title: Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.
abstract: Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases.
authors.affiliation: Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.
authors.forename: Vito
authors.initials: V
authors.lastname: Genna
authors.affiliation: CONCEPT Lab., Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Gaspari
authors.affiliation: Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland.
authors.forename: Matteo
authors.initials: M
authors.lastname: Dal Peraro
authors.affiliation: Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy IAS-5 / INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße 52428 Jülich, Germany marco.devivo@iit.it.
authors.forename: Marco
authors.initials: M
authors.lastname: De Vivo
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D020816:Amino Acid Motifs; D001120:Arginine / Q000737:chemistry* / Q000378:metabolism; D055162:Biocatalysis; D002413:Cations, Divalent; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism; D011756:Diphosphates / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008274:Magnesium / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D013816:Thermodynamics; D000099270:Y-Family DNA Polymerases
chemical_list: D000255:Adenosine Triphosphate; D001120:Arginine; D002413:Cations, Divalent; D004247:DNA; D004259:DNA-Directed DNA Polymerase; D011756:Diphosphates; D008274:Magnesium; C107241:diphosphoric acid; C112338:Rad30 protein; D000099270:Y-Family DNA Polymerases