Exploring the Identity of the General Base for a DNA Polymerase Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase eta

• Type: Article in International Scientific Journal
• Date: 2019

Authors

Wilson, KA (Author) Other; Pedro A Fernandes (Author) FCUP; Ramos, MJ (Author) FCUP; Wetmore, SD (Author) Other

Journal

Title: Acs Catalysis

Vol. 9

Pages: 2543-2551

ISSN: 2155-5435

Publisher: American Chemical Society

Indexing

ISI Web of Knowledge - 14 Citations

Scopus - 14 Citations

Other information

Authenticus ID: P-00Q-AHM

DOI: 10.1021/acscatal.8b04889

Abstract (EN): DNA replication is a fundamental process for life. Despite previous experimental and computational studies of the reaction pathway catalyzed by a variety of DNA polymerases, certain features of the mechanism remain unclear, especially for the more recently identified translesion synthesis (TLS) polymerases. A pressing question in the TLS polymerase literature is: what is the identity of the general base that initiates the reaction? The current work uses computational techniques to shed light on this topic by exploring the mechanism for the chemical step catalyzed by a human TLS polymerase, namely polymerase This enzyme was chosen due to its critical role in the replication of damaged DNA and its biomedical importance. A consistent theoretical framework is used to investigate all possibilities for the general base based on previous proposals from experimental and computational studies on polymerase eta and other DNA polymerases. Our MD and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations suggest that the dNTP alpha-phosphate moiety and active site water interacting with bulk solvent or the catalytic Mg2+ ion are not optimal choices for the general base due to high energy intermediates. Although proton transfer to an active site hydroxide ion or to Glu116 through Ser113 is energetically feasible, the pathway that best aligns with our dynamical (MD/umbrella sampling) structural information and available experimental kinetic and mutational data invokes Glu116 directly abstracting a proton to initiate the nucleotidyl transfer reaction. Together, these results help answer a long-standing question in the DNA replication literature.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 17