Alan Frankel, PhD

PROF-HCOMP
Biochemistry and Biophysics
+1 415 476-9994
Publications: 

The HIV-1 Nuclear Export Complex Reveals the Role of RNA in Crm1 Cargo Recognition.

bioRxiv : the preprint server for biology

Smith AM, Li Y, Velarde A, Cheng Y, Frankel AD

Enhanced NF-κB activation via HIV-1 Tat-TRAF6 cross-talk.

Science advances

Li Y, Liu X, Fujinaga K, Gross JD, Frankel AD

Functional and structural segregation of overlapping helices in HIV-1.

eLife

Safari M, Jayaraman B, Yang S, Smith C, Fernandes JD, Frankel AD

Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling.

Cell reports

Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, Fregoso OI, Young JAT, Krogan NJ

Phosphoregulation of Phase Separation by the SARS-CoV-2 N Protein Suggests a Biophysical Basis for its Dual Functions.

Molecular cell

Carlson CR, Asfaha JB, Ghent CM, Howard CJ, Hartooni N, Safari M, Frankel AD, Morgan DO

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Nature

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

A Quantitative Genetic Interaction Map of HIV Infection.

Molecular cell

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

ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection.

Cell host & microbe

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

Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability.

Scientific reports

Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD

Discovery of a Branched Peptide That Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication.

Journal of medicinal chemistry

Dai Y, Wynn JE, Peralta AN, Sherpa C, Jayaraman B, Li H, Verma A, Frankel AD, Le Grice SF, Santos WL

The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation.

eLife

Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD

Identification and Optimization of Thienopyridine Carboxamides as Inhibitors of HIV Regulatory Complexes.

Antimicrobial agents and chemotherapy

Nakamura RL, Burlingame MA, Yang S, Crosby DC, Talbot DJ, Chui K, Frankel AD, Renslo AR

PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription.

Scientific reports

Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel AD

Functional Segregation of Overlapping Genes in HIV.

Cell

Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD

Oligomeric viral proteins: small in size, large in presence.

Critical reviews in biochemistry and molecular biology

Jayaraman B, Smith AM, Fernandes JD, Frankel AD

A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1.

Wiley interdisciplinary reviews. RNA

Fernandes JD, Booth DS, Frankel AD

Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly.

Biochemistry

Jayaraman B, Mavor D, Gross JD, Frankel AD

Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA.

Molecular and cellular biology

D'Orso I, Jang GM, Pastuszak AW, Faust TB, Quezada E, Booth DS, Frankel AD

Transcription control by long non-coding RNAs.

Transcription

Faust T, Frankel A, D'Orso I

Global landscape of HIV-human protein complexes.

Nature

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

GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.

BMC bioinformatics

Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ

Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1.

Biophysical journal

Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel AD, Musier-Forsyth K, Barbara PF

An SF1 affinity model to identify branch point sequences in human introns.

Nucleic acids research

Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD

Structural basis for cooperative RNA binding and export complex assembly by HIV Rev.

Nature structural & molecular biology

Daugherty MD, Liu B, Frankel AD

Purification and characterization of HIV-human protein complexes.

Methods (San Diego, Calif.)

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

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

Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD

Host cell factors in HIV replication: meta-analysis of genome-wide studies.

PLoS pathogens

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

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

D'Orso I, Frankel AD

Nucleocapsid Protein Locally Melts The Iib Region Of Hiv-1 Rre Rna, But Rev Protein Does Not: A Single-molecule Spectroscopic Study.

Biophysical journal

Yu-shan Yeh, Hui Wang, Paul F. Barbara, Matthew D. Daugherty, Alan D. Frankel, Karin Musier-Forsyth

Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes.

Journal of virology

D'Orso I, Grunwell JR, Nakamura RL, Das C, Frankel AD

An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction.

Journal of the American Chemical Society

Mills NL, Daugherty MD, Frankel AD, Guy RK

A simple motif for protein recognition in DNA secondary structures.

Journal of molecular biology

Landt SG, Ramirez A, Daugherty MD, Frankel AD

Viral RNA gymnastics.

Nature chemical biology

Calabro V, 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

Calabro V, Daugherty MD, Frankel AD

Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system.

Journal of virology

Xie B, Calabro V, Wainberg MA, Frankel AD

Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1.

Virology

Das C, Edgcomb SP, Peteranderl R, Chen L, Frankel AD

Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains.

Journal of molecular biology

Cheng AC, Chen WW, Fuhrmann CN, Frankel AD

Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids.

Journal of molecular biology

Walberer BJ, Cheng AC, Frankel AD

Selection of RRE RNA binding peptides using a kanamycin antitermination assay.

RNA (New York, N.Y.)

Peled-Zehavi H, Horiya S, Das C, Harada K, Frankel AD

Design of RNA-binding proteins and ligands.

Current opinion in structural biology

Cheng AC, Calabro V, Frankel AD

Structural characterization of the complex of the Rev response element RNA with a selected peptide.

Chemistry & biology

Zhang Q, Harada K, Cho HS, Frankel AD, Wemmer DE

Structure-based design of a dimeric RNA-peptide complex.

The EMBO journal

Campisi DM, Calabro V, Frankel AD

An RNA-binding chameleon.

Molecular cell

Smith CA, Calabro V, Frankel AD

Fitting peptides into the RNA world.

Current opinion in structural biology

Frankel AD

Structure determination and binding kinetics of a DNA aptamer-argininamide complex.

Biochemistry

Robertson SA, Harada K, Frankel AD, Wemmer DE

Screening RNA-binding libraries by transcriptional antitermination in bacteria.

Methods in enzymology

Peled-Zehavi H, Smith CA, Harada K, Frankel AD

Screening RNA-binding libraries using Tat-fusion system in mammalian cells.

Methods in enzymology

Landt SG, Tan R, Frankel AD

Screening in vivo for RNA-binding peptides from combinatorial libraries.

Nucleic acids symposium series

Harada K, Horiya S, Zehavi H, Frankel AD

Using peptides as models of RNA-protein interactions.

Methods in enzymology

Smith CA, Chen L, Frankel AD

If the loop fits...

Nature structural biology

Frankel AD

Structure-based design of an RNA-binding zinc finger.

Proceedings of the National Academy of Sciences of the United States of America

McColl DJ, Honchell CD, Frankel AD

In vivo selection of RNA-binding peptides from combinatorial libraries.

Nucleic acids symposium series

Harada K, Martin SS, Frankel AD

Screening RNA-binding libraries using a bacterial transcription antitermination assay.

Methods in molecular biology (Clifton, N.J.)

Harada K, 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

Tan R, Frankel AD

HIV-1: fifteen proteins and an RNA.

Annual review of biochemistry

Frankel AD, Young JA

Molding a peptide into an RNA site by in vivo peptide evolution.

Proceedings of the National Academy of Sciences of the United States of America

Harada K, Martin SS, Tan R, Frankel AD

RNA Recognition by HIV-1 Tat and Rev.

Seminars in Virology

Ruoying Tan, Alexander Brodsky, James R. Williamson, Alan D. Frankel

Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex.

Science (New York, N.Y.)

Battiste JL, Mao H, Rao NS, Tan R, Muhandiram DR, Kay LE, Frankel AD, Williamson JR

Selection of RNA-binding peptides in vivo.

Nature

Harada K, Martin SS, Frankel AD

Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR.

Journal of biomolecular NMR

Battiste JL, Tan R, Frankel AD, Williamson JR

Identification of two novel arginine binding DNAs.

The EMBO journal

Harada K, Frankel AD

Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex.

Science (New York, N.Y.)

Puglisi JD, Chen L, Blanchard S, Frankel AD

Structural variety of arginine-rich RNA-binding peptides.

Proceedings of the National Academy of Sciences of the United States of America

Tan R, Frankel AD

A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA.

Proceedings of the National Academy of Sciences of the United States of America

Chen L, Frankel AD

Increased cellular uptake of the human immunodeficiency virus-1 Tat protein after modification with biotin.

Analytical biochemistry

Chen LL, Frankel AD, Harder JL, Fawell S, Barsoum J, Pepinsky B

Rapamycin enhances apoptosis and increases sensitivity to cisplatin in vitro.

Cancer research

Shi Y, Frankel A, Radvanyi LG, Penn LZ, Miller RG, Mills GB

Interaction of HIV Rev peptides with the Rev response element RNA.

Nucleic acids symposium series

Williamson JR, Battiste JL, Mao H, Frankel AD

Factors associated with airway colonisation and invasion due to Klebsiella spp.

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde

Feldman C, Smith C, Kaka S, de Jong P, Goolam Mahomed A, Frankel A, Koornhof HJ

ChemInform Abstract: Tactics and Strategies in Solid Phase Peptide Synthesis: New Directions, Methods and Applications.

ChemInform

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.

RNA recognition by an isolated alpha helix.

Cell

Tan R, Chen L, Buettner JA, Hudson D, Frankel AD

Role of RNA structure in arginine recognition of TAR RNA.

Proceedings of the National Academy of Sciences of the United States of America

Puglisi JD, Chen L, Frankel AD, Williamson JR

ChemInform Abstract: Approaches Towards the Automated Synthesis of Genes and Proteins.

ChemInform

R. M. COOK, S. BIANCALANA, D. HUDSON, A. D. FRANKEL, D. S. TSOU, M. LYTTLE, N. SINHA

The importance of being flexible.

Proceedings of the National Academy of Sciences of the United States of America

Frankel AD

Peptide models of the Tat-TAR protein-RNA interaction.

Protein science : a publication of the Protein Society

Frankel AD

Conformation of the TAR RNA-arginine complex by NMR spectroscopy.

Science (New York, N.Y.)

Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR

Activation of HIV transcription by Tat.

Current opinion in genetics & development

Frankel AD

Specific binding of arginine to TAR RNA.

Proceedings of the National Academy of Sciences of the United States of America

Tao J, Frankel AD

Structure of a ricin mutant showing rescue of activity by a noncatalytic residue.

Biochemistry

Kim Y, Mlsna D, Monzingo AF, Ready MP, Frankel A, Robertus JD

Specific binding of a basic peptide from HIV-1 Rev.

The EMBO journal

Kjems J, Calnan BJ, Frankel AD, Sharp PA

The Arginine Fork: Correction.

Science

Alan D. Frankel, Jianshi Tao

RNA binding by the HIV-1 Tat protein.

Peptides

Barbara J. Calnan, Sara Biancalana, Bruce Tidor, Derek Hudson, Alan D. Frankel

RNA-protein interactions.

Cell

Frankel AD, Mattaj IW, Rio DC

Endocytosis and targeting of exogenous HIV-1 Tat protein.

The EMBO journal

Mann DA, Frankel AD

Arginine-mediated RNA recognition: the arginine fork.

Science (New York, N.Y.)

Calnan BJ, Tidor B, Biancalana S, Hudson D, Frankel AD

The role of Tat in the human immunodeficiency virus life cycle indicates a primary effect on transcriptional elongation.

Proceedings of the National Academy of Sciences of the United States of America

Feinberg MB, Baltimore D, Frankel AD

Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes.

Molecular and cellular biology

Frankel A, Welsh P, Richardson J, Robertus JD

HIV-1 Tat protein trans-activates transcription in vitro.

Cell

Marciniak RA, Calnan BJ, Frankel AD, Sharp PA

Inhibition of antigen-induced lymphocyte proliferation by Tat protein from HIV-1.

Science (New York, N.Y.)

Viscidi RP, Mayur K, Lederman HM, Frankel AD

Activity of synthetic peptides from the Tat protein of human immunodeficiency virus type 1.

Proceedings of the National Academy of Sciences of the United States of America

Frankel AD, Biancalana S, Hudson D

Selection and characterization of ricin toxin A-chain mutations in Saccharomyces cerevisiae.

Molecular and cellular biology

Frankel A, Schlossman D, Welsh P, Hertler A, Withers D, Johnston S

Combining thermostable mutations increases the stability of lambda repressor.

Biochemistry

Stearman RS, Frankel AD, Freire E, Liu BS, 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

Frankel AD, Chen L, Cotter RJ, Pabo CO

Fingering too many proteins.

Cell

Frankel AD, Pabo CO

Tat protein from human immunodeficiency virus forms a metal-linked dimer.

Science (New York, N.Y.)

Frankel AD, Bredt DS, Pabo CO

Systematic analysis of possible hydrogen bonds between amino acid side chains and B-form DNA.

Journal of biomolecular structure & dynamics

Pabo CO, Jordan SR, Frankel AD

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