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A
Tareen A, Wingreen NS, Mukhopadhyay R. Asymmetry between Activators and Deactivators in Functional Protein Networks. Sci Rep. 2020 ;10(1):10131.
Stevens AJ, Sekar G, Gramespacher JA, Cowburn D, Muir TW. An Atypical Mechanism of Split Intein Molecular Recognition and Folding. J Am Chem Soc. 2018 ;140(37):11791-11799.
B
Ochoa A, Storey JD, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol. 2015 ;11(11):e1004509.
Taylor N, Elbaum-Garfinkle S, Vaidya N, Zhang H, Stone HA, Brangwynne CP. Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. Soft Matter. 2016 ;12(45):9142-9150.
Goglia AG, Toettcher JE. A bright future: optogenetics to dissect the spatiotemporal control of cell behavior. Curr Opin Chem Biol. 2019 ;48:106-113.
C
Stadlmeier M, Runtsch LSimon, 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.
Federspiel JD, Cristea IM. Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol. 2019 ;1977:115-143.
D
Hoegler KJ, Hecht MH. A de novo protein confers copper resistance in Escherichia coli. Protein Sci. 2016 ;25(7):1249-59.
Murphy GS, Greisman JB, Hecht MH. De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic. J Mol Biol. 2016 ;428(2 Pt A):399-411.
Wühr M, Freeman RM, Presler M, Horb ME, Peshkin L, Gygi S, et al.. Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol. 2014 ;24(13):1467-1475.
Greco TM, Guise AJ, Cristea IM. 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.
Carrasco-López C, Zhao EM, Gil AA, Alam N, Toettcher JE, Avalos JL. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun. 2020 ;11(1):4045.
Davidson SM, Jonas O, Keibler MA, Hou HWei, Luengo A, Mayers JR, et al. Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors. Nat Med. 2017 ;23(2):235-241.
Smith BA, Mularz AE, Hecht MH. Divergent evolution of a bifunctional de novo protein. Protein Sci. 2015 ;24(2):246-52.
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Carey J. Globularity and protein function. J Biomol Struct Dyn. 2000 ;17 Suppl 1:87-8.
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Nechay M, Kleiner RE. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020 ;54:37-44.
Aebersold R, Agar JN, I Amster J, Baker MS, Bertozzi CR, Boja ES, et al. How many human proteoforms are there?. Nat Chem Biol. 2018 ;14(3):206-214.
I
Gramespacher JA, Stevens AJ, Thompson RE, Muir TW. Improved protein splicing using embedded split inteins. Protein Sci. 2018 ;27(3):614-619.
Bradley LH, Kleiner RE, Wang AF, Hecht MH, Wood DW. 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.
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Cook KC, Cristea IM. Location is everything: protein translocations as a viral infection strategy. Curr Opin Chem Biol. 2019 ;48:34-43.
Rubinstein BY, Mattingly HH, Berezhkovskii AM, Shvartsman SY. Long-term dynamics of multisite phosphorylation. Mol Biol Cell. 2016 ;27(14):2331-40.
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Murray LA, Combs AN, Rekapalli P, Cristea IM. Methods for characterizing protein acetylation during viral infection. Methods Enzymol. 2019 ;626:587-620.
Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014 ;30(14):2081-3.
Nofal M, Zhang K, Han S, Rabinowitz JD. mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein. Mol Cell. 2017 ;67(6):936-946.e5.
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Liszczak G, Muir TW. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl. 2019 ;58(13):4144-4162.