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Proteins

  • 1.
    Sekar G, Stevens A, Mostafavi A, Sashi P, Muir T, Cowburn D. A Conserved Histidine Residue Drives Extein Dependence in an Enhanced Atypically Split Intein. J Am Chem Soc. 2022;144(41):19196–19203. PMID: 36194550
    Reference Link
  • 1.
    Kayrouz C, Huang J, Hauser N, Seyedsayamdost M. Biosynthesis of selenium-containing small molecules in diverse microorganisms. Nature. 2022;610(7930):199–204. PMCID: 2881734
    Reference Link
  • 1.
    Ronceray P, Zhang Y, Liu X, Wingreen N. Stoichiometry Controls the Dynamics of Liquid Condensates of Associative Proteins. Phys Rev Lett. 2022;128(3):038102. PMID: 35119898
    Reference Link
  • 1.
    Farahani P, Reed E, Underhill E, Aoki K, Toettcher J. Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annu Rev Biomed Eng. 2021;23:61–87. PMID: 33722063
    Reference Link
  • 1.
    Seath C, Trowbridge A, Muir T, MacMillan D. Reactive intermediates for interactome mapping. Chem Soc Rev. 2021;50(5):2911–2926. PMID: 33458734
    Reference Link
  • 1.
    Carrasco-López C, Zhao E, Gil A, Alam N, Toettcher J, Avalos J. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun. 2020;11(1):4045. PMCID: PMC7427095
    Reference Link
  • 1.
    Kichuk T, Carrasco-López C, Avalos J. Lights up on organelles: Optogenetic tools to control subcellular structure and organization. WIREs Mech Dis. 2021;13(1):e1500. PMID: 32715616
    Reference Link
  • 1.
    Stadlmeier M, Runtsch L, Streshnev F, Wühr M, Carell T. A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry. Chembiochem. 2020;21(1-2):103–107. PMCID: PMC6980279
    Reference Link
  • 1.
    Tareen A, Wingreen N, Mukhopadhyay R. Asymmetry between Activators and Deactivators in Functional Protein Networks. Sci Rep. 2020;10(1):10131. PMCID: PMC7311538
    Reference Link
  • 1.
    Kennedy M, Hofstadter W, Cristea I. TRANSPIRE: A Computational Pipeline to Elucidate Intracellular Protein Movements from Spatial Proteomics Data Sets. J Am Soc Mass Spectrom. 2020;31(7):1422–1439. PMCID: PMC7737664
    Reference Link
  • 1.
    Greco T, Kennedy M, Cristea I. Proteomic Technologies for Deciphering Local and Global Protein Interactions. Trends Biochem Sci. 2020;45(5):454–455. PMID: 32035732
    Reference Link
  • 1.
    Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871
    Reference Link
  • 1.
    Thompson R, Muir T. Chemoenzymatic Semisynthesis of Proteins. Chem Rev. 2020;120(6):3051–3126. PMCID: PMC7101271
    Reference Link
  • 1.
    Murray L, Combs A, Rekapalli P, Cristea I. Methods for characterizing protein acetylation during viral infection. Methods Enzymol. 2019;626:587–620. PMCID: PMC6889803
    Reference Link
  • 1.
    Stevens A, Sekar G, Gramespacher J, Cowburn D, Muir T. An Atypical Mechanism of Split Intein Molecular Recognition and Folding. J Am Chem Soc. 2018;140(37):11791–11799. PMCID: PMC7232844
    Reference Link
  • 1.
    Gramespacher J, Burton A, Guerra L, Muir T. Proximity Induced Splicing Utilizing Caged Split Inteins. J Am Chem Soc. 2019;141(35):13708–13712. PMCID: PMC6903685
    Reference Link
  • 1.
    Federspiel J, Cristea I. Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol. 2019;1977:115–143. PMID: 30980326
    Reference Link
  • 1.
    Wang S-W, Bitbol A-F, Wingreen N. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Comput Biol. 2019;15(4):e1007010. PMCID: PMC6502352
    Reference Link
  • 1.
    Goglia A, Toettcher J. A bright future: optogenetics to dissect the spatiotemporal control of cell behavior. Curr Opin Chem Biol. 2019;48:106–113. PMCID: PMC6382565
    Reference Link
  • 1.
    Pappireddi N, Martin L, Wühr M. A Review on Quantitative Multiplexed Proteomics. Chembiochem. 2019;20(10):1210–1224. PMCID: PMC6520187
    Reference Link
  • 1.
    Murray L, Sheng X, Cristea I. Orchestration of protein acetylation as a toggle for cellular defense and virus replication. Nat Commun. 2018;9(1):4967. PMCID: PMC6251895
    Reference Link
  • 1.
    Cook K, Cristea I. Location is everything: protein translocations as a viral infection strategy. Curr Opin Chem Biol. 2019;48:34–43. PMCID: PMC6382524
    Reference Link
  • 1.
    Liszczak G, Muir T. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl. 2019;58(13):4144–4162. PMCID: PMC6748390
    Reference Link
  • 1.
    Dine E, Gil A, Uribe G, Brangwynne C, Toettcher J. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018;6(6):655–663.e5. PMCID: PMC6023754
    Reference Link
  • 1.
    Bradley L, Kleiner R, Wang A, Hecht M, Wood D. An intein-based genetic selection allows the construction of a high-quality library of binary patterned de novo protein sequences. Protein Eng Des Sel. 2005;18(4):201–7. PMID: 15849217
    Reference Link
  • 1.
    Carey J. Globularity and protein function. J Biomol Struct Dyn. 2000;17 Suppl 1:87–8. PMID: 22607410
    Reference Link
  • 1.
    Aebersold R, Agar J, Amster J, Baker M, Bertozzi C, Boja E, Costello C, Cravatt B, Fenselau C, Garcia B, Ge Y, Gunawardena J, Hendrickson R, Hergenrother P, Huber C, Ivanov A, Jensen O, Jewett M, Kelleher N, Kiessling L, Krogan N, Larsen M, Loo J, Loo R, Lundberg E, MacCoss M, Mallick P, Mootha V, Mrksich M, Muir T, Patrie S, Pesavento J, Pitteri S, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff S, Smith L, Snyder M, Thomas P, Uhlén M, Van Eyk J, Vidal M, Walt D, White F, Williams E, Wohlschlager T, Wysocki V, Yates N, Young N, Zhang B. How many human proteoforms are there?. Nat Chem Biol. 2018;14(3):206–214. PMCID: PMC5837046
    Reference Link
  • 1.
    Dine E, Toettcher J. Optogenetic Reconstitution for Determining the Form and Function of Membraneless Organelles. Biochemistry. 2018;57(17):2432–2436. PMCID: PMC5972035
    Reference Link
  • 1.
    Gramespacher J, Stevens A, Thompson R, Muir T. Improved protein splicing using embedded split inteins. Protein Sci. 2018;27(3):614–619. PMCID: PMC5818749
    Reference Link
  • 1.
    Rowland E, Snowden C, Cristea I. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol. 2018;42:76–85. PMCID: PMC5965299
    Reference Link
  • 1.
    Nofal M, Zhang K, Han S, Rabinowitz J. mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein. Mol Cell. 2017;67(6):936–946.e5. PMCID: PMC5612669
    Reference Link
  • 1.
    Rubinstein B, Mattingly H, Berezhkovskii A, Shvartsman S. Long-term dynamics of multisite phosphorylation. Mol Biol Cell. 2016;27(14):2331–40. PMCID: PMC4945148
    Reference Link
  • 1.
    Davidson S, Jonas O, Keibler M, Hou H, Luengo A, Mayers J, Wyckoff J, Del Rosario A, Whitman M, Chin C, Condon K, Lammers A, Kellersberger K, Stall B, Stephanopoulos G, Bar-Sagi D, Han J, Rabinowitz J, Cima M, Langer R, Heiden M. Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors. Nat Med. 2017;23(2):235–241. PMCID: PMC5407288
    Reference Link
  • 1.
    Esposito M, Kang Y. RAI2: Linking Retinoic Acid Signaling with Metastasis Suppression. Cancer Discov. 2015;5(5):466–8. PMCID: PMC4422076
    Reference Link
  • 1.
    Taylor N, Elbaum-Garfinkle S, Vaidya N, Zhang H, Stone H, Brangwynne C. Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. Soft Matter. 2016;12(45):9142–9150. PMCID: PMC6724727
    Reference Link
  • 1.
    Shin Y, Berry J, Pannucci N, Haataja M, Toettcher J, Brangwynne C. Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. Cell. 2017;168(1-2):159–171.e14. PMCID: PMC5562165
    Reference Link
  • 1.
    Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014;30(14):2081–3. PMCID: PMC4080744
    Reference Link
  • 1.
    Ochoa A, Storey J, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol. 2015;11(11):e1004509. PMCID: PMC4648515
    Reference Link
  • 1.
    Smith B, Mularz A, Hecht M. Divergent evolution of a bifunctional de novo protein. Protein Sci. 2015;24(2):246–52. PMCID: PMC4315662
    Reference Link
  • 1.
    Murphy G, Greisman J, Hecht M. De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic. J Mol Biol. 2016;428(2 Pt A):399–411. PMCID: PMC4744525
    Reference Link
  • 1.
    Hoegler K, Hecht M. A de novo protein confers copper resistance in Escherichia coli. Protein Sci. 2016;25(7):1249–59. PMCID: PMC4918413
    Reference Link
  • 1.
    Carey J, Lindman S, Bauer M, Linse S. Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci. 2007;16(11):2317–33. PMCID: PMC2211703
    Reference Link
  • 1.
    Wühr M, Freeman R, Presler M, Horb M, Peshkin L, Gygi S, Kirschner M. Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol. 2014;24(13):1467–1475. PMCID: PMC4090281
    Reference Link
  • 1.
    Greco T, Guise A, Cristea I. Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy. Methods Mol Biol. 2016;1410:39–63. PMCID: PMC4916643
    Reference Link

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