PeptideCutter - References

PeptideCutter tool reference

Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.;
Protein Identification and Analysis Tools on the Expasy Server;
(In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005).
Full text - Copyright Humana Press.

Protease references

• Barrett A., Rawlings N.D., Woessner J.F.
  Handbook of proteolytic enzymes.
  Academic Press (1998)
• Birktoft J.J., Breddam K.
  Glutamyl endopeptidases.
  Methods of Enzymology (1994) 244: 114-126.
• Bornstein P., Balian G.
  Cleavage at Asn-Gly bonds with hydroxylamine.
  Methods in Enzymology (1977) 47: 132- 144
• Degani Y., Patchornik A.
  Cyanylation of sulfhydryl groups by 2-nitro-5-thiocyanobenzoic acid. High-yield modification and cleavage of peptides at cysteine residues.
  Biochemistry (1974) 13: 1-11.
• Earnshaw W.C., Martins L.M., Kaufmann S.H.
  Mammalian caspases: Structure, activation, substrates, and functions during apoptosis.
  Annual Review of Biochemistry (1999) 68: 383-424.
• Fulop V., Bocskei Z., Polgar L.
  Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis
  Cell (1998) 94: 161-170.
• Fujikawa K., Titani K., Davie E.W.
  Activation of bovine factor X (Stuart factor): conversion of factor Xa alpha to factor Xa beta.
  Proceedings of the National Academy of Science of the United States of America. (1975) 72: 3359-3363.
• Houmard J., Drapeau G.R.
  Staphylococcal protease: a proteolytic enzyme specific for glutamoyl bonds.
  Proceedings of the National Academy of Science of the United States of America (1972) 69: 3506-3509.
• Han, K.K et al.
  Current developments in chemical cleavage of proteins.
  International Journal of Biochemistry (1983) 15(7): 875-884.
• Keil, B.
  Protein and Nucleic Acid Enzymology (1986) 6: 11.
• Keil, B.
  Proteolysis Data Bank: specificity of alpha-chymotrypsin from computation of protein cleavages.
  Protein Sequence Data Analysis (1987 ) 1: 13-21.
• Keil, B.
  Specificity of proteolysis.
  Springer-Verlag Berlin-Heidelberg-NewYork, pp.335. (1992)
• Keil, B., Tong T.N.
  LYSIS.
  Springer-Verlag Berlin-Heidelberg-NewYork, diskette set. (1992)
• Li, A. et al.
  Chemical cleavage at aspartyl residues for protein identification.
  Anal Chem. (2001) 73: 5395-5402
• Roche
  Enterokinase product description
  http://www.roche-applied-science.com/proddata/gpip/3_1_3_7_10_1.html
• Schechter I. & Berger A.
  On the size of the active site in proteases. I. Papain.
  Biochemical and Biophysical Research Communication (1967) 27: 157.
  
• Schechter I. & Berger A.
  On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain.
  Biochemical and Biophysical Research Communication (1968) 32: 898.
  
• Schroeder W.A., Shelton J.B., Shelton J.R.
  An examination of conditions for the cleavage of polypeptide chains with cyanogen bromide: application to catalase.
  Archives of Biochemistry and Biophysics (1969) 130: 551-556.
• Stennicke H.R., Renatus M., Meldal M., Salvesen G.S.
  Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1,3,6,7 and 8.
  Biochem. J. (2000) 350: 563-568.
• Talanian R.V., Quinlan C., Trautz S., Hackett M.C., Mankovich J.A., Banach D., Ghayur T., Brady K.D., Wong W.W.
  Substrate specificities of caspase family proteases.
  Journal of Biological Chemistry (1997) 272: 9677- 9682.
• Thornberry N.A., Rano T.A., Peterson E.P., Rasper D.M., Timkey T. et al.
  A combinatorial approach defines specificities of members of the caspase family and Granzyme B.
  Journal of Biological Chemistry (1997) 272: 17907- 17911.
• Kapust R.B., Tozser J., Copeland T.D., Waugh D.S.
  The P1' specificity of tobacco etch virus protease.
  Biochem Biophys Res Commun. (2002) 294: 949-955.
• Waugh D.S.
  TEV protease FAQ.
  http://mcl1.ncifcrf.gov/waugh_tech/faq/tev.pdf