Publications

PROTEIN UNFOLDING IN THE CELL

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., Sanchez 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 Sep 25; 8(6): 1832-44

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

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

Inobe T., Matouschek A.
Paradigms of protein degradation by the proteasome
Curr Opin Struct Biol. 2014 Feb; 24(2): 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 Feb; 15(2): 122-33

Matouschek A., Finley D.
Cell Biology. An ancient portal to proteolysis
Science. 2012 Aug; 337(6096) 813-814

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

Schrader E.K., Harstad K.G., Holmgren R.A.,Matouschek A.
A three-part signal governs differential processing of Gli1 and Gli3 proteins by the proteosome
J. Mol. Biol. 2011 Nov; 286(45) 39051-8

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

Kraut D.A., Matouschek A.
Proteasomal degradation from internal sites favors partial proteolysis via remote domain stabilization
ACS Chem. Biol 2011 Oct; 6(10) 1087-95

Fishbain S., Prakash S., Herrig A., Elsasser S., Matouschek A.
Rad 23 escapes degradation because it lacks a proteasome initiation region
Nat. Commun. 2011 Feb; 2:192

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

Schrader E.K, Wilmington S.R, 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. 2010 Apr;29(7):1163-1164.

Schrader, E.K., Harstad, K.G. & Matouschek, A.
Targeting proteins for degradation.
Nature Chem. Biol. 2009 Nov;5(11):815-22.

Koodathingal, P., Jaffe, N.E., Kraut, D.A., 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, A.J. & Matouschek, A.
Substrate selection by the proteasome during degradation of protein complexes.
Nature Chem. Biol. 2009 Jan;5(1):29-36.

Inobe, T., Kraut, D.A. & 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, D.A., 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. [PDF]

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.[PDF]

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 [PDF]

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 [PDF]

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

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 [PDF]

Prakash S., Tian L., Ratliff K.S., Lehotzky R. L., Matouschek A.
An unstructured initiation site is required for efficient proteasome-mediated degradation
Nature Struct. Mol. Biol. 2004 Sept; 11(9), 830-837. [PDF]
News and Views by Kenniston JA and Sauer RT in Nature Struct. Mol. Biol. 2004 Sep;11(9):800-2.

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. [PDF]

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

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

Herman C., Prakash S., Lu C.Z., Matouschek A., Gross C.A.
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. [PDF]

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. [PDF]

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. [PDF]

Huang S., Ratliff K.S., Matouschek A..
Protein unfolding by the mitochondrial membrane potential
Nature Struct. Biol. 2002 Apr; 9(4), 301 – 307. [PDF]
News and Views by Pfanner N and Truscott KN in Nature Struct. Biol. 2002 Apr;9(4):234-6.

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

Lee C.*, Schwartz M.P.*, Prakash S., Iwakura M., Matouschek A. ( * :- co-authors )
ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal
Mol. Cell. 2001 Mar;7(3):627-37. [PDF]
News and Views by Hochstrasser M and Wang J in Nature Struct. Biol. 2001 Apr;8(4):294-6.

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

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. [PDF]

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

Huang S., Ratliff K.S., Schwartz M.P., Spenner J.M., Matouschek A.
Mitochondria unfold precursor proteins by unraveling them from their N-termini
Nature Struct. Biol. 1999 Dec;6(12):1132-8. [PDF]
News and Views by Hebert DN. in Nature Struct. Biol. 1999 Dec;6(12):1084-5

Schwartz M.P., 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. [PDF]

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. [PDF]

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

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PROTEIN FOLDING IN THE CELL

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, Rospert S, Schmid K, Glick BS, Schatz G.
Cyclophilin catalyzes protein folding in yeast mitochondria.
Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6319-23.

Lithgow T, Horst M, Rospert S, Matouschek A, Haucke V, Schatz G
Import and folding of proteins by mitochondria.
Cold Spring Harb Symp Quant Biol. 1995;60:609-17

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PROTEIN FOLDING IN VITRO

Matouschek A, Otzen DE, Itzhaki LS, Jackson SE, Fersht AR.
Movement of the position of the transition state in protein folding.
Biochemistry. 1995 Oct 17;34(41):13656-62

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, 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.

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.

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