Research Interest Statement:
My research is focused on understanding the fundamental mechanisms of a family of enzymes that regulate DNA repair. Misregulation of DNA repair, and these enzymes specifically, is associated with multiple types of cancer. The molecular mechanisms of these proteins, both individually and as components of multi-protein complexes, are of interest, as are the effects of posttranslational modifications on their activity. Increased understanding of the regulation of these DNA repair processes that are critical for maintaining genomic integrity could ultimately lead to the design of better cancer therapies.
Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. International journal of molecular sciences. 2022 23(7). PMID: 35409096. PMCID: PMC8998199.
Byrd AK, Malone EG, Hazeslip L, [et al.]. A structural feature of Dda helicase which enhances displacement of streptavidin and trp repressor from DNA. Protein science : a publication of the Protein Society. 2021. PMID: 34761452.
Gao J, Gao Z, Putnam AA, [et al., including Byrd AK]. G-quadruplex DNA inhibits unwinding activity but promotes liquid-liquid phase separation by the DEAD-box helicase Ded1p. Chemical communications (Cambridge, England). 2021. PMID: 34232232.
Chappell K, Tackett A, Manna K, [et al., including Byrd AK]. Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer. Molecular omics. 2021. PMID: 34142686.
Graw S, Tang J, Zafar MK, [et al., including Byrd AK]. proteiNorm - A User-Friendly Tool for Normalization and Analysis of TMT and Label-Free Protein Quantification. ACS omega. 2020 5(40):25625-25633. PMID: 33073088. PMCID: PMC7557219.
Zafar MK, Hazeslip L, Chauhan MZ, Byrd AK. The Expression of Human DNA Helicase B Is Affected by G-Quadruplexes in the Promoter. Biochemistry. 2020 59(26):2401-2409. PMID: 32478505. PMCID: PMC7346868.
Butler TJ, Estep KN, Sommers JA, [et al., including Byrd AK]. Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro. Human molecular genetics. 2020 29(8):1292-1309. PMID: 32191790. PMCID: PMC7254849.
Hazeslip L, Zafar MK, Chauhan MZ, Byrd AK. Genome Maintenance by DNA Helicase B. Genes. 2020 11(5). PMID: 32455610. PMCID: PMC7290933.
Su N, Byrd AK, Bharath SR, [et al.]. Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases. Nature communications. 2019 10(1):5375. PMID: 31772234. PMCID: PMC6879534.
Lu C, Le S, Chen J, [et al., including Byrd AK]. Direct quantification of the translocation activities of Saccharomyces cerevisiae Pif1 helicase. Nucleic acids research. 2019 47(14):7494-7501. PMID: 31216020. PMCID: PMC6698741.
Gao J, Byrd AK, Zybailov BL, [et al.]. DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chemical communications (Cambridge, England). 2019 55(31):4467-4470. PMID: 30855040. PMCID: PMC6459694.
Marecki JC, Aarattuthodiyil S, Byrd AK, [et al.]. N-Naphthoyl-substituted indole thio-barbituric acid analogs inhibit the helicase activity of the hepatitis C virus NS3. Bioorganic & medicinal chemistry letters. 2019 29(3):430-434. PMID: 30578035. PMCID: PMC6377802.
Byrd AK, Bell MR, Raney KD. Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. The Journal of biological chemistry. 2018 293(46):17792-17802. PMID: 30257865. PMCID: PMC6240867.
Byrd AK, Raney KD. Structure and function of Pif1 helicase. Biochemical Society transactions. 2017 45(5):1159-1171. PMID: 28900015. PMCID: PMC5870758.
Griffin WC, Gao J, Byrd AK, [et al.]. A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4. The Journal of biological chemistry. 2017 292(23):9567-9582. PMID: 28416612. PMCID: PMC5465483.
Zybailov BL, Byrd AK, Glazko GV, [et al.]. Protein-protein interaction analysis for functional characterization of helicases. Methods (San Diego, Calif.). 2016 108:56-64. PMID: 27090004. PMCID: PMC5035562.
Byrd AK, Zybailov BL, Maddukuri L, [et al.]. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. The Journal of biological chemistry. 2016 291(34):18041-57. PMID: 27369081. PMCID: PMC5016190.
Chib S, Byrd AK, Raney KD. Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes. The Journal of biological chemistry. 2016 291(11):5889-901. PMID: 26733194. PMCID: PMC4786723.
Yu C, Tan HY, Choi M, [et al., including Byrd AK]. SSB binds to the RecG and PriA helicases in vivo in the absence of DNA. Genes to cells : devoted to molecular & cellular mechanisms. 2016 21(2):163-84. PMID: 26766785. PMCID: PMC4738028.
Byrd AK, Raney KD. Fine tuning of a DNA fork by the RecQ helicase. Proceedings of the National Academy of Sciences of the United States of America. 2015 112(50):15263-4. PMID: 26582797. PMCID: PMC4687568.
Zybailov B, Gokulan K, Wiese J, [et al., including Byrd AK]. Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. Journal of proteomics & bioinformatics. 2015 8(11):243-252. PMID: 26807012. PMCID: PMC4722957.