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A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

preprint
submitted on 28.08.2018, 20:29 and posted on 29.08.2018, 13:24 by Walker M. Jones, Aaron G. Davis, R. Hunter Wilson, Katherine L. Elliott, Isaiah Sumner
We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Funding

NSF-REU CHE-1461175, CHE-1062629; XSEDE NSF ACI-1548562; NSF CHE-1229354, CHE-1662030; The Thomas F. and Kate Miller Jeffress Memorial Trust, Bank of America, N.A., Trustee; and a Research Corporation Department Development Award #7957

History

Email Address of Submitting Author

sumneric@jmu.edu

Institution

James Madison University

Country

United States of America

ORCID For Submitting Author

0000-0002-1422-5476

Declaration of Conflict of Interest

no conflict of interest

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