Alan D. Frankel - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
Biochemistry

77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, ... ... Frankel AD, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/s41586-020-2286-9  0.4
2020 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, et al. A Quantitative Genetic Interaction Map of HIV Infection. Molecular Cell. PMID 32084337 DOI: 10.1016/j.molcel.2020.02.004  0.4
2019 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, et al. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. Cell Host & Microbe. PMID 31253590 DOI: 10.1016/j.chom.2019.05.008  0.36
2019 Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD. Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability. Scientific Reports. 9: 5139. PMID 30914719 DOI: 10.1038/s41598-019-41582-7  0.96
2018 Dai Y, Wynn J, Peralta A, Sherpa C, Jayaraman B, Li H, Verma A, Frankel AD, Le Grice SFJ, Santos WL. Discovery of a Branched Peptide that Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication. Journal of Medicinal Chemistry. PMID 30289719 DOI: 10.1021/acs.jmedchem.8b01076  0.68
2018 Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. Elife. 7. PMID 29845934 DOI: 10.7554/eLife.31879  0.68
2017 Faust TB, Binning JM, Gross JD, Frankel AD. Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription. Annual Review of Virology. 4: 241-260. PMID 28961413 DOI: 10.1146/annurev-virology-101416-041654  0.4
2017 Nakamura RL, Burlingame MA, Yang S, Crosby DC, Talbot DJ, Chui K, Frankel AD, Renslo AR. Identification and optimization of thienopyridine carboxamides as inhibitors of HIV regulatory complexes. Antimicrobial Agents and Chemotherapy. PMID 28416550 DOI: 10.1128/AAC.02366-16  0.52
2017 Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel AD. PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription. Scientific Reports. 7: 45394. PMID 28345603 DOI: 10.1038/srep45394  0.4
2016 Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Functional Segregation of Overlapping Genes in HIV. Cell. 167: 1762-1773.e12. PMID 27984726 DOI: 10.1016/j.cell.2016.11.031  0.96
2016 Jayaraman B, Smith AM, Fernandes JD, Frankel AD. Oligomeric viral proteins: small in size, large in presence. Critical Reviews in Biochemistry and Molecular Biology. 1-16. PMID 27685368 DOI: 10.1080/10409238.2016.1215406  0.96
2016 Fernandes JD, Booth DS, Frankel AD. A structurally plastic ribonuceloprotein complex mediates post-transcriptional gene regulation in HIV-1. Wiley Interdisciplinary Reviews. Rna. PMID 26929078 DOI: 10.1002/wrna.1342  1
2015 Jayaraman B, Mavor D, Gross JD, Frankel AD. Thermodynamics of Rev-RNA Interactions in HIV-1 Rev-RRE Assembly. Biochemistry. 54: 6545-54. PMID 26422686 DOI: 10.1021/acs.biochem.5b00876  1
2015 Dunyak BM, Nakamura RL, Frankel AD, Gestwicki JE. Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. Acs Chemical Biology. PMID 26322864 DOI: 10.1021/acschembio.5b00426  0.4
2014 Booth DS, Cheng Y, Frankel AD. The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA. Elife. 3: e04121. PMID 25486595 DOI: 10.7554/eLife.04121  1
2014 Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. Elife. 3: e04120. PMID 25486594 DOI: 10.7554/eLife.04120  0.68
2012 Nakamura RL, Landt SG, Mai E, Nejim J, Chen L, Frankel AD. A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins. Plos One. 7: e48194. PMID 23133567 DOI: 10.1371/journal.pone.0048194  1
2012 D'Orso I, Jang GM, Pastuszak AW, Faust TB, Quezada E, Booth DS, Frankel AD. Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA. Molecular and Cellular Biology. 32: 4780-93. PMID 23007159 DOI: 10.1128/MCB.00206-12  1
2012 Faust T, Frankel A, D'Orso I. Transcription control by long non-coding RNAs. Transcription. 3: 78-86. PMID 22414755 DOI: 10.4161/trns.19349  1
2012 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 Biology. 9: 6-11. PMID 22258145 DOI: 10.4161/rna.9.1.18178  1
2012 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, ... ... Frankel AD, et al. Global landscape of HIV-human protein complexes. Nature. 481: 365-70. PMID 22190034 DOI: 10.1038/nature10719  1
2011 Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. Bmc Bioinformatics. 12: 298. PMID 21777475 DOI: 10.1186/1471-2105-12-298  1
2011 Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Research. 39: 2344-56. PMID 21071404 DOI: 10.1093/nar/gkq1046  1
2011 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. Purification and characterization of HIV-human protein complexes. Methods (San Diego, Calif.). 53: 13-9. PMID 20708689 DOI: 10.1016/j.ymeth.2010.08.007  1
2010 D'Orso I, Frankel AD. HIV-1 Tat: Its Dependence on Host Factors is Crystal Clear. Viruses. 2: 2226-2234. PMID 21709748 DOI: 10.3390/v2102226  1
2010 Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel AD, 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. Biophysical Journal. 99: 3454-62. PMID 21081095 DOI: 10.1016/j.bpj.2010.09.051  1
2010 Daugherty MD, Liu B, Frankel AD. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nature Structural & Molecular Biology. 17: 1337-42. PMID 20953181 DOI: 10.1038/nsmb.1902  1
2010 Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD. HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proceedings of the National Academy of Sciences of the United States of America. 107: 12481-6. PMID 20616058 DOI: 10.1073/pnas.1007022107  1
2010 D'Orso I, Frankel AD. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nature Structural & Molecular Biology. 17: 815-21. PMID 20562857 DOI: 10.1038/nsmb.1827  1
2009 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, et al. Host cell factors in HIV replication: meta-analysis of genome-wide studies. Plos Pathogens. 5: e1000437. PMID 19478882 DOI: 10.1371/journal.ppat.1000437  1
2009 D'Orso I, Frankel AD. Tat acetylation modulates assembly of a viral-host RNA-protein transcription complex. Proceedings of the National Academy of Sciences of the United States of America. 106: 3101-6. PMID 19223581 DOI: 10.1073/pnas.0900012106  0.52
2008 Daugherty MD, D'Orso I, Frankel AD. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Molecular Cell. 31: 824-34. PMID 18922466 DOI: 10.1016/j.molcel.2008.07.016  1
2008 D'Orso I, Grunwell JR, Nakamura RL, Das C, Frankel AD. Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes. Journal of Virology. 82: 9492-504. PMID 18667497 DOI: 10.1128/JVI.00763-08  1
2008 Mokdad A, Frankel AD. ISFOLD: Structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments Journal of Biomolecular Structure and Dynamics. 25: 467-472. PMID 18282001  1
2006 Mills NL, Daugherty MD, Frankel AD, Guy RK. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. Journal of the American Chemical Society. 128: 3496-7. PMID 16536504 DOI: 10.1021/ja0582051  1
2005 Calabro V, Frankel AD. Viral RNA gymnastics. Nature Chemical Biology. 1: 67-8. PMID 16407998 DOI: 10.1038/nchembio0705-67  0.4
2005 Landt SG, Ramirez A, Daugherty MD, Frankel AD. A simple motif for protein recognition in DNA secondary structures. Journal of Molecular Biology. 351: 982-94. PMID 16055152 DOI: 10.1016/j.jmb.2005.07.001  1
2005 Calabro V, Daugherty MD, Frankel AD. A single intermolecular contact mediates intramolecular stabilization of both RNA and protein. Proceedings of the National Academy of Sciences of the United States of America. 102: 6849-54. PMID 15857951 DOI: 10.1073/pnas.0409282102  1
2005 Landt SG, Tipton AR, Frankel AD. Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove. Biochemistry. 44: 6547-58. PMID 15850388 DOI: 10.1021/bi047916t  1
2004 Das C, Edgcomb SP, Peteranderl R, Chen L, Frankel AD. Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1. Virology. 318: 306-17. PMID 14972556 DOI: 10.1016/j.virol.2003.10.003  1
2004 Xie B, Calabro V, Wainberg MA, Frankel AD. Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system. Journal of Virology. 78: 1456-63. PMID 14722301 DOI: 10.1128/JVI.78.3.1456-1463.2004  0.4
2004 Cheng AC, Frankel AD. Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions. Journal of the American Chemical Society. 126: 434-5. PMID 14719918 DOI: 10.1021/ja037264g  1
2003 Das C, Frankel AD. Sequence and structure space of RNA-binding peptides. Biopolymers. 70: 80-5. PMID 12925994 DOI: 10.1002/bip.10429  1
2003 Harada K, Horiya S, Zehavi H, Frankel AD. Screening in vivo for RNA-binding peptides from combinatorial libraries. Nucleic Acids Symposium Series. 269-70. PMID 12903372 DOI: 10.1093/nass/44.1.269  0.48
2003 Cheng AC, Chen WW, Fuhrmann CN, Frankel AD. Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains. Journal of Molecular Biology. 327: 781-96. PMID 12654263 DOI: 10.1016/S0022-2836(03)00091-3  1
2003 Walberer BJ, Cheng AC, Frankel AD. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. Journal of Molecular Biology. 327: 767-80. PMID 12654262 DOI: 10.1016/S0022-2836(03)00090-1  1
2003 Peled-Zehavi H, Horiya S, Das C, Harada K, Frankel AD. Selection of RRE RNA binding peptides using a kanamycin antitermination assay. Rna (New York, N.Y.). 9: 252-61. PMID 12554868  1
2003 Xie B, Wainberg MA, Frankel AD. Replication of human immunodeficiency viruses engineered with heterologous Tat-transactivation response element interactions. Journal of Virology. 77: 1984-91. PMID 12525632 DOI: 10.1128/JVI.77.3.1984-1991.2003  1
2001 Cheng AC, Calabro V, Frankel AD. Design of RNA-binding proteins and ligands Current Opinion in Structural Biology. 11: 478-484. PMID 11495742 DOI: 10.1016/S0959-440X(00)00236-0  1
2001 Peled-Zehavi H, Berglund JA, Rosbash M, Frankel AD. Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex. Molecular and Cellular Biology. 21: 5232-41. PMID 11438677 DOI: 10.1128/MCB.21.15.5232-5241.2001  1
2001 Reyes CM, Nifosì R, Frankel AD, Kollman PA. Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophysical Journal. 80: 2833-42. PMID 11371457 DOI: 10.1016/S0006-3495(01)76250-9  1
2001 Zhang Q, Harada K, Cho HS, Frankel AD, Wemmer DE. Structural characterization of the complex of the Rev response element RNA with a selected peptide. Chemistry & Biology. 8: 511-20. PMID 11358697 DOI: 10.1016/S1074-5521(01)00027-8  1
2000 Landt SG, Tan R, Frankel AD. Screening RNA-binding libraries using Tat-fusion system in mammalian cells. Methods in Enzymology. 318: 350-63. PMID 10889998  0.44
2000 Peled-Zehavi H, Smith CA, Harada K, Frankel AD. Screening RNA-binding libraries by transcriptional antitermination in bacteria. Methods in Enzymology. 318: 297-308. PMID 10889995 DOI: 10.1016/S0076-6879(00)18059-0  0.36
2000 Harada K, Martin SS, Frankel AD. In vivo selection of RNA-binding peptides from combinatorial libraries. Nucleic Acids Symposium Series. 213-4. PMID 10780455 DOI: 10.1093/nass/42.1.213  0.4
2000 Robertson SA, Harada K, Frankel AD, Wemmer DE. Structure determination and binding kinetics of a DNA aptamer-argininamide complex. Biochemistry. 39: 946-54. PMID 10653638 DOI: 10.1021/bi9915061  1
1999 Harada K, Frankel AD. Screening RNA-binding libraries using a bacterial transcription antitermination assay. Methods in Molecular Biology (Clifton, N.J.). 118: 177-87. PMID 10549523 DOI: 10.1385/1-59259-676-2:177  0.56
1998 Smith CA, Crotty S, Harada Y, Frankel AD. Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins Biochemistry. 37: 10808-10814. PMID 9692971 DOI: 10.1021/bi980382+  1
1998 Tan R, Frankel AD. A novel glutamine-RNA interaction identified by screening libraries in mammalian cells Proceedings of the National Academy of Sciences of the United States of America. 95: 4247-4252. PMID 9539722 DOI: 10.1073/pnas.95.8.4247  1
1995 Tan R, Frankel AD. Structural variety of arginine-rich RNA-binding peptides Proceedings of the National Academy of Sciences of the United States of America. 92: 5282-5286. PMID 7777498 DOI: 10.1073/pnas.92.12.5282  1
1995 Puglisi JD, Chen L, Blanchard S, Frankel AD. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex Science. 270: 1200-1203. PMID 7502045 DOI: 10.1126/science.270.5239.1200  1
1994 Tan R, Frankel AD. Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex Biochemistry. 33: 14579-14585. PMID 7981219 DOI: 10.1021/bi00252a025  1
1993 Puglisi JD, Chen L, Frankel AD, Williamson JR. Role of RNA structure in arginine recognition of TAR RNA. Proceedings of the National Academy of Sciences of the United States of America. 90: 3680-4. PMID 7682716 DOI: 10.1073/pnas.90.8.3680  0.44
1992 Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science (New York, N.Y.). 257: 76-80. PMID 1621097 DOI: 10.1126/science.1621097  0.44
1992 Tan R, Frankel AD. Circular dichroism studies suggest that TAR RNA changes conformation upon specific binding of arginine or guanidine Biochemistry. 31: 10288-10294. PMID 1384695 DOI: 10.1021/bi00157a016  1
1991 Frankel AD, Mattaj IW, Rio DC. RNA-protein interactions. Cell. 67: 1041-6. PMID 1722140  1
1991 Calnan BJ, Tidor B, Biancalana S, Hudson D, Frankel AD. Arginine-mediated RNA recognition: the arginine fork. Science (New York, N.Y.). 252: 1167-71. PMID 1709522 DOI: 10.1126/science.252.5009.1167  1
1990 Daly TJ, Rusche JR, Maione TE, Frankel AD. Circular dichroism studies of the HIV-1 Rev protein and its specific RNA binding site Biochemistry. 29: 9791-9795. PMID 2125482 DOI: 10.1021/bi00494a005  1
1988 Frankel AD, Pabo CO. Fingering too many proteins. Cell. 53: 675. PMID 3370671 DOI: 10.1016/0092-8674(88)90083-9  1
1988 Stearman RS, Frankel AD, Freire E, Liu BS, Pabo CO. Combining thermostable mutations increases the stability of lambda repressor. Biochemistry. 27: 7571-4. PMID 3061460 DOI: 10.1021/bi00419a059  1
1988 Frankel AD, Pabo CO. Cellular uptake of the tat protein from human immunodeficiency virus. Cell. 55: 1189-93. PMID 2849510 DOI: 10.1016/0092-8674(88)90263-2  1
1988 Frankel AD, Chen L, Cotter RJ, Pabo CO. Dimerization of the tat protein from human immunodeficiency virus: a cysteine-rich peptide mimics the normal metal-linked dimer interface. Proceedings of the National Academy of Sciences of the United States of America. 85: 6297-300. PMID 2842763 DOI: 10.1073/pnas.85.17.6297  1
1988 Frankel AD, Bredt DS, Pabo CO. Tat protein from human immunodeficiency virus forms a metal-linked dimer. Science (New York, N.Y.). 240: 70-3. PMID 2832944 DOI: 10.1126/science.2832944  1
1987 Frankel AD, Berg JM, Pabo CO. Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proceedings of the National Academy of Sciences of the United States of America. 84: 4841-5. PMID 3474629 DOI: 10.1073/pnas.84.14.4841  1
1985 Frankel AD, Ackers GK, Smith HO. Measurement of DNA-protein equilibria using gel chromatography: Application to the HinfI restriction endonuclease Biochemistry. 24: 3049-3054. PMID 2990540  1
1983 Pabo CO, Jordan SR, Frankel AD. Systematic analysis of possible hydrogen bonds between amino acid side chains and B-form DNA. Journal of Biomolecular Structure & Dynamics. 1: 1039-49. PMID 6400903 DOI: 10.1080/07391102.1983.10507501  1
1981 Frankel AD, Smith HO. Restriction and modification enzymes detect no allosteric changes in DNA with bound lac repressor or RNA polymerase. Journal of Molecular Biology. 146: 611-9. PMID 6268796 DOI: 10.1016/0022-2836(81)90049-8  0.6
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