Probing the effect of point mutations at protein-protein interfaces with free energy calculations - PubMed (original) (raw)

Probing the effect of point mutations at protein-protein interfaces with free energy calculations

Martin Almlöf et al. Biophys J. 2006.

Abstract

We have studied the effect of point mutations of the primary binding residue (P1) at the protein-protein interface in complexes of chymotrypsin and elastase with the third domain of the turkey ovomucoid inhibitor and in trypsin with the bovine pancreatic trypsin inhibitor, using molecular dynamics simulations combined with the linear interaction energy (LIE) approach. A total of 56 mutants have been constructed and docked into their host proteins. The free energy of binding could be reliably calculated for 52 of these mutants that could unambiguously be fitted into the binding sites. We find that the predicted binding free energies are in very good agreement with experimental data with mean unsigned errors between 0.50 and 1.03 kcal/mol. It is also evident that the standard LIE model used to study small drug-like ligand binding to proteins is not suitable for protein-protein interactions. Three different LIE models were therefore tested for each of the series of protein-protein complexes included, and the best models for each system turn out to be very similar. The difference in parameterization between small drug-like compounds and protein point mutations is attributed to the preorganization of the binding surface. Our results clearly demonstrate the potential of free energy calculations for probing the effect of point mutations at protein-protein interfaces and for exploring the principles of specificity of hot spots at the interface.

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Figures

FIGURE 1

Scatter diagrams of the calculated versus the experimental binding free energy (kcal/mol) using model A for binding of P1 variants of OMTKY3 to chymotrypsin and elastase and BPTI to trypsin.

FIGURE 2

Surface representation of the crystal structure of trypsin in complex with the P1 Trp variant of BPTI (Protein Data Bank accession code 3BTW). BPTI is shown in tan with the P1 residue colored red.

FIGURE 3

Representative snapshot of most and least favored P1 variants bound to chymotrypsin (A and B), elastase (C and D), and trypsin (E and F). Only the binding loop of the inhibitors and the molecular surface of the proteinases are shown for clarity.

FIGURE 4

Binding of OMTKY3 P1 Trp (A) results in major structural rearrangements at the S1 site of elastase compared to accommodation of OMTKY3 P1 Ala (B). Only the binding loop of OMTKY3 and the molecular surface of HLE are shown for clarity.

FIGURE 5

(A) The contribution of binding-site preorganization to the binding free energy versus the difference in Lennard-Jones energies between bound and free states. The P1 variants of OMTKY3 complexed with chymotrypsin are shown as diamonds. Small ligands (ligands to p450cam and benzamidine-like ligands) are shown as stars. (B) The size dependence of the electrostatic preorganization energy contribution to the binding free energy for P1 variants of OMTKY3 binding to chymotrypsin (⋄) and small ligands binding to their receptors (▴). On the horizontal axis is the number of heavy atoms in the P1 amino acid or small ligand.

References

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Probing the effect of point mutations at protein-protein interfaces with free energy calculations - PubMed (original) (raw)