Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain

Abstract

Protein-protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains, such as Src Homology 2 and 3 (SH2 and SH3) domains, which bind to specific sequence and structural motifs. It is important but challenging to determine the binding specificity of these domains accurately and to predict their physiological interacting partners. In this study, the interactions between 35 peptide ligands (15 binders and 20 non-binders) and the Abl SH3 domain were analyzed using molecular dynamics simulation and the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. The calculated binding free energies correlated well with the rank order of the binding peptides and clearly distinguished binders from non-binders. Free energy component analysis revealed that the van der Waals interactions dictate the binding strength of peptides, whereas the binding specificity is determined by the electrostatic interaction and the polar contribution of desolvation. The binding motif of the Abl SH3 domain was then determined by a virtual mutagenesis method, which mutates the residue at each position of the template peptide relative to all other 19 amino acids and calculates the binding free energy difference between the template and the mutated peptides using the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. A single position mutation free energy profile was thus established and used as a scoring matrix to search peptides recognized by the Abl SH3 domain in the human genome. Our approach successfully picked ten out of 13 experimentally determined binding partners of the Abl SH3 domain among the top 600 candidates from the 218,540 decapeptides with the PXXP motif in the SWISS-PROT database. We expect that this physical-principle based method can be applied to other protein domains as well.

The Capable ABL: What Is Its Biological Function?

“…The field searched for ABL-SH3-binding proteins and discovered the PXXP motif for binding to the SH3 domain (26). A large number of ABL-SH3-binding proteins have now been identified either empirically or by computational prediction (1,27). Although initially reported as "inhibitors," many of those ABL-SH3-binding proteins have turned out to be ABL substrates (1).…”

Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models

“…Recently, the bindings between the Abl SH3 domain and 35 peptide ligands (10 binders and 20 non-binders) were analyzed using MD simulations and MM-PBSA calculations by Hou et al [80]. The calculated binding free energies correlated well with the rank order of the binding peptides and clearly distinguished binders and non-binders.…”

Proteome-wide Detection of Abl1 SH3-binding Peptides by Integrating Computational Prediction and Peptide Microarray

“…All 10-residue-long peptides in the UniProt database (7) were scored using the position-specific scoring matrix (PSSM) 1 that we developed in a previous study (8). The PSSM was a 10 ϫ 20 matrix that represented the difference in binding free energies between the mutated peptides and the template peptide APSYSPPPPP (see details in Ref.…”

“…The PSSM was a 10 ϫ 20 matrix that represented the difference in binding free energies between the mutated peptides and the template peptide APSYSPPPPP (see details in Ref. 8). Briefly, we calculated the binding free energy of the template peptide based on the crystal structure (Protein Data Bank entry 1bbz) using molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA).…”