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How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

01 July 2020, Version 1
Working Paper
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

In this contribution, the phosphoryl transfer reaction in CDK2 has been studied in detail considering the presence of an additional Mg2+ ion in the active site. For this purpose, QM/MM (quantum mechanics/molecular mechanics) free energy calculations with the adaptive string method were performed, which showed that indeed the system containing two Mg2+ ions exhibits a lower activation free energy, corroborating the experimental observations.

Keywords

QMMM
cdks
Free energy calculations
Adaptive String Method
Enzyme catalysis
phosphoryl tranfer

Supplementary materials

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SI Manuscript CDK2 V 3
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Now Published

How a Second Mg2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study [opens in a new tab]
Rodrigo Recabarren, Kirill Zinovjev, Iñaki Tuñón, Jans Alzate-Morales journal article
ACS Catalysis , Volume 11, Issue 1
Online publication date: Dec 15, 2020

Version History

Jul 01, 2020 Version 1

Version Notes

First version

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The content is available under CC BY NC ND 4.0 [opens in a new tab]

DOI

10.26434/chemrxiv.12560153.v1
D O I: 10.26434/chemrxiv.12560153.v1 [opens in a new tab]

Funding

CONICYT-PCHA/Folio 846 21130949
Spanish Ministerio de Economía y 847 Competitividad and FEDER funds (project PGC2018-094852-B-C22)
FONDECYT Nº 1181253

Author’s competing interest statement

No conflict of interest

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