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Protein Engineering, Vol. 13, No. 8, 551-555, August 2000
© 2000 Oxford University Press

Structural and interactional homology of clinically potential trypsin inhibitors: molecular modelling of Cucurbitaceae family peptides using the X-ray structure of MCTI-II

S. Chakraborty, S. Bhattacharya, S. Ghosh, A.K. Bera, U. Haldar, A.K. Pal, B.P. Mukhopadhyay and Asok Banerjee1

Department of Biophysics, Bose Institute, P1/2 C.I.T. Scheme VII M, Calcutta-700054, India

Several trypsin inhibitor peptides (with 28–32 amino acid residues) belonging to the Cucurbitaceae (LA-1, LA-2, MCTI-I, CMTI-I, CMTI-III, CMTI-IV), characterized by a distinctive tertiary fold with three conserved disulphide bonds and with mostly arginine at their active centre, were modelled using the high-resolution X-ray structure of a homologous inhibitor, MCTI-II, isolated from bitter gourd. All the inhibitors were modelled in both their native and complexed state with the trypsin molecule, keeping the active site the same as was observed in the trypsin–MCTI-II complex, by homology modelling using the InsightII program. The minimized energy profile supported the binding constants (binding behaviour) of the inhibitor–trypsin complexes in the solution state. A difference accessible surface area (DASA) study of the trypsin with and without inhibitors revealed the subsites of trypsin where the inhibitors bind. It revealed that the role of mutation of these peptides through evolution is to modulate their inhibitory function depending on the biological need rather than changing the overall structural folding characteristics which are highly conserved. The minor changes of amino acids in the non-conserved regions do not influence significantly the basic conformational and interactional sequences at the trypsin binding subsites during complex formation.


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