.1126/science.270.5234.293 Lee, 2010, Tertiary and secondary structure elasticity of a Six-Ig titin chain, Biophys. J., 98, 1085, 10.1016/j.bpj.2009.12.4192 Lu, 1999, Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations, Chem. Phys., 247, 141, 10.1016/S0301-0104(99)00164-0