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Co-Authors

This is a "connection" page, showing publications co-authored by Alicia Byrd and Kevin Raney.

 
Connection Strength
 
 
 
8.834
 
  1. Byrd AK, Malone EG, Hazeslip L, Zafar MK, Harrison DK, Thompson MD, Gao J, Perumal SK, Marecki JC, Raney KD. A structural feature of Dda helicase which enhances displacement of streptavidin and trp repressor from DNA. Protein Sci. 2022 02; 31(2):407-421.
    View in: PubMed
    Score: 0.816
  2. Byrd AK, Bell MR, Raney KD. Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. J Biol Chem. 2018 11 16; 293(46):17792-17802.
    View in: PubMed
    Score: 0.656
  3. Byrd AK, Raney KD. Structure and function of Pif1 helicase. Biochem Soc Trans. 2017 Oct 15; 45(5):1159-1171.
    View in: PubMed
    Score: 0.610
  4. 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. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem. 2016 08 19; 291(34):18041-57.
    View in: PubMed
    Score: 0.562
  5. Byrd AK, Raney KD. Fine tuning of a DNA fork by the RecQ helicase. Proc Natl Acad Sci U S A. 2015 Dec 15; 112(50):15263-4.
    View in: PubMed
    Score: 0.538
  6. Byrd AK, Raney KD. A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase. J Biol Chem. 2015 Mar 06; 290(10):6482-94.
    View in: PubMed
    Score: 0.507
  7. Byrd AK, Raney KD. Superfamily 2 helicases. Front Biosci (Landmark Ed). 2012 06 01; 17(6):2070-88.
    View in: PubMed
    Score: 0.423
  8. Byrd AK, Matlock DL, Bagchi D, Aarattuthodiyil S, Harrison D, Croquette V, Raney KD. Dda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase. J Mol Biol. 2012 Jul 13; 420(3):141-54.
    View in: PubMed
    Score: 0.419
  9. Byrd AK, Raney KD. Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 2006; 34(10):3020-9.
    View in: PubMed
    Score: 0.279
  10. Byrd AK, Raney KD. Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase. Biochemistry. 2005 Oct 04; 44(39):12990-7.
    View in: PubMed
    Score: 0.267
  11. Gao J, Proffitt DR, Marecki JC, Protacio RU, Wahls WP, Byrd AK, Raney KD. Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth. Nucleic Acids Res. 2024 Jun 24; 52(11):6543-6557.
    View in: PubMed
    Score: 0.244
  12. Byrd AK, Raney KD. Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA. Nat Struct Mol Biol. 2004 Jun; 11(6):531-8.
    View in: PubMed
    Score: 0.242
  13. Chib S, Griffin WC, Gao J, Proffitt DR, Byrd AK, Raney KD. Pif1 Helicase Mediates Remodeling of Protein-Nucleic Acid Complexes by Promoting Dissociation of Sub1 from G-Quadruplex DNA and Cdc13 from G-Rich Single-Stranded DNA. Biochemistry. 2023 12 05; 62(23):3360-3372.
    View in: PubMed
    Score: 0.234
  14. Belachew B, Gao J, Byrd AK, Raney KD. Hepatitis C virus nonstructural protein NS3 unfolds viral G-quadruplex RNA structures. J Biol Chem. 2022 11; 298(11):102486.
    View in: PubMed
    Score: 0.216
  15. Ozaslan D, Byrd AK, Belachew B, Raney KD. Alignment of helicases on single-stranded DNA increases activity. Methods Enzymol. 2022; 672:29-54.
    View in: PubMed
    Score: 0.210
  16. Gao J, Gao Z, Putnam AA, Byrd AK, Venus SL, Marecki JC, Edwards AD, Lowe HM, Jankowsky E, Raney KD. G-quadruplex DNA inhibits unwinding activity but promotes liquid-liquid phase separation by the DEAD-box helicase Ded1p. Chem Commun (Camb). 2021 Jul 27; 57(60):7445-7448.
    View in: PubMed
    Score: 0.200
  17. Edwards AD, Marecki JC, Byrd AK, Gao J, Raney KD. G-Quadruplex loops regulate PARP-1 enzymatic activation. Nucleic Acids Res. 2021 01 11; 49(1):416-431.
    View in: PubMed
    Score: 0.192
  18. Marecki JC, Byrd AK, Raney KD. Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays. Methods Mol Biol. 2021; 2209:53-72.
    View in: PubMed
    Score: 0.192
  19. Gao J, Byrd AK, Zybailov BL, Marecki JC, Guderyon MJ, Edwards AD, Chib S, West KL, Waldrip ZJ, Mackintosh SG, Gao Z, Putnam AA, Jankowsky E, Raney KD. DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chem Commun (Camb). 2019 Apr 11; 55(31):4467-4470.
    View in: PubMed
    Score: 0.170
  20. Marecki JC, Aarattuthodiyil S, Byrd AK, Penthala NR, Crooks PA, Raney KD. N-Naphthoyl-substituted indole thio-barbituric acid analogs inhibit the helicase activity of the hepatitis C virus NS3. Bioorg Med Chem Lett. 2019 02 01; 29(3):430-434.
    View in: PubMed
    Score: 0.166
  21. Griffin WC, Gao J, Byrd AK, Chib S, Raney KD. A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4. J Biol Chem. 2017 06 09; 292(23):9567-9582.
    View in: PubMed
    Score: 0.148
  22. Zybailov BL, Byrd AK, Glazko GV, Rahmatallah Y, Raney KD. Protein-protein interaction analysis for functional characterization of helicases. Methods. 2016 10 01; 108:56-64.
    View in: PubMed
    Score: 0.138
  23. Chib S, Byrd AK, Raney KD. Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes. J Biol Chem. 2016 Mar 11; 291(11):5889-5901.
    View in: PubMed
    Score: 0.136
  24. Zybailov B, Gokulan K, Wiese J, Ramanagoudr-Bhojappa R, Byrd AK, Glazko G, Jaiswal M, Mackintosh S, Varughese KI, Raney KD. Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. J Proteomics Bioinform. 2015 Nov; 8(11):243-252.
    View in: PubMed
    Score: 0.135
  25. Gao J, Zybailov BL, Byrd AK, Griffin WC, Chib S, Mackintosh SG, Tackett AJ, Raney KD. Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb). 2015 Apr 28; 51(33):7242-4.
    View in: PubMed
    Score: 0.129
  26. Ramanagoudr-Bhojappa R, Byrd AK, Dahl C, Raney KD. Yeast Pif1 accelerates annealing of complementary DNA strands. Biochemistry. 2014 Dec 09; 53(48):7659-69.
    View in: PubMed
    Score: 0.126
  27. Aarattuthodiyil S, Byrd AK, Raney KD. Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase. Nucleic Acids Res. 2014 Oct; 42(18):11707-20.
    View in: PubMed
    Score: 0.124
  28. Ramanagoudr-Bhojappa R, Chib S, Byrd AK, Aarattuthodiyil S, Pandey M, Patel SS, Raney KD. Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem. 2013 May 31; 288(22):16185-95.
    View in: PubMed
    Score: 0.112
  29. Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol. 2013; 767:17-46.
    View in: PubMed
    Score: 0.110
  30. Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol. 2013; 973:E1.
    View in: PubMed
    Score: 0.110
  31. Matlock DL, Yeruva L, Byrd AK, Mackintosh SG, Langston C, Brown C, Cameron CE, Fischer CJ, Raney KD. Investigation of translocation, DNA unwinding, and protein displacement by NS3h, the helicase domain from the hepatitis C virus helicase. Biochemistry. 2010 Mar 16; 49(10):2097-109.
    View in: PubMed
    Score: 0.091
  32. Hong Z, Byrd AK, Gao J, Das P, Tan VQ, Malone EG, Osei B, Marecki JC, Protacio RU, Wahls WP, Raney KD, Song H. Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge. Nat Commun. 2024 Jul 19; 15(1):6104.
    View in: PubMed
    Score: 0.061
  33. Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):14722-7.
    View in: PubMed
    Score: 0.054
  34. Butler TJ, Estep KN, Sommers JA, Maul RW, Moore AZ, Bandinelli S, Cucca F, Tuke MA, Wood AR, Bharti SK, Bogenhagen DF, Yakubovskaya E, Garcia-Diaz M, Guilliam TA, Byrd AK, Raney KD, Doherty AJ, Ferrucci L, Schlessinger D, Ding J, Brosh RM. Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro. Hum Mol Genet. 2020 05 28; 29(8):1292-1309.
    View in: PubMed
    Score: 0.046
  35. Su N, Byrd AK, Bharath SR, Yang O, Jia Y, Tang X, Ha T, Raney KD, Song H. Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases. Nat Commun. 2019 11 26; 10(1):5375.
    View in: PubMed
    Score: 0.044
  36. Lu C, Le S, Chen J, Byrd AK, Rhodes D, Raney KD, Yan J. Direct quantification of the translocation activities of Saccharomyces cerevisiae Pif1 helicase. Nucleic Acids Res. 2019 08 22; 47(14):7494-7501.
    View in: PubMed
    Score: 0.044
  37. Waldrip ZJ, Byrum SD, Storey AJ, Gao J, Byrd AK, Mackintosh SG, Wahls WP, Taverna SD, Raney KD, Tackett AJ. A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics. 2014 Sep; 9(9):1207-11.
    View in: PubMed
    Score: 0.031
  38. He X, Byrd AK, Yun MK, Pemble CW, Harrison D, Yeruva L, Dahl C, Kreuzer KN, Raney KD, White SW. The T4 phage SF1B helicase Dda is structurally optimized to perform DNA strand separation. Structure. 2012 Jul 03; 20(7):1189-200.
    View in: PubMed
    Score: 0.026
  39. Liu J, Choi M, Stanenas AG, Byrd AK, Raney KD, Cohan C, Bianco PR. Novel, fluorescent, SSB protein chimeras with broad utility. Protein Sci. 2011 Jun; 20(6):1005-20.
    View in: PubMed
    Score: 0.025
Connection Strength

The connection strength for concepts is the sum of the scores for each matching publication.

Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.