Steered molecular dynamics simulations

It is interesting to note that the free energy profiles obtained with ABF are essentially identical to those derived by Park et al. [53] from a reversible, 200-ns steered molecular dynamics simulation and from a set of 100 shorter runs, pulling very... 

Lu, H. Isralewitz, B. Krammer, A. Vogel, V. Schulten, K., Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation, Biophys. J. 1998, 75, 662-671... 

Lu, H. Schulten, K., Steered molecular dynamics simulations of force-induced protein domain unfolding, Proteins Struct. Funct. Gene. 1999, 35, 453 163... 

Park, S. Khalili-Araghi, F. Tajkhorshid, E. Schulten, K., Free energy calculation from steered molecular dynamics simulations using Jarzynski s equality, J. Chem. Phys. 

S. Park and K. Schulten, Calculating potentials of mean force from steered molecular dynamics simulation. J. Chem. Phys. 13, 5946—5961 (2004). 

Allen WJ, Bevan DR (2011) Steered molecular dynamics simulations reveal important mechanisms in reversible monoamine oxidase B inhibition. Biochemistry 50(29) 6441-6454... 

Yang LJ, Zou J, Xie HZ et al (2009) Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl. PloS One 4(12) e8470... 

Recently Calderon introduced a surrogate process approximation (SPA) to improve the sampling in calculation of the JE. The scheme is applied to the study of the unravelling of deca-alanine at constant temperature in a steered molecular dynamics simulation. The distribution of the work is approximated by developing a model for the dynamics using a relatively small number of real trajectories in conjunction with stochastic differential equations selected to model the process. The... 

Figure 6 Visualisation of a steered molecular dynamics simulation of the Avidin-Biotin complex" ...

J. Gullingsrud, R. Braun, and K. Schulten (1999) Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comp. Phys. 151, pp. 190-211... 

Li W, Liu H, Scott EE, Grater F, Halpert JR, Luo X, et al. Possible pathway(s) of testosterone egress from the active site of cytochrome 2B1 A steered molecular dynamics simulation. Drug Metab Dispos 2005 33 910-9. 

Fig. 14. Rotation of the mobile [2Fe 2S] cluster in the Cyt be, complex upon binding of the inhibitor stigmatellin. Cytb[bH,orb(HP) and bi or b(LP)], Cyt c and ISP (the [2Fe 2S]) are as indicated. (A) Arrangement oftheCyt bo, complex subunits when stigmatellin is bound to the Qo site. (B) Arrangement of the Cyt be, complex subunits in the absence of the inhibitor. Figure source Izrailev, Crofts, Berry and Schulten (1999) Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome be, complex. Biophys J 77 1754.

Liu, Z., Xu, Y, Tang, P. (2006). Steered molecular dynamics simulations of Na permeation across Gramicidin A channel. The Journal of Physical Chemistry, 110, 12789—12795. 

Xu YC, Shen JH, Luo XM, Silman I, Sussman JL, Chen KX, Jiang HL (2003) How does Huperzine A enter and leave the binding gorge of acetylcholinesterase Steered molecular dynamics simulations. J Am Chem Soc 125(37) 11340-11349. doi 10.1021/ja029775t... 

To facilitate understanding the low tensile force behavior of CKA and calmodulin upon forced uniaxial extension from their two ends, a steered molecular dynamics simulation (SMD) was carried out by the same group. The SMD tries to simulate the uniaxial pulling experiment by inserting a virtual harmonic spring between one end of the sample polymer and a hard surface representing cantilever or substrate surfaces. 

In Fig. 14, some results of steered molecular dynamics simulation are given. 

Peplowski, L., Kubiak, K., 8c Nowak, W. (2008). Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chemical Physics Letters, 467,144. 

Strzelecki, J., Mikulska, K., Lekka, M., Kulik, A., Balter, A., 8c Nowak, W. (2009). AFM force spectroscopy and steered molecular dynamics simulation of protein contactin 4. Acta Physica Polonica A, 116, S156. 

H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten, Biop/ ys./., 75, 662 (1998). Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics Simulation. 

H. Lu and K. Schulten, Chem. Phys., 247,141 (1999). Steered Molecular Dynamics Simulation of Conformational Changes of Immunoglobulin Domain 127 Interpret Atomic Force... 

A. Das and C. Mukhopadhyay, Proteins Struct., Funct., Bioinf, 75, 1024 (2009). Mechanical Unfolding Pathway and Origin of Mechanical Stability of Proteins of Ubiquitin Family An Investigation by Steered Molecular Dynamics Simulation. 

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