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For a full list of publications, please visit PubMed
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  • Zhao B, Reilly CP, Davis C, Matouschek A, and Reilly JP. Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms. J. Proteome Res. 2020 June 4.

  • Tomita, T., Huibregtse, J.M. & Matouschek, A. A masked initiation region in retinoblastoma protein regulates its proteasomal degradation. Nat Commun 11, 2019 (2020).

  • Martinez-Fonts K, Davis C, Tomita T, Elsasser S, Nager AR, Shi Y, Finley D, Matouschek A. The proteasome 19S cap and its ubiquitin receptors provide a versatile recognition platform for substrates. Nature Comm. 2020 Jan 24;11(1):477. PMID: 31980598

  • Tomita T, Matouschek A. Substrate selection by the proteasome through initiation regions. Protein Sci. 2019

  • Singh Gautam AK, Matouschek A. Decoding without the cipher. Nat Chem Biol. 2019;15(3):210-212.

  • Singh Gautam AK, Martinez-Fonts K, Matouschek A. Scalable In Vitro Proteasome Activity Assay. Methods Mol Biol. 2018;1844:321-341.

  • Byun H, Das P, Yu H, et al. Mouse Mammary Tumor Virus Signal Peptide Uses a Novel p97-Dependent and Derlin-Independent Retrotranslocation Mechanism To Escape Proteasomal Degradation. MBio. 2017;8(2)

  • Yu H, Matouschek A. Recognition of Client Proteins by the Proteasome. Annu Rev Biophys. 2017;46:149-173.

  • Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A. An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates. Anal. Biochem. 2016, 509:50-59

  • Yu H, Kago G, Yellman CM, Matouschek A. Ubiquitin-like domains can target proteins to the proteasome but proteolysis requires an unstructured initiation sequence. EMBO J. 2016, 35(14):1522-1536

  • Yu H, Gautam AKS,  Wilmington SR, Wylie D, Martinez-Fonts K, Kago G, Warburton M, Chavali S, Inobe T, Finkelstein IJ, Babu MM, and Matouschek A. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome. J. Bio. Chem. 2016, 291(28):14526-14539

  • Wilmington SR, Matouschek A. An Inducible System for Rapid Degradation of Specific Cellular Proteins Using Proteasome Adaptors. PLoS One. 2016, 11(4)

  • Martinez-Fonts K, Matouschek A. A Rapid and Versatile Method for Generating Proteins with Defined Ubiquitin Chains. Biochemistry. 2016, 55(12):1898-1908

  • Huibregtse JM, Matouschek A. Ramping up degradation for proliferation. Nat Cell Biol. 2016, 18(2):141-142.

  • Takahashi K, Matouschek A, Inobe T. Regulation of Proteasomal Degradation by Modulating Proteasomal Initiation Regions. ACS Chem Biol. 2015, 10(11):2537-2543.

  • Fuxreiter M, Toth-Petroczy A, Kraut DA, Matouschek AT, Lim RY, Xue B, Kurgan L, Uversky VN. Disordered Proteinaceous Machines. Chem Rev. 2014, July; 114(13): 6806-43

  • Fishbain S, Inobe T, Israeli E, Chavali S, Yu H, Kago G, Babu MM, Matouschek A. Sequence composition of disordered regions fine-tunes protein half-life. Nature Struct. Molec. Biol. 2015 Feb 02

  • Cannon JR, Martinez-Fonts K, Robotham SA, Matouschek A, Brodbelt JS. Top-Down 193nm Ultraviolet Photodissociation Mass Spectrometry for Simultaneous Determination of Polyubiquitin Chain Length and Topology. Analyt. Chem. 2015 Jan 15

  • Van der Lee R, Lang B, Kruse K, Gsponer J, Sánchez de Groot N, Huynen MA, Matouschek A, Fuxreiter M, Babu MM. Intrinsically disordered segments affect protein half-life in the cell and during evolution. Cell Rep. 2014, 8(6):1832-1844.

  • Russell R, Matouschek A. Chance, Destiny, and the inner workings of CplXP. Cell. 2014, July; 158(3): 479-80

  • Inobe T, Matouschek A. Paradigms of protein degradation by the proteasome. Curr Opin Struct Biol. 2014, 24:156-64

  • Bhattacharyya S, Yu H, Mim C, Matouschek A. Regulated protein turnover: snapshots of the proteasome in action. Nat. Rev. Mol. Cell Biol. 2014, 15(2):122-133

  • Matouschek A, Finley D. Cell biology. An ancient portal to proteolysis. Science. 2012, 3, 37(6096):813-814.

  • Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A. Sequence- and species-dependence of proteasomal processivity. ACS Chem Biol. 2012, 7(8):1444-53

  • Schrader EK, Harstad KG, Holmgren RA, Matouschek A. A three-part signal governs differential processing of Gli1 and Gli3 proteins by the proteasome. J Biol Chem. 2011, 286(45):39051-39058.

  • Kraut DA, Matouschek A. How ClpX unfolds GFP in stages by pulling. J. Mol. Biol. 2011, Oct; 413(1) 1-3

  • Kraut DA, Matouschek A. Proteasomal degradation from internal sites favors partial proteolysis via remote domain stabilization. ACS Chem Biol. 2011, 6(10):1087-1095.

  • Fishbain S, Prakash S, Herrig A, Elsasser S, Matouschek A. Rad23 escapes degradation because it lacks a proteasome initiation region. Nat Commun. 2011, 2:192.

  • Inobe T, Fishbain S, Prakash S, Matouschek A. Defining the geometry of the two-component proteasome degron. Nat Chem Biol. 2011, 7(3):161-7.

  • Schrader EK, Wilmington SR, Matouschek A. Making it easier to regulate protein stability. Chem. Biol. 2010, Sept;17(9):917-8

  • Kraut DA, Matouschek A. Pup grows up: in vitro characterization of the degradation of pupylated proteins. EMBO J. 2010, Apr;29(7):1163-1164.

  • Schrader EK, Harstad KG, Matouschek A. Targeting proteins for degradation. Nature Chem. Biol. 2009 Nov;5(11):815-22.

  • Koodathingal P, Jaffe NE, Kraut DA, Prakash S, Fishbain S, Herman C, Matouschek A. ATP-dependent proteases differ substantially in their ability to unfold globular proteins. J. Biol. Chem. 2009 Jul 10;284(28):18674-84.

  • Prakash S, Inobe T, Hatch AJ, Matouschek A. Substrate selection by the proteasome during degradation of protein complexes. Nature Chem. Biol. 2009 Jan;5(1):29-36.

  • Inobe T, Kraut DA, Matouschek A. How to pick a protein and pull at it. Nature Struct. Molec. Biol. 2008 Nov;15(11):1135-6

  • Mohammad M, Prakash S, Matouschek A, Movileanu L. Controlling a single protein in a nanopore through electrostatic traps. J. Amer. Chem. Soc. 2008 Mar 26;130(12):4081-8.

  • Inobe T, Matouschek A. Protein targeting to ATP-dependent proteases. Curr. Opin. Struct. Biol. 2008 Feb;18(1):43-51.

  • Kraut DA, Prakash S, Matouschek A. To degrade or release: ubiquitin chain remodeling. Trends Cell Biol. 2007 Sep;17(9):419-21.

  • Tian L, Matouschek A. Where to start and when to stop. Nature Struct. Mol. Biol. 2006 Aug;13(8), 668-70. 

  • Tian L, Holmgren RA, Matouschek A. A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-kappaB. Nature Struct. Mol. Biol. 2005 Dec;12(12):1045-53.

  • Wilcox AJ, Choy J, Bustamante C, Matouschek A. Effect of protein structure on mitochondrial import. Proc. Natl. Acad. Sci. U S A. 2005 Oct 25;102(43):15435-40.

  • Snyder H, Mensah K, Hsu C, Hashimoto M, Surgucheva IG, Festoff B, Surguchov A, Masliah E, Matouschek A, Wolozin B. Beta-synuclein reduces proteasomal inhibition by alpha-synuclein but not gamma -synuclein. J. Biol. Chem. 2005 Mar 4;280(9):7562-9.

  • Prakash S, Matouschek A. Protein unfolding in the cell. Trends Biochem. Sci. 2004 Nov; 29(11), 593-600.

  • Holmberg CI, Staniszewski KE, Mensah KN, Matouschek A, Morimoto RI. Inefficient degradation of truncated polyglutamine proteins by the proteasome. EMBO J. 2004 Oct 27;23(21):4307-18.

  • Prakash S, Tian L, Ratliff KS, Lehotzky RL, Matouschek A. An unstructured initiation site is required for efficient proteasome-mediated degradation. Nature Struct. Mol. Biol. 2004 Sept; 11(9), 830-837. 

  • Shariff K, Ghosal S, Matouschek A. The Force Exerted by the Membrane Potential during Protein Import into the Mitochondrial Matrix. Biophys. J. 2004 Jun; 86(6), 3647-3652. 

  • Matouschek A. and Bustamante C. Finding a protein’s Achilles heel. Nature Struct. Biol. 2003 Sep;10(9):674-6.

  • Matouschek A. Protein unfolding – an important process in vivo. Curr. Opin. Struct. Biol. 2003 Feb; 13(1), 98-109. 

  • Herman C, Prakash S, Lu CZ, Matouschek A, Gross CA. Lack of a Robust Unfoldase Activity Confers a Unique Level of Substrate Specificity to the Universal AAA Protease FtsH. Mol. Cell. 2003, Mar; 11(3), 659-669. 

  • Snyder H., Mensah K., Theisler C., Lee J.M., Matouschek A., Wolozin B. Aggregated and monomeric alpha-synuclein bind to the S6′ proteasomal protein and inhibit proteasomal function. J. Biol. Chem. 2003, Mar; 278(14), 11753-59.

  • Lee C, Prakash S, Matouschek A. Concurrent translocation of multiple polypeptide chains through the proteasomal degradation channel. J. Biol. Chem. 2002, Sept; 277(38), 34760-34765.

  • Huang S, Ratliff KS, Matouschek A. Protein unfolding by the mitochondrial membrane potential. Nature Struct. Biol. 2002 Apr; 9(4), 301 – 307.

  • Matouschek A, Glick BS. Barreling through the outer membrane. Nature Struct. Biol. 2001, Apr;8(4):284-6.

  • Lee C*, Schwartz MP*, Prakash S, Iwakura M, Matouschek A. ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Mol. Cell. 2001 Mar;7(3):627-37.

  • Matouschek A., Pfanner N., Voos W. Protein unfolding by mitochondria. The Hsp70 import motor. EMBO Rep. 2000, Nov;1(5):404-10. 

  • Huang S, Murphy S, Matouschek A. Effect of the protein import machinery at the mitochondrial surface on precursor stability. Proc. Natl. Acad. Sci. U S A. 2000, Nov 21;97(24):12991-6. 

  • Matouschek A. Recognizing misfolded proteins in the endoplasmic reticulum. Nature Struct. Biol. 2000, Apr;7(4):265-6.

  • Huang S, Ratliff KS, Schwartz MP, Spenner JM, Matouschek A. Mitochondria unfold precursor proteins by unraveling them from their N-termini. Nature Struct. Biol. 1999, Dec;6(12):1132-8.

  • Schwartz MP, Matouschek A. The dimensions of the protein import channels in the outer and inner mitochondrial membranes. Proc. Natl. Acad. Sci. U S A. 1999, Nov 9;96(23):13086-90.

  • Schwartz M.P., Huang S., Matouschek A. The structure of precursor proteins during import into mitochondria. J. Biol. Chem. 1999, Apr 30;274(18):12759-64. 

  • Matouschek A. Recognizing misfolded proteins in the endoplasmic reticulum. Nature Struct. Biol. 2000, Apr;7(4):265-6.

  • Matouschek A, Azem A, Ratliff K, Glick BS, Schmid K, Schatz G. Active unfolding of precursor proteins during mitochondrial protein import. EMBO J. 1997 Nov 17;16(22):6727-36. 

  • Matouschek, A. (1997). Saccharomyces cerevisiae mitochondrial cyclophilin Cpr3/Cyp3. Guidebook to Molecular chaperones and Protein Folding Catalysts. Edited by Gething MJ. Oxford University Press.

  • Rospert S, Looser R, Dubaquie Y, Matouschek A, Glick BS, Schatz G. Hsp60-independent protein folding in the matrix of yeast mitochondria. EMBO J. 1996 Feb 15;15(4):764-74.

  • Matouschek A, Matthews JM, Johnson CM, Fersht AR. Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions. Protein Eng. 1994 Sep;7(9):1089-95.

  • Matouschek A, Serrano L, Fersht AR. (1994). Analysis of Protein Folding by Protein Engineering. in “Protein Folding”, Frontiers in Molecular Biology Series, IRL Press, Oxford 1994.

  • Matouschek A, Fersht AR. Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding. Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7814-8. 

  • Fersht AR, Matouschek A, Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol. 1992 Apr 5;224(3):771-82.

  • Serrano L, Kellis JT Jr, Cann P, Matouschek A, Fersht AR. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J Mol Biol. 1992 Apr 5;224(3):783-804.

  • Serrano L, Matouschek A, Fersht AR. The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure. J Mol Biol. 1992 Apr 5;224(3):805-18.

  • Matouschek A, Serrano L, Fersht AR. The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure. J Mol Biol. 1992 Apr 5;224(3):819-35.

  • Matouschek A, Serrano L, Meiering EM, Bycroft M, Fersht AR. The folding of an enzyme. V. H/2H exchange-nuclear magnetic resonance studies on the folding pathway of barnase: complementarity to and agreement with protein engineering studies. J Mol Biol. 1992 Apr 5;224(3):837-45.

  • Serrano L, Matouschek A, Fersht AR. The folding of an enzyme. VI. The folding pathway of barnase: comparison with theoretical models. J Mol Biol. 1992 Apr 5;224(3):847-59.

  • Fersht AR, Matouschek A, Sancho J, Serrano L, Vuilleumier S. Pathway of protein folding. Faraday Discuss. 1992;(93):183-93.

  • Fersht AR, Bycroft M, Horovitz A, Kellis JT Jr, Matouschek A, Serrano L. Pathway and stability of protein folding. Philos Trans R Soc Lond B Biol Sci. 1991 May 29;332(1263):171-6.

  • Matouschek A, Fersht AR. Protein engineering in analysis of protein folding pathways and stability. Methods Enzymol. 1991;202:82-112.

  • Matouschek, A. & Fersht, A.R. (1991). Use of protein engineering for mapping the transition state and protein folding pathway. Methods in Enzymology 202, 82-112.

  • Bycroft M, Matouschek A, Kellis JT Jr, Serrano L, Fersht AR. Detection and characterization of a folding intermediate in barnase by NMR. Nature. 1990 Aug 2;346(6283):488-90.

  • Matouschek A, Kellis JT Jr, Serrano L, Bycroft M, Fersht AR. Transient folding intermediates characterized by protein engineering. Nature. 1990 Aug 2;346(6283):440-5.

  • Matouschek A, Kellis JT Jr, Serrano L, Fersht AR. Mapping the transition state and pathway of protein folding by protein engineering. Nature. 1989 Jul 13;340(6229):122-6.

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