Format

Send to

Choose Destination
J Am Chem Soc. 2019 Jul 10;141(27):10821-10829. doi: 10.1021/jacs.9b04655. Epub 2019 Jun 28.

Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase.

Author information

1
Program of Quantitative and Computational Biosciences , Baylor College of Medicine , Houston , Texas 71115 , United States.
2
Department of Biology , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States.

Abstract

High fidelity human mitochondrial DNA polymerase (Pol γ) contains two active sites, a DNA polymerization site (pol) and a 3'-5' exonuclease site (exo) for proofreading. Although separated by 35 Å, coordination between the pol and exo sites is crucial to high fidelity replication. The biophysical mechanisms for this coordination are not completely understood. To understand the communication between the two active sites, we used a statistical-mechanical model of the protein ensemble to calculate the energetic landscape and local stability. We compared a series of structures of Pol γ, complexed with primer/template DNA, and either a nucleotide substrate or a series of nucleotide analogues, which are differentially incorporated and excised by pol and exo activity. Despite the nucleotide or its analogues being bound in the pol, Pol γ residue stability varied across the protein, particularly in the exo domain. This suggests that substrate presence in the pol can be "sensed" in the exo domain. Consistent with this hypothesis, in silico mutations made in one active site mutually perturbed the energetics of the other. To identify specific regions of the polymerase that contributed to this communication, we constructed an allosteric network connectivity map that further demonstrates specific pol-exo cooperativity. Thus, a cooperative network underlies energetic connectivity. We propose that Pol γ and other dual-function polymerases exploit an energetic coupling network that facilitates domain-domain communication to enhance discrimination between correct and incorrect nucleotides.

PMID:
31251605
DOI:
10.1021/jacs.9b04655

Supplemental Content

Full text links

Icon for American Chemical Society
Loading ...
Support Center