Steered molecular dynamics investigations of protein function
نویسندگان
چکیده
منابع مشابه
Steered molecular dynamics investigations of protein function.
Molecular recognition and mechanical properties of proteins govern molecular processes in the cell that can cause disease and can be targeted for drug design. Single molecule measurement techniques have greatly advanced knowledge but cannot resolve enough detail to be interpreted in terms of protein structure. We seek to complement the observations through so-called Steered Molecular Dynamics (...
متن کاملSteered Molecular Dynamics
Steered molecular dynamics (SMD) induces unbinding of ligands and conformational changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed. SMD has already provided important qualitative insights into biologically relevant problems, as demonstrated here for application...
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Steered molecular dynamics (SMD), a computer simulation method for studying force-induced reactions in biopolymers, has been applied to investigate the response of protein domains to stretching apart of their terminal ends. The simulations mimic atomic force microscopy and optical tweezer experiments, but proceed on much shorter time scales. The simulations on different domains for 0.6 nanoseco...
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Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently pr...
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A molecular dynamics simulation approximates the motion of atoms in a system of molecules over short intervals of simulated time, typically on the order of picoseconds to nanoseconds. Such simulations may run for days or weeks on a computer when used to investigate the dynamic behavior of small proteins in biological systems. By adding additional restraints, a simulation may be “steered” to obs...
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ژورنال
عنوان ژورنال: Journal of Molecular Graphics and Modelling
سال: 2001
ISSN: 1093-3263
DOI: 10.1016/s1093-3263(00)00133-9