Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations
نویسندگان
چکیده
منابع مشابه
Protein Folding Properties from Molecular Dynamics Simulations
Our understanding of protein folding has improved tremendously due to computer simulations of molecular dynamics (MD), but determining protein folding kinetics and thermodynamics from all-atom MD simulations without using experimental data still represents a formidable scientific challenge. Simulations can easily get trapped in local minima on rough free energy landscapes and folding events may...
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Putative transition-state ensemble (TSE) conformations of src SH3 were identified by monitoring the deviation from the experimental phi values along molecular dynamics (MD) simulations of unfolding. Sixty MD trajectories (for a total of about 7 micros) were then started from the putative TSE. About one-half of the 60 runs reached the folded state while unfolding was observed in the remaining ha...
متن کاملLong-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations
Protein folding involves physical timescales—microseconds to seconds—that are too long to be studied directly by straightforward molecular dynamics simulation, where the fundamental timestep is constrained to femtoseconds. Here we show how the long-time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete-state Markov chain model constructed from tra...
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A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-weighted ensemble of microcanonical molecular dynamics simulations has been developed as a way to study the kinetics of protein folding in the context of a Markov chain. Analysis of these transition functions for signatures of Markovian behavior is described. The method has been applied to an example...
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We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotrypsin inhibitor 2 (CI2) with an implicit solvation model for a total simulation time of 0.4 microseconds. Folding requires that the three-dimensional structure of the native state is known. It was simulated at 300 K by supplementing the force field with a harmonic restraint which acts on the root-mean-square deviat...
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ژورنال
عنوان ژورنال: Multiscale Modeling & Simulation
سال: 2006
ISSN: 1540-3459,1540-3467
DOI: 10.1137/06065146x