Helicases are ubiquitous enzymes involved in virtually every aspect of DNA and RNA metabolism. This project focuses on one of the largest classes of this family of enzymes, superfamily 1B (SF1B). Limited structural information has slowed progress of our understanding of this class of enzymes. SF1B helicases couple ATP hydrolysis to DNA unwinding, but the rate limiting steps in this process are unknown. Specific amino acid motifs are known to make contact with DNA, but the dynamic role of these motifs has only been inferred. SF1B helicases interact with other proteins such as single-stranded binding proteins, but the biochemical and biological roles of these interactions are largely unaddressed. The importance of filling in these gaps in our knowledge relates to the many roles that helicases play in DNA metabolism including replication, repair, and recombination. Molecular defects in helicase activity have been directly linked to numerous human genetic diseases characterized by genome instability, premature aging, and cancer. Therefore, it is critical that we understand the mechanisms of these enzymes in order to understand how defects at the molecular level can lead to such devastating diseases. Dda helicase from bacteriophage T4 has served as the prototypical model system for the SF1B helicases. New structural data for Dda has led us to propose a mechano-chemical coupling mechanism that involves domains that include the standard helicase motifs along with novel domains that are uncharacterized. Helicase assays and DNA footprinting will be used to test this mechanism. We will determine the kinetic mechanism for ATP hydrolysis during DNA unwinding to determine the overall rate-limiting step in the process, which is currently unknown. Protein domains that are proposed to drive the helicase through conformational changes will be examined by rapid chemical footprinting methods that reveal whether DNA is bound tightly or loosely within the active site. High mobility protein motifs will be identified by hydrogen-deuterium exchange in order to determine the relationship between protein structure and dynamics. One of the major unanswered questions in helicase enzymology relates to the interaction between the enzyme and each individual strand of DNA. A combination of x-ray crystallographic, mass spectrometric and kinetic approaches will be used to identify all of the DNA binding sites on the surface of the enzyme. The structure-function relationship of these novel DNA binding sites will be determined through DNA unwinding experiments. The mechanism by which helicases remove proteins from DNA will be investigated using single molecule approaches. The role of protein-protein interactions will be determined by creating a tethered, dimeric form of the helicase and examining the ability of this enzyme to displace DNA-bound proteins. Answers to the questions posed in this proposal will advance the field in depth (helicase enzymology) and breadth (helicase interactions with protein partners), each of which will facilitate understanding of the role that these enzymes play in normal and pathogenic pathways of DNA metabolism. This work will provide experimental and conceptual tools to investigate other classes of helicases.

Public Health Relevance

Helicases are ubiquitous enzymes that fill many different roles in virtually each step in the metabolism of DNA and RNA. The mechanism by which these enzymes function is important to understand because defects in these enzymes at the molecular level have been directly linked to numerous human genetic diseases characterized by genome instability, premature aging, and cancer. Work in this funding cycle will fill in gaps in our knowledge so that the relationship between helicase function and disease states can be understood at the molecular level. This research project will define molecular mechanisms for physiologically relevant reactions that have been poorly characterized thus far. The work will enable investigation of the biological function of several physiologically significant interactions between helicases and other proteins. This work will also provide experimental and conceptual tools to investigate any helicase.

National Institute of Health (NIH)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Arkansas for Medical Sciences
Schools of Medicine
Little Rock
United States
Zip Code
Waldrip, Zachary J; Byrum, Stephanie D; Storey, Aaron J et al. (2014) A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics 9:1207-11
Raney, Kevin D; Byrd, Alicia K; Aarattuthodiyil, Suja (2013) Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol 973:E1
Ramanagoudr-Bhojappa, Ramanagouda; Blair, Lauren P; Tackett, Alan J et al. (2013) Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. Nucleic Acids Res 41:1029-46
Ramanagoudr-Bhojappa, Ramanagouda; Chib, Shubeena; Byrd, Alicia K et al. (2013) Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem 288:16185-95
Byrd, Alicia K; Matlock, Dennis L; Bagchi, Debjani et al. (2012) Dda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase. J Mol Biol 420:141-54