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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM098922-03
Application #
8539805
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2011-09-01
Project End
2015-08-31
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
3
Fiscal Year
2013
Total Cost
$266,326
Indirect Cost
$82,976
Name
University of Arkansas for Medical Sciences
Department
Biochemistry
Type
Schools of Medicine
DUNS #
122452563
City
Little Rock
State
AR
Country
United States
Zip Code
72205
Byrd, Alicia K; Zybailov, Boris L; Maddukuri, Leena et al. (2016) Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem 291:18041-57
Chib, Shubeena; Byrd, Alicia K; Raney, Kevin D (2016) Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes. J Biol Chem 291:5889-901
Ramachandran, Aparna; Nandakumar, Divya; Deshpande, Aishwarya P et al. (2016) The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA. J Biol Chem 291:16828-39
Zybailov, Boris L; Byrd, Alicia K; Glazko, Galina V et al. (2016) Protein-protein interaction analysis for functional characterization of helicases. Methods 108:56-64
Zybailov, Boris; Gokulan, Kuppan; Wiese, Jadon et al. (2015) Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. J Proteomics Bioinform 8:243-252
Gao, Jun; Zybailov, Boris L; Byrd, Alicia K et al. (2015) Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb) 51:7242-4
Byrd, Alicia K; Raney, Kevin D (2015) A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase. J Biol Chem 290:6482-94
Byrd, Alicia K; Raney, Kevin D (2015) Fine tuning of a DNA fork by the RecQ helicase. Proc Natl Acad Sci U S A 112:15263-4
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
Aarattuthodiyil, Suja; Byrd, Alicia K; Raney, Kevin D (2014) Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase. Nucleic Acids Res 42:11707-20

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