Kinetics of Loop Closure in Disordered Proteins: Theory vs Simulations vs Experiments
- Rohit Satija
Rohit SatijaDepartment of Chemistry, University of Texas at Austin, Austin, Texas 78712, United StatesMore by Rohit Satija
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- Atanu Das
Atanu DasDepartment of Chemistry, University of Texas at Austin, Austin, Texas 78712, United StatesMore by Atanu Das
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- Steffen Mühle
Steffen MühleIII. Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, GermanyCluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells’ (MBExC), Georg August University, Göttingen, GermanyMore by Steffen Mühle
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- Jörg Enderlein
Jörg EnderleinIII. Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, GermanyCluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells’ (MBExC), Georg August University, Göttingen, GermanyMore by Jörg Enderlein
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- Dmitrii E. Makarov*
Dmitrii E. Makarov*Email: [email protected]. Phone: (512) 471-4575.Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United StatesOden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United StatesMore by Dmitrii E. Makarov
Abstract
We study intrachain dynamics of intrinsically disordered proteins, as manifested by the time scales of loop formation, using atomistic simulations, experiment-parametrized coarse-grained models, and one-dimensional theories assuming Markov or non-Markov dynamics along the reaction coordinate. Despite the generally non-Markov character of monomer dynamics in polymers, we find that the simplest model of one-dimensional diffusion along the reaction coordinate (equated to the distance between the loop-forming monomers) well captures the mean first passage times to loop closure measured in coarse-grained and atomistic simulations, which, in turn, agree with the experimental values. This justifies use of the one-dimensional diffusion model in interpretation of experimental data. At the same time, the transition path times for loop closure in longer polypeptide chains show significant non-Markov effects; at intermediate times, these effects are better captured by the generalized Langevin equation model. At long times, however, atomistic simulations predict long tails in the distributions of transition path times, which are at odds with both the one-dimensional diffusion model and the generalized Langevin equation model.
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