Prediction of protein-protein interaction sites using electrostatic desolvation profiles

Abstract

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces.

Figure 1

Calculation of the electrostatic desolvation of a neutral probe placed at the protein surface. (Upper) Electrostatic energies of protein + probe (left) and protein alone (right) are calculated from solutions of the finite-difference Poisson equation (see Methods), and the difference corresponds to the electrostatic penalty of placing the probe at the protein surface (dotted lines indicate the solvent-accessible surface used to define the dielectric boundary). The procedure is repeated for approximately evenly distributed probe placements at the protein surface (distance between probes ∼3 Å). Regions with the lowest electrostatic desolvation energy appear in red (light gray) and those with the highest penalty in blue (dark gray).

Figure 2

(A) Example of an enzyme inhibitor complex (pdb2MTA; blue (dark gray) for enzyme and green (light gray) for inhibitor). (B) Color-coded surface representation of the calculated electrostatic desolvation energy of neutral probes placed at the surface of the inhibitor (same view as in A). (C) Same as in B, but for the enzyme molecule. Red (light gray) indicates surface regions of low probe desolvation penalty and blue (dark gray) those of high desolvation penalties.

Figure 3

Mean electrostatic desolvation energy (in kJ·mol⁻¹ per residue and per probe) and standard deviation (error bars) for amino acids accessible to solvent (blue/dark gray) and those located at the protein-protein interface (red/light gray). Each probe is associated with the closest residue, and the energy value of a given amino acid is the average considering the total number of probes/residue. The energy/residue gives the average cost of desolvating a neutral probe in contact with the type of amino acid.

Figure 4

(Upper) Superposition of lysozyme/antibody complexes highlights the three different epitopes (includes pdb entries 1MLC, 1DQJ, 1FBI, 1BQL, 2IFF, 1JHL, 1KIQ, 1G7J, 1A2Y, and 1FDL), showing the lysozyme proteins and their solvent-accessible surface (blue/dark gray), the antibody Fab fragments (red/light gray), and the predicted sites of low electrostatic desolvation penalty (green/gray). The three different epitope regions are labeled A–C as explained in the text. (Lower) Prediction of centers of low probe desolvation (I, green/gray spheres) at the surface of the lysozyme, based on surface desolvation profiles obtained for the unbound lysozyme structure (pdb3LZH) shown in II. For comparison, the surface profiles calculated for two lysozyme structures in the bound form are shown (III, taken from pdb1MLC in complex with antibody D44.1, and IV, taken from pdb1DQJ in complex with antibody Hyhel-63). The surface is colored (gray-scale) according to the electrostatic desolvation energy, using VMD viewer software (54) (blue/dark gray, high probe desolvation penalties; red/light gray, low probe desolvation penalties). The view is approximately the same for each structure).