Instructor

Ph.D., University of Arkansas for Medical SciencesAlicia K. Byrd, Ph.D.
B.S., University of Missouri-Rolla (now Missouri University of Science and Technology)

E-mail:  AKByrd@uams.edu
Office:  (501)526-7520 – Biomedical Research Center B421G
Lab:  (501)686-7254 – Biomedical Research Center 2 433-2
Fax:  (501)686-8169

 

DNA damage response and cellular response to stress

DNA damage occurs tens of thousands of times per day in human cells from both endogenous and environmental sources.  In order to preserve the genetic material, cells have evolved multiple mechanisms to detect and repair DNA damage.  However, inaccurate DNA repair can cause genomic instability such as chromosomal rearrangements and expansion of repetitive sequences which can lead to the development of cancer or diseases such as Fragile X Syndrome.  One area my research focuses on is the enzymes that regulate the DNA damage response.  In particular, I am interested in a family of enzymes called helicases which remove secondary structures from DNA and RNA.   At least 10 different human helicases are involved in DNA repair.

In addition to DNA damage, events such as viral infection or oxidative stress can cause extensive changes in the cell including widespread changes in translation which increase the cell’s ability to withstand the stress.  This process is related to the formation of pathological granules in diseases such as ALS and Alzheimer’s disease and involves a number of proteins including multiple helicases.

My research is focused on understanding the fundamental mechanisms of these enzymes using biophysical and biochemical techniques including ensemble and single molecule kinetics, proteomics, and genomics. 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.

 

Selected Publications

Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD. (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(34):18041-57 PMID: 27369081 [Abstract]

Byrd, AK and Raney, KD (2015) “A parallel quadruplex DNA is bound tightly but unfolded slowly by Pif1 helicase” J. Biol. Chem. 290(10):6482-94 PMID:25589786. [Abstract]

Aarattuthodiyil, S., Byrd, A.K., and Raney, K.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(18):11707-20. PMID:25249618 [Abstract]

Ramanagoudr-Bhojappa R., Chib, S., Byrd, A.K., Pandey, M., Patel, S.S., and Raney, K.D. (2013) “Yeast Pif1 Helicase Exhibits a One-base-pair Stepping Mechanism for Unwinding Duplex DNA” J. Biol. Chem. 288, 16185-16195. PMID:23596008 [Abstract]

He, X.*, Byrd, A.K.*, Yun, M.-K., Pemble, C.W., Harrison, D., Yeruva, L., Dahl, C., Kreuzer, K.N., Raney, K.D., and White, S.W. (2012) “The T4 Phage SF1B Helicase Dda is Structurally Optimized to Perform DNA Strand Separation” Structure. 20(7):1189-200. *co-first authors [Abstract]

Byrd, A.K., Matlock, D.L., Bagchi, D., Aarattuthodiyil, S., Harrison, D.K., Croquette, V., and Raney, K.D. (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(3):141-54. PMID: 22504228 [Abstract]

Byrd AK and Raney KD. (2006) “Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 34(10):3020-9. PMID: 16738140 [Abstract]

Byrd AK and Raney KD. (2005) “Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase.” Biochemistry. 44(39):12990-7. PMID: 16185067 [Abstract]

Byrd AK and Raney KD. (2004) “Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA.” Nat Struct Mol Biol. 11(6):531-8. PMID:15146172 [Abstract]

Complete List of Published Work in My Bibliography