Alan Frankel, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Address600 16th St
San Francisco CA 94158
Phone415-463-7877
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    HARC Center: HIV Accessory and Regulatory Complexes
    NIH P50GM082250Aug 27, 2007 - Aug 31, 2022
    Role: Co-Principal Investigator
    Genetic Assay for Inhibitors of RNA-Protein Interactions
    NIH R42CA103407Sep 12, 2003 - Mar 31, 2008
    Role: Principal Investigator
    Genetic Assay for Inhibitors of RNA-Protein Interactions
    NIH R41CA103407Sep 12, 2003 - Mar 31, 2005
    Role: Principal Investigator
    Structure Biology and Targeted Drug Design for AIDS
    NIH P01GM056531Sep 1, 1997 - Aug 31, 2007
    Role: Co-Investigator
    Structural Diversity of RNA-Binding Proteins
    NIH R01GM047478Jan 1, 1993 - Apr 30, 2007
    Role: Principal Investigator
    Activity and inhibition of the TAT protein from HIV
    NIH R01AI029135Sep 30, 1989 - Nov 30, 2010
    Role: Principal Investigator
    STRUCTURE, MECHANISM AND INHIBITION OF HIV PROTEINS
    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

    Collapse ORNG Applications 
    Collapse Global Health

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    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. to make corrections and additions.
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    1. Phosphoregulation of Phase Separation by the SARS-CoV-2 N Protein Suggests a Biophysical Basis for its Dual Functions. Mol Cell. 2020 12 17; 80(6):1092-1103.e4. Carlson CR, Asfaha JB, Ghent CM, Howard CJ, Hartooni N, Safari M, Frankel AD, Morgan DO. PMID: 33248025.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    2. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. PMID: 32353859.
      View in: PubMed   Mentions: 879     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    3. A Quantitative Genetic Interaction Map of HIV Infection. Mol Cell. 2020 04 16; 78(2):197-209.e7. Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, Marson A, Marazzi I, Cagney G, Krogan NJ. PMID: 32084337.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    4. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. . 2019 07 10; 26(1):86-99.e7. Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF, Johnson JR, Satkamp L, Hiatt J, Rhee DY, Baek K, Crosby DC, Frankel AD, Marson A, Harper JW, Alpi AF, Schulman BA, Gross JD, Krogan NJ. PMID: 31253590.
      View in: PubMed   Mentions:
    5. Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability. Sci Rep. 2019 03 26; 9(1):5139. Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD. PMID: 30914719.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    6. Discovery of a Branched Peptide That Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication. J Med Chem. 2018 11 08; 61(21):9611-9620. Dai Y, Wynn JE, Peralta AN, Sherpa C, Jayaraman B, Li H, Verma A, Frankel AD, Le Grice SF, Santos WL. PMID: 30289719.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    7. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. Elife. 2018 05 30; 7. Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD. PMID: 29845934.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    8. Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription. Annu Rev Virol. 2017 09 29; 4(1):241-260. Faust TB, Binning JM, Gross JD, Frankel AD. PMID: 28961413.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    9. Identification and Optimization of Thienopyridine Carboxamides as Inhibitors of HIV Regulatory Complexes. Antimicrob Agents Chemother. 2017 07; 61(7). Nakamura RL, Burlingame MA, Yang S, Crosby DC, Talbot DJ, Chui K, Frankel AD, Renslo AR. PMID: 28416550.
      View in: PubMed   Mentions: 2     Fields:    
    10. PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription. Sci Rep. 2017 03 27; 7:45394. Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel AD. PMID: 28345603.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    11. Functional Segregation of Overlapping Genes in HIV. Cell. 2016 Dec 15; 167(7):1762-1773.e12. Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. PMID: 27984726.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    12. Oligomeric viral proteins: small in size, large in presence. Crit Rev Biochem Mol Biol. 2016 Sep; 51(5):379-394. Jayaraman B, Smith AM, Fernandes JD, Frankel AD. PMID: 27685368.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    13. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. Wiley Interdiscip Rev RNA. 2016 07; 7(4):470-86. Fernandes JD, Booth DS, Frankel AD. PMID: 26929078.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    14. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly. Biochemistry. 2015 Oct 27; 54(42):6545-54. Jayaraman B, Mavor D, Gross JD, Frankel AD. PMID: 26422686.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    15. Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. ACS Chem Biol. 2015 Nov 20; 10(11):2441-7. Dunyak BM, Nakamura RL, Frankel AD, Gestwicki JE. PMID: 26322864.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    16. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. Elife. 2014 Dec 08; 3:e04120. Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD. PMID: 25486594.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    17. The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA. Elife. 2014 Dec 08; 3:e04121. Booth DS, Cheng Y, Frankel AD. PMID: 25486595.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    18. A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins. PLoS One. 2012; 7(10):e48194. Nakamura RL, Landt SG, Mai E, Nejim J, Chen L, Frankel AD. PMID: 23133567.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    19. 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. D'Orso I, Jang GM, Pastuszak AW, Faust TB, Quezada E, Booth DS, Frankel AD. PMID: 23007159.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    20. Transcription control by long non-coding RNAs. Transcription. 2012 Mar-Apr; 3(2):78-86. Faust T, Frankel A, D'Orso I. PMID: 22414755.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    21. 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. Fernandes J, Jayaraman B, Frankel A. PMID: 22258145.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    22. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. 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 AD, Krogan NJ. PMID: 22190034.
      View in: PubMed   Mentions: 310     Fields:    Translation:HumansCells
    23. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics. 2011 Jul 22; 12:298. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. PMID: 21777475.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    24. 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. Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel AD, Musier-Forsyth K, Barbara PF. PMID: 21081095.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    25. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res. 2011 Mar; 39(6):2344-56. Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. PMID: 21071404.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    26. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol. 2010 Nov; 17(11):1337-42. Daugherty MD, Liu B, Frankel AD. PMID: 20953181.
      View in: PubMed   Mentions: 88     Fields:    Translation:Cells
    27. HIV-1 Tat: Its Dependence on Host Factors is Crystal Clear. Viruses. 2010 Oct 01; 2(10):2226-2234. D'Orso I, Frankel AD. PMID: 21709748.
      View in: PubMed   Mentions: 10     Fields:    
    28. Purification and characterization of HIV-human protein complexes. Methods. 2011 Jan; 53(1):13-9. Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ. PMID: 20708689.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    29. 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. Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD. PMID: 20616058.
      View in: PubMed   Mentions: 47     Fields:    Translation:Cells
    30. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol. 2010 Jul; 17(7):815-21. D'Orso I, Frankel AD. PMID: 20562857.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCells
    31. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437. 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 AD, Young JA, Chanda SK. PMID: 19478882.
      View in: PubMed   Mentions: 239     Fields:    Translation:HumansCells
    32. 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. D'Orso I, Frankel AD. PMID: 19223581.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    33. Nucleocapsid Protein Locally Melts The Iib Region Of Hiv-1 Rre Rna, But Rev Protein Does Not: A Single-molecule Spectroscopic Study. Biophysical Journal. 2009 Feb 1; 96(3):292a. Yu-shan Yeh, Hui Wang, Paul F. Barbara, Matthew D. Daugherty, Alan D. Frankel, Karin Musier-Forsyth. .
      View in: Publisher Site   Mentions:
    34. 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. Daugherty MD, D'Orso I, Frankel AD. PMID: 18922466.
      View in: PubMed   Mentions: 64     Fields:    Translation:Cells
    35. Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes. J Virol. 2008 Oct; 82(19):9492-504. D'Orso I, Grunwell JR, Nakamura RL, Das C, Frankel AD. PMID: 18667497.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    36. 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. Mokdad A, Frankel AD. PMID: 18282001.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    37. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. J Am Chem Soc. 2006 Mar 22; 128(11):3496-7. Mills NL, Daugherty MD, Frankel AD, Guy RK. PMID: 16536504.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    38. A simple motif for protein recognition in DNA secondary structures. J Mol Biol. 2005 Sep 02; 351(5):982-94. Landt SG, Ramirez A, Daugherty MD, Frankel AD. PMID: 16055152.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    39. Viral RNA gymnastics. Nat Chem Biol. 2005 Jul; 1(2):67-8. Calabro V, Frankel AD. PMID: 16407998.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    40. 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. Landt SG, Tipton AR, Frankel AD. PMID: 15850388.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    41. 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. Calabro V, Daugherty MD, Frankel AD. PMID: 15857951.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    42. Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system. J Virol. 2004 Feb; 78(3):1456-63. Xie B, Calabro V, Wainberg MA, Frankel AD. PMID: 14722301.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    43. 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. Cheng AC, Frankel AD. PMID: 14719918.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    44. Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1. Virology. 2004 Jan 05; 318(1):306-17. Das C, Edgcomb SP, Peteranderl R, Chen L, Frankel AD. PMID: 14972556.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    45. Sequence and structure space of RNA-binding peptides. Biopolymers. 2003 Sep; 70(1):80-5. Das C, Frankel AD. PMID: 12925994.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    46. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. J Mol Biol. 2003 Apr 04; 327(4):767-80. Walberer BJ, Cheng AC, Frankel AD. PMID: 12654262.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    47. 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. Cheng AC, Chen WW, Fuhrmann CN, Frankel AD. PMID: 12654263.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    48. Replication of human immunodeficiency viruses engineered with heterologous Tat-transactivation response element interactions. J Virol. 2003 Feb; 77(3):1984-91. Xie B, Wainberg MA, Frankel AD. PMID: 12525632.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    49. Selection of RRE RNA binding peptides using a kanamycin antitermination assay. RNA. 2003 Feb; 9(2):252-61. Peled-Zehavi H, Horiya S, Das C, Harada K, Frankel AD. PMID: 12554868.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    50. Design of RNA-binding proteins and ligands. Curr Opin Struct Biol. 2001 Aug; 11(4):478-84. Cheng AC, Calabro V, Frankel AD. PMID: 11495742.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    51. HIV-1: fifteen proteins and an RNA. Annu Rev Biochem. 1998; 67:1-25. Frankel AD, Young JA. PMID: 9759480.
      View in: PubMed   Mentions: 243     Fields:    Translation:Cells
    52. RNA Recognition by HIV-1 Tat and Rev. Seminars in Virology. 1997 Jan 1; 8(3):186-193. Ruoying Tan, Alexander Brodsky, James R. Williamson, Alan D. Frankel. .
      View in: Publisher Site   Mentions:
    53. ChemInform Abstract: Tactics and Strategies in Solid Phase Peptide Synthesis: New Directions, Methods and Applications. ChemInform. 1993 Jun 22; 24(25):no-no. S. BIANCALANA, D. HUDSON, M. H. LYTTLE, C. R. JOHNSON, D. S. TSOU, P. B. WRIGHT, G. BARANY, B. J. CALNAN, A. D. FRANKEL, ET AL. ET AL.
      View in: Publisher Site   Mentions:
    54. ChemInform Abstract: Approaches Towards the Automated Synthesis of Genes and Proteins. ChemInform. 1993 Mar 16; 24(11):no-no. R. M. COOK, S. BIANCALANA, D. HUDSON, A. D. FRANKEL, D. S. TSOU, M. LYTTLE, N. SINHA. .
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    55. RNA binding by the HIV-1 Tat protein. Peptides. 1992 Jan 1; 685-687. Barbara J. Calnan, Sara Biancalana, Bruce Tidor, Derek Hudson, Alan D. Frankel. .
      View in: Publisher Site   Mentions:
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