Alan Frankel, PhD

InstitutionUniversity of California San Francisco
DepartmentBiochemistry and Biophysics
Address600 16th St
San Francisco CA 94158
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    Collapse Research 
    Collapse Research Activities and Funding
    HARC Center: HIV Accessory and Regulatory Complexes
    NIH/NIGMS P50GM082250Aug 27, 2007 - Aug 31, 2022
    Role: Co-Principal Investigator
    Genetic Assay for Inhibitors of RNA-Protein Interactions
    NIH/NCI R42CA103407Sep 12, 2003 - Mar 31, 2008
    Role: Principal Investigator
    Genetic Assay for Inhibitors of RNA-Protein Interactions
    NIH/NCI R41CA103407Sep 12, 2003 - Mar 31, 2005
    Role: Principal Investigator
    Structure Biology and Targeted Drug Design for AIDS
    NIH/NIGMS P01GM056531Sep 1, 1997 - Aug 31, 2007
    Role: Co-Investigator
    Structural Diversity of RNA-Binding Proteins
    NIH/NIGMS R01GM047478Jan 1, 1993 - Apr 30, 2007
    Role: Principal Investigator
    Activity and inhibition of the TAT protein from HIV
    NIH/NIAID R01AI029135Sep 30, 1989 - Nov 30, 2010
    Role: Principal Investigator
    NIH P01GM039589Sep 1, 1987 - Jul 31, 2004
    Role: Co-Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel A. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. Elife. 2018 May 30; 7. PMID: 29845934.
      View in: PubMed
    2. Faust TB, Binning JM, Gross JD, Frankel A. Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription. Annu Rev Virol. 2017 Sep 29; 4(1):241-260. PMID: 28961413.
      View in: PubMed
    3. Nakamura RL, Burlingame MA, Yang S, Crosby DC, Talbot DJ, Chui K, Frankel A, Renslo AR. Identification and Optimization of Thienopyridine Carboxamides as Inhibitors of HIV Regulatory Complexes. Antimicrob Agents Chemother. 2017 07; 61(7). PMID: 28416550.
      View in: PubMed
    4. Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel A. PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription. Sci Rep. 2017 Mar 27; 7:45394. PMID: 28345603.
      View in: PubMed
    5. Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel A. Functional Segregation of Overlapping Genes in HIV. Cell. 2016 Dec 15; 167(7):1762-1773.e12. PMID: 27984726.
      View in: PubMed
    6. Jayaraman B, Smith AM, Fernandes JD, Frankel A. Oligomeric viral proteins: small in size, large in presence. Crit Rev Biochem Mol Biol. 2016 Sep; 51(5):379-394. PMID: 27685368.
      View in: PubMed
    7. Fernandes JD, Booth DS, Frankel A. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. Wiley Interdiscip Rev RNA. 2016 07; 7(4):470-86. PMID: 26929078; PMCID: PMC5026123.
    8. Jayaraman B, Mavor D, Gross JD, Frankel A. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly. Biochemistry. 2015 Oct 27; 54(42):6545-54. PMID: 26422686; PMCID: PMC4801481.
    9. Dunyak BM, Nakamura RL, Frankel A, Gestwicki JE. Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. ACS Chem Biol. 2015 Nov 20; 10(11):2441-7. PMID: 26322864; PMCID: PMC4714926 [Available on 11/20/16].
    10. Booth DS, Cheng Y, Frankel A. The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA. Elife. 2014 Dec 08; 3:e04121. PMID: 25486595; PMCID: PMC4360530.
    11. Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel A. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. Elife. 2014 Dec 08; 3:e04120. PMID: 25486594; PMCID: PMC4360532.
    12. Nakamura RL, Landt SG, Mai E, Nejim J, Chen L, Frankel A. A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins. PLoS One. 2012; 7(10):e48194. PMID: 23133567; PMCID: PMC3485056.
    13. D'Orso I, Jang GM, Pastuszak AW, Faust TB, Quezada E, Booth DS, Frankel A. Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA. Mol Cell Biol. 2012 Dec; 32(23):4780-93. PMID: 23007159; PMCID: PMC3497596.
    14. Faust T, Frankel A, D'Orso I. Transcription control by long non-coding RNAs. Transcription. 2012 Mar-Apr; 3(2):78-86. PMID: 22414755; PMCID: PMC3337829.
    15. Fernandes J, Jayaraman B, Frankel A. The HIV-1 Rev response element: an RNA scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complex. RNA Biol. 2012 Jan; 9(1):6-11. PMID: 22258145; PMCID: PMC3342944.
    16. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel A, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
    17. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel A, Krogan NJ. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics. 2011 Jul 22; 12:298. PMID: 21777475; PMCID: PMC3213248.
    18. Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel A, Musier-Forsyth K, Barbara PF. Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1. Biophys J. 2010 Nov 17; 99(10):3454-62. PMID: 21081095; PMCID: PMC2980704.
    19. Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel A. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res. 2011 Mar; 39(6):2344-56. PMID: 21071404; PMCID: PMC3064769.
    20. Daugherty MD, Liu B, Frankel A. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol. 2010 Nov; 17(11):1337-42. PMID: 20953181; PMCID: PMC2988976.
    21. D'Orso I, Frankel A. HIV-1 Tat: Its Dependence on Host Factors is Crystal Clear. Viruses. 2010 Oct 01; 2(10):2226-2234. PMID: 21709748.
      View in: PubMed
    22. Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel A, Alber T, Zhou Q, Krogan NJ. Purification and characterization of HIV-human protein complexes. Methods. 2011 Jan; 53(1):13-9. PMID: 20708689; PMCID: PMC3076283.
    23. Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel A. HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12481-6. PMID: 20616058; PMCID: PMC2906596.
    24. D'Orso I, Frankel A. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol. 2010 Jul; 17(7):815-21. PMID: 20562857; PMCID: PMC2921552.
    25. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel A, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437. PMID: 19478882; PMCID: PMC2682202.
    26. D'Orso I, Frankel A. Tat acetylation modulates assembly of a viral-host RNA-protein transcription complex. Proc Natl Acad Sci U S A. 2009 Mar 03; 106(9):3101-6. PMID: 19223581; PMCID: PMC2651313.
    27. Daugherty MD, D'Orso I, Frankel A. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Mol Cell. 2008 Sep 26; 31(6):824-34. PMID: 18922466; PMCID: PMC2651398.
    28. D'Orso I, Grunwell JR, Nakamura RL, Das C, Frankel A. Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes. J Virol. 2008 Oct; 82(19):9492-504. PMID: 18667497; PMCID: PMC2546947.
    29. Mokdad A, Frankel A. ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments. J Biomol Struct Dyn. 2008 Apr; 25(5):467-72. PMID: 18282001.
      View in: PubMed
    30. Mills NL, Daugherty MD, Frankel A, Guy RK. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. J Am Chem Soc. 2006 Mar 22; 128(11):3496-7. PMID: 16536504; PMCID: PMC2566309.
    31. Landt SG, Ramirez A, Daugherty MD, Frankel A. A simple motif for protein recognition in DNA secondary structures. J Mol Biol. 2005 Sep 02; 351(5):982-94. PMID: 16055152.
      View in: PubMed
    32. Calabro V, Frankel A. Viral RNA gymnastics. Nat Chem Biol. 2005 Jul; 1(2):67-8. PMID: 16407998.
      View in: PubMed
    33. Landt SG, Tipton AR, Frankel A. Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove. Biochemistry. 2005 May 03; 44(17):6547-58. PMID: 15850388.
      View in: PubMed
    34. Calabro V, Daugherty MD, Frankel A. A single intermolecular contact mediates intramolecular stabilization of both RNA and protein. Proc Natl Acad Sci U S A. 2005 May 10; 102(19):6849-54. PMID: 15857951; PMCID: PMC1100766.
    35. Xie B, Calabro V, Wainberg MA, Frankel A. Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system. J Virol. 2004 Feb; 78(3):1456-63. PMID: 14722301; PMCID: PMC321383.
    36. Cheng AC, Frankel A. Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions. J Am Chem Soc. 2004 Jan 21; 126(2):434-5. PMID: 14719918.
      View in: PubMed
    37. Das C, Edgcomb SP, Peteranderl R, Chen L, Frankel A. Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1. Virology. 2004 Jan 05; 318(1):306-17. PMID: 14972556.
      View in: PubMed
    38. Das C, Frankel A. Sequence and structure space of RNA-binding peptides. Biopolymers. 2003 Sep; 70(1):80-5. PMID: 12925994.
      View in: PubMed
    39. Cheng AC, Chen WW, Fuhrmann CN, Frankel A. Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains. J Mol Biol. 2003 Apr 04; 327(4):781-96. PMID: 12654263.
      View in: PubMed
    40. Walberer BJ, Cheng AC, Frankel A. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. J Mol Biol. 2003 Apr 04; 327(4):767-80. PMID: 12654262.
      View in: PubMed
    41. Peled-Zehavi H, Horiya S, Das C, Harada K, Frankel A. Selection of RRE RNA binding peptides using a kanamycin antitermination assay. RNA. 2003 Feb; 9(2):252-61. PMID: 12554868; PMCID: PMC1370391.
    42. Xie B, Wainberg MA, Frankel A. Replication of human immunodeficiency viruses engineered with heterologous Tat-transactivation response element interactions. J Virol. 2003 Feb; 77(3):1984-91. PMID: 12525632; PMCID: PMC140932.
    43. Cheng AC, Calabro V, Frankel A. Design of RNA-binding proteins and ligands. Curr Opin Struct Biol. 2001 Aug; 11(4):478-84. PMID: 11495742.
      View in: PubMed
    44. Frankel A, Young JA. HIV-1: fifteen proteins and an RNA. Annu Rev Biochem. 1998; 67:1-25. PMID: 9759480.
      View in: PubMed