Notable publications

Altschuler

• GSK-3 modulates cellular responses to a broad spectrum of kinase inhibitors.
  Thorne CA, Wichaidit C, Coster AD, Posner BA, Wu LF, Altschuler SJ. Nat Chem Biol.

• A simple image correction method for high-throughput microscopy.
  Coster AD, Wichaidit C, Rajaram S, Altschuler SJ, Wu LF. Nat Methods.

• On comparing heterogeneity across biomarkers.
  Steininger RJ 3rd, Rajaram S, Girard L, Minna JD, Wu LF, Altschuler SJ. Cytometry Part A.

Arkin

• Screening for noise in gene expression identifies drug synergies.
  Dar RD, Hosmane NN, Arkin MR, Siliciano RF, Weinberger LS. Science.
• Specific inhibition of p97/VCP ATPase and kinetic analysis demonstrate interaction between D1 and D2 ATPase domains.
  Chou TF, Bulfer SL, Weihl CC, Li K, Lis LG, Walters MA, Schoenen FJ, Lin HJ, Deshaies RJ, Arkin MR. J Mol Biol.
• Small-molecule inhibitors of protein-protein interactions: progressing toward the reality.
  Arkin MR, Tang Y, Wells JA. Chem Biol.

Burlingame

• MST3 kinase phosphorylates TAO1/2 to enable Myosin Va function in promoting spine synapse development.
  Ultanir SK, Yadav S, Hertz NT, Oses-Prieto JA, Claxton S, Burlingame AL, Shokat KM, Jan LY, Jan YN. Neuron.
• Mass spectrometry-based detection and assignment of protein posttranslational modifications.
  Doll S, Burlingame AL. ACS Chem Biol.
• A20 Restricts Ubiquitination of Pro-Interleukin-1β Protein Complexes and Suppresses NLRP3 Inflammasome Activity.
  Duong BH, Onizawa M, Oses-Prieto JA, Advincula R, Burlingame A, Malynn BA, Ma A. Immunity.

Craik

• Sensitive and selective plasmon ruler nanosensors for monitoring the apoptotic drug response in leukemia.
  Tajon CA, Seo D, Asmussen J, Shah N, Jun YW, Craik CS. ACS Nano.
• Broad-spectrum allosteric inhibition of herpesvirus proteases.Biochemistry.
  Gable JE, Lee GM, Jaishankar P, Hearn BR, Waddling CA, Renslo AR, Craik CS. Biochemistry.
• Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter.
  Kim J, Wu S, Tomasiak TM, Mergel C, Winter MB, Stiller SB, Robles-Colmanares Y, Stroud RM, Tampé R, Craik CS, Cheng Y. Nature.

DeGrado

• De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.
  Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. Science.
• Short peptides self-assemble to produce catalytic amyloids.
  Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, DeGrado WF, Korendovych IV. Nat Chem.
• Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel.
  Wu Y, Canturk B, Jo H, Ma C, Gianti E, Klein ML, Pinto LH, Lamb RA, Fiorin G, Wang J, DeGrado WF. J Am Chem Soc.

Ding

• Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens.
  Jin C, Yang L, Xie M, Lin C, Merkurjev D, Yang JC, Tanasa B, Oh S, Zhang J, Ohgi KA, Zhou H, Li W, Evans CP, Ding S, Rosenfeld MG. Proc Natl Acad Sci USA.
• Mouse liver repopulation with hepatocytes generated from human fibroblasts.
  Zhu S, Rezvani M, Harbell J, Mattis AN, Wolfe AR, Benet LZ, Willenbring H, Ding S. Nature.

• Small molecules facilitate the reprogramming of mouse fibroblasts into pancreatic lineages.
  Li K, Zhu S, Russ HA, Xu S, Xu T, Zhang Y, Ma T, Hebrok M, Ding S. Cell Stem Cell.

Ferrin

• Enhancing UCSF Chimera through web services.
  Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res.

• setsApp: Set operations for Cytoscape Nodes and Edges.
  Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. F1000Res.

• RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps.
  Chen JE, Huang CC, Ferrin TE. Bioinformatics.

Fujimori

• Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism.
  Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG. Nat Commun.

Gartner

• A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity.
  Cerchiari AE, Garbe JC, Jee NY, Todhunter ME, Broaders KE, Peehl DM, Desai TA, LaBarge MA, Thomson M, Gartner ZJ. Proc Natl Acad Sci USA.

Gestwicki

• Validation of the hsp70-bag3 protein-protein interaction as a potential therapeutic target in cancer.
  Li X, Colvin T, Rauch JN, Acosta-Alvear D, Kampmann M, Dunyak B, Hann B, Aftab BT, Murnane M, Cho M, Walter P, Weissman JS, Sherman MY, Gestwicki JE. Mol Cancer Ther.
• Binding of human nucleotide exchange factors to heat shock protein 70 (Hsp70) generates functionally distinct complexes in vitro.
  Rauch JN, Gestwicki JE. J Biol Chem.

Grabe

• Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1.
  Choudhary OP, Paz A, Adelman JL, Colletier JP, Abramson J, Grabe M. Nat Struct Mol Biol.

• Antibacterial membrane attack by a pore-forming intestinal C-type lectin.
  Mukherjee S, Zheng H, Derebe MG, Callenberg KM, Partch CL, Rollins D, Propheter DC, Rizo J, Grabe, M. Jiang QX, Hooper LV. Nature.

• Simulating current-voltage relationships for a single-file ion channel using the weighted ensemble method.
  Adelman, J.L, Grabe M. J. Chem.

Gross

• A mutually assured destruction mechanism attenuates light signaling in Arabidopsis.
  Ni W, Xu SL, Tepperman JM, Stanley DJ, Maltby DA, Gross JD, Burlingame AL, Wang ZY, Quail PH. Science.

Huang

• Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.
  Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. Cell.

Jacobson

• Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.
  Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Elife.
• Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.
  Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. PLoS Comput Biol.
• Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis.
  Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. J Am Chem Soc.

Keiser

• Systems pharmacology augments drug safety surveillance.
  Lorberbaum T, Nasir M, Keiser M, Vilar S, Hripcsak G, Tatonetti N. Clin Pharmacol Ther.

Miller

• Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase.
  Hong L, Sharp MA, Poblete S, Biehl R, Zamponi M, Szekely N, Appavou MS, Winkler RG, Nauss RE, Johs A, Parks JM, Yi Z, Cheng X, Liang L, Ohl M, Miller SM, Richter D, Gompper G, Smith JC. Biophys J.
• X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and quantum mechanical/molecular mechanical study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs.
  Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H. Biochemistry.

Ortiz de Montellano

• Cholesterol ester oxidation by mycobacterial cytochrome P450.
  Frank DJ, Madrona Y, Ortiz de Montellano PR. J Biol Chem.

• Analysis of Cytochrome P450 CYP119 Ligand-Dependent Conformational Dynamics by Two-Dimensional NMR and X-Ray Crystallography.
  Basudhar D, Madrona Y, Kandel S, Lampe JN, Nishida CR, Ortiz de Montellano PR. J Biol Chem.

Renslo

• Fontaine SD, DiPasquale AG, Renslo AR. Efficient and stereocontrolled synthesis of 1,2,4-trioxolanes useful for ferrous iron-dependent drug delivery. Org Lett.
• Tailoring small molecules for an allosteric site on procaspase-6.
  Murray J, Giannetti AM, Steffek M, Gibbons P, Hearn BR, Cohen F, Tam C, Pozniak C, Bravo B, Lewcock J, Jaishankar P, Ly CQ, Zhao X, Tang Y, Chugha P, Arkin MR, Flygare J, Renslo AR. ChemMedChem.
• Simple plate-based, parallel synthesis of disulfide fragments using the CuAAC click reaction. Turner DM, Tom CT, Renslo AR. ACS Comb Sci.

Shoichet

• Covalent docking of large libraries for the discovery of chemical probes.
  London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J. Nat Chem Biol.
• Substrate deconstruction and the nonadditivity of enzyme recognition.
  Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK. J Am Chem Soc.
• Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
  Fischer M, Coleman RG, Fraser JS, Shoichet BK. Nat Chem.

Shu

• Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo.
  To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X. Proc Natl Acad Sci USA.
• Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells.
  To TL, Fadul MJ, Shu X. Nat Commun.
• An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging.
  Yu D, Gustafson WC, Han C, Lafaye C, Noirclerc-Savoye M, Ge WP, Thayer DA, Huang H, Kornberg TB, Royant A, Jan LY, Jan YN, Weiss WA, Shu X. Nat Commun.

Wang

• Genetically encoding an electrophilic amino acid for protein stapling and covalent binding to native receptors.
  Chen XH, Xiang Z, Hu YS, Lacey VK, Cang H, Wang L. ACS Chem Biol.
• Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells.
  Hoppmann C, Lacey VK, Louie GV, Wei J, Noel JP, Wang L. Angew Chem Int Ed Engl.
• Proximity-enabled protein crosslinking through genetically encoding haloalkane unnatural amino acids.
  Xiang Z, Lacey VK, Ren H, Xu J, Burban DJ, Jennings PA, Wang L. Angew Chem Int Ed Engl.

Wells

• A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1.
  Rettenmaier TJ, Sadowsky JD, Thomsen ND, Chen SC, Doak AK, Arkin MR, Wells JA. Proc Natl Acad Sci U S A.
• An improved single-chain fab platform for efficient display and recombinant expression.
  Koerber JT, Hornsby MJ, Wells JA. J Mol Biol.
• Unraveling the mechanism of cell death induced by chemical fibrils.
  Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA. Nat Chem Biol.