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  Variational Identification of Markovian Transition States

Martini, L., Covino, R., Hummer, G., Buchete, N.-V., & Rosta, E. (2017). Variational Identification of Markovian Transition States. Physical Review X, 7(3): 031060. doi:10.1103/PhysRevX.7.031060.

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 Creators:
Martini, Linda1, Author
Covino, Roberto2, Author           
Hummer, Gerhard2, 3, Author           
Buchete, Nicolae-Viorel4, Author
Rosta, Edina1, Author
Affiliations:
1Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom, ou_persistent22              
2Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              
3Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany, ou_persistent22              
4School of Physics and Institute for Discovery, University College Dublin, Dublin 4, Ireland, ou_persistent22              

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 Abstract: We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5, and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

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Language(s): eng - English
 Dates: 2017-03-172016-06-162017-09-28
 Publication Status: Published online
 Pages: 14
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1103/PhysRevX.7.031060
 Degree: -

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Title: Physical Review X
  Abbreviation : Phys. Rev. X
Source Genre: Journal
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Publ. Info: New York, NY : American Physical Society
Pages: - Volume / Issue: 7 (3) Sequence Number: 031060 Start / End Page: - Identifier: Other: 2160-3308
CoNE: https://pure.mpg.de/cone/journals/resource/2160-3308