Genetics and Molecular Research 6 (4): 846-858 (2007) FUNPEC-RP www.funpecrp.com.br Proteinase inhibition using small Bowman-Birk- type structures J.H. Fernandez 1 *, M.O. Mello 2 *, L. Galgaro 2 , A.S. Tanaka 3 , M.C. Silva-Filho 2 and G. Neshich 4 1 LabInfo, LNCC, Petrópolis, RJ, Brasil 2 Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, SP, Brasil 3 Departamento de Bioquímica, Escola Paulista de Medicina, UNIFESP, São Paulo, SP, Brasil 4 Laboratório de Bioinformática Estrutural, EMBRAPA, Campinas, SP, Brasil Corresponding author: G. Neshich E-mail: neshich@cbi.cnptia.embrapa.br *These authors contributed equally to this study. ABSTrACT. Bowman-Birk inhibitors (BBIs) are cysteine-rich and highly cross-linked small proteins that function as specifc pseudosub- strates for digestive proteinases. They typically display a “double-head- ed” structure containing an independent proteinase-binding loop that can bind and inhibit trypsin, chymotrypsin and elastase. In the present study, we used computational biology to study the structural charac- teristics and dynamics of the inhibition mechanism of the small BBI loop expressing a 35-amino acid polypeptide (ChyTB2 inhibitor) which Genet. Mol. Res. 6 (4): 846-858 (2007) Received August 03, 2007 Accepted September 25, 2007 Published October 05, 2007