Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD

Here, we demonstrate a method to capture local dynamics on a time scale 3 orders of magnitude beyond state-of-the-art simulation approaches. We apply accelerated molecular dynamics simulations for conformational sampling and extract reweighted backbone dihedral distributions. Local dynamics are char...

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Published inJournal of chemical theory and computation Vol. 12; no. 8; pp. 3449 - 3455
Main Authors Kamenik, Anna S, Kahler, Ursula, Fuchs, Julian E, Liedl, Klaus R
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 09.08.2016
Subjects
Alanine - chemistry
Animals
Antigens, Plant - chemistry
Antigens, Plant - metabolism
Aprotinin - chemistry
Aprotinin - metabolism
Backbone
Cattle
Computer simulation
Dipeptides - chemistry
Dipeptides - metabolism
Dynamical systems
Dynamics
Entropy
Magnetic Resonance Spectroscopy
Molecular Dynamics Simulation
Pollen
Proteins
Time
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Summary:Here, we demonstrate a method to capture local dynamics on a time scale 3 orders of magnitude beyond state-of-the-art simulation approaches. We apply accelerated molecular dynamics simulations for conformational sampling and extract reweighted backbone dihedral distributions. Local dynamics are characterized by torsional probabilities, resulting in residue-wise dihedral entropies. Our approach is successfully validated for three different protein systems of increasing size: alanine dipeptide, bovine pancreatic trypsin inhibitor (BPTI), and the major birch pollen allergen Bet v 1a. We demonstrate excellent agreement of flexibility profiles with both large-scale computer simulations and NMR experiments. Thus, our method provides efficient access to local protein dynamics on extended time scales of high biological relevance.
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ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.6b00231