Integrating All-Atom and Coarse-Grained Simulations-Toward Understanding of IDPs at Surfaces.

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ID: 97525
2020
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Abstract
We present a scheme for transferring conformational degrees of freedom from all-atom (AA) simulations of an intrinsically disordered protein (IDP) to coarse-grained (CG) Monte Carlo (MC) simulations using conformational swap moves. AA simulations of a single histatin 5 peptide in water were used to obtain a structural ensemble, which is reweighted in a CGMC simulation in the presence of a negatively charged surface. For efficient sampling, the AA trajectory was condensed using two approaches: RMSD clustering (based on the root-mean-square difference in atom positions) and a "naı̈ve" truncation, where only every 100th frame of the trajectory was included in the library. The results show that even libraries with few structures well reproduce the radius of gyration and interaction free energy as functions of the distance from the surface. We further observe that the surface slightly promotes the secondary structure of histatin 5 and more so if using explicit surface charges rather than smeared charges.
Reference Key
hyltegren2020integratingjournal Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Hyltegren, Kristin;Polimeni, Marco;Skepö, Marie;Lund, Mikael;
Journal journal of chemical theory and computation
Year 2020
DOI
10.1021/acs.jctc.9b01041
URL
Keywords
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