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Title: An MD simulation of the decoy action of Epstein–Barr virus LMP1 protein mimicking the CD40 interaction with TRAF3
Authors: Chung, Wilfredo Credo
Ishida, Toshimasa
Author's alias: 石田, 俊正
Keywords: Epstein–Barr virus
Essential dynamics
Molecular dynamics
Issue Date: Oct-2011
Publisher: Springer-Verlag
Journal title: Theoretical Chemistry Accounts
Volume: 130
Issue: 2-3
Start page: 401
End page: 410
Abstract: The Epstein–Barr virus (EBV) is associated with a variety of malignancies and chronic active EBV infection is a severe systemic disease associated with high rates of mortality and morbidity. In this paper, the dynamics of the interaction of EBV-expressed latent membrane protein 1 (LMP1) with cellular signaling intermediate tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) is simulated using standard classical molecular dynamics (MD) protocols. For comparison, the dynamics of the interaction of TRAF3 with CD40, a TNFR mimicked by LMP1 to effect EBV infection is also calculated under similar conditions. Essential dynamics (ED) analysis is carried out to identify important degrees of vibrational freedom that relate to protein function and virus infection. Both the MD simulation and ED analysis reveal novel interactions that help explain the structural decoy action of LMP1 over CD40. These interactions involve the consensus sequence PXQXTXX shared by CD40 and LMP1. In LMP1, we have found novel interaction of Asp 209 with TRAF3 and the interaction is crucial although the adjacent Asp 210 was suggested to be essential by the X-ray analysis. In CD40, it is found that the hairpin formation is not indispensable for the interaction with TRAF3.
Rights: The final publication is available at
This is not the published version. Please cite only the published version. この論文は出版社版でありません。引用の際には出版社版をご確認ご利用ください。
DOI(Published Version): 10.1007/s00214-011-1006-9
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