Journal Article

FZJ-2017-06039

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase

Ciupka, D. ; Gohlke, H. (Corresponding author)FZJ*

2017
Nature Publishing Group London

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Please use a persistent id in citations: http://hdl.handle.net/2128/15158  doi:10.1038/s41598-017-08521-w

Abstract: The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational changes involving an opening-closing motion of the nucleotide-binding domain (NBD) and a swiveling motion of the central domain (CD). However, why PPDK is active only in a dimeric form and to what extent an alternate binding change mechanism could underlie this fact has remained elusive. We performed unbiased molecular dynamics simulations, configurational free energy computations, and rigidity analysis to address this question. Our results support the hypothesis that PPDK dimerization influences the opening-closing motion of the NBDs, and that this influence is mediated via the CDs of both chains. Such an influence would be a prerequisite for an alternate binding change mechanism to occur. To the best of our knowledge, this is the first time that a possible explanation has been suggested as to why only dimeric PPDK is active.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. John von Neumann - Institut für Computing (NIC)
3. Strukturbiochemie (ICS-6)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. Investigating the swiveling domain mechanism of the Pyruvate phosphate dikinase (PPDK) (hdd14_20140501) (hdd14_20140501)
3. 553 - Physical Basis of Diseases (POF3-553) (POF3-553)

Appears in the scientific report 2017

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