The binding of P1 variants of bovine pancreatic trypsin inhibitor (BPTI) to
trypsin has been investigated by means of molecular dynamics simulations.
The specific interaction formed between the amino acid at the primary bindi
ng (P1) position of the binding loop of BPTI and the specificity pocket of
trypsin was estimated by use of the linear interaction energy (LTE) method.
Calculations for 13 of the naturally occurring amino acids at the P1 posit
ion were carried out, and the results obtained were found to correlate well
with the experimental binding free energies. The LIE calculations rank the
majority of the 13 variants correctly according to the experimental associ
ation energies and the mean error between calculated and experimental bindi
ng free energies is only 0.38 kcal/mole, excluding the Glu and Asp variants
, which Me associated with some uncertainties regarding protonation and the
possible presence of counter-ions. The three-dimensional structures of the
complex with three of the P1 variants (Asn, Tyr, and Ser) included in this
study have not at present been solved by any experimental techniques and,
therefore, were modeled on the basis of experimental data from pi variants
of similar size. Average structures were calculated from the MD simulations
, from which specific interactions explaining the broad variation in associ
ation energies were identified. The present study also shows that explicit
treatment of the complex water-mediated hydrogen bonding network at the pro
tein-protein interface is of crucial importance for obtaining reliable bind
ing free energies, The successful reproduction of relative binding energies
shows that this type of methodology can be very useful as an aid in ration
al design and redesign of biologically active macromolecules.