Protein Engineering, Vol. 14, No. 1, 7-15,
January 2001
© 2001 Oxford University Press
Assessing the role of tryptophan residues in the binding site
Department of Biochemistry and Bioinformatics Centre, Bose Institute,P-1/12, CIT Scheme VIIM, Calcutta 700 054, India
Instead of looking at the interfacial area as a measure of the extent of a protein–protein recognition site, a new procedure has been developed to identify the importance of a specific residue, namely tryptophan, in the binding process. Trp residues which contribute more towards the free energy of binding have their accessible surface area reduced, on complex formation, for both the main-chain and side-chain atoms, whereas for the less important residues the reduction is restricted only to the aromatic ring of the side chain. The two categories of residues are also distinguished by the presence or absence of hydrogen bonds involving the Trp residue in the complex. A comparison of the observed change in the accessible surface area with the value calculated using an analytical expression provides another way of characterizing the Trp residues critical for binding and this has been used to identify such residues involved in binding non-proteinaceous molecules in protein structures.
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