Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.
Skip Nav Destination
Follow us on Twitter @Biochem_Journal
Article navigation
March 2018
-
Cover Image
Cover Image
The human immunodeficiency virus. In this issue of the Biochemical Journal, Parajuli et al. report that restricted the HIV Env (envelope glycoprotein) glycan engagement by a lectin reengineered DAVEI protein chimera is sufficient for virolysis. For details, see pages 931–957.
Review Article|
March 09 2018
Using molecular simulation to explore the nanoscale dynamics of the plant kinome
Alexander S. Moffett;
Alexander S. Moffett
1Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL, U.S.A.
Search for other works by this author on:
Diwakar Shukla
1Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL, U.S.A.
2Department of Plant Biology, University of Illinois, Urbana, IL, U.S.A.
3Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, U.S.A.
Correspondence: Diwakar Shukla ([email protected])
Search for other works by this author on:
Publisher: Portland Press Ltd
Received:
October 02 2017
Revision Received:
February 01 2018
Accepted:
February 02 2018
Online ISSN: 1470-8728
Print ISSN: 0264-6021
© 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society
2018
Biochem J (2018) 475 (5): 905–921.
Article history
Received:
October 02 2017
Revision Received:
February 01 2018
Accepted:
February 02 2018
Citation
Alexander S. Moffett, Diwakar Shukla; Using molecular simulation to explore the nanoscale dynamics of the plant kinome. Biochem J 15 March 2018; 475 (5): 905–921. doi: https://doi.org/10.1042/BCJ20170299
Download citation file:
Sign in
Don't already have an account? Register
Sign in to your personal account
You could not be signed in. Please check your email address / username and password and try again.
Could not validate captcha. Please try again.
Biochemical Society Member Sign in
Sign InSign in via your Institution
Sign in via your InstitutionGet Access To This Article
Follow us on Twitter @Biochem_Journal
Open Access for all
We offer compliant routes for all authors from 2025. With library support, there will be no author nor reader charges in 5 journals. Check here |
![]() View past webinars > |