Role of Interfacial Water Molecules in Proline-rich Ligand Recognition by the Src Homology 3 Domain of Abl

Abstract

The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.The recognition of proline-rich sequences by protein-protein interaction modules, such as SH3 3 or WW domains, is one of the most common mechanisms by which specific, transient protein-protein interactions are established within the cell. SH3 domains are found in oncoproteins and proteins overexpressed in deregulated signaling pathways during cancer development and are also associated with other pathologies such as AIDS, osteoporosis, or inflammatory processes (1-2). Inhibitors of the interactions between SH3 domains and their partners have proved to be promising therapeutic agents, validating these domains as attractive targets for drug design (3-6). Nevertheless, despite the wealth of structural and functional information collected during the last 2 decades, the forces driving proline-rich ligand recognition by SH3 domains are still not fully understood.SH3 domains fold into a ␤-barrel structure composed of two orthogonal anti-parallel three-stranded ␤-sheets connected by three main loops (RT, n-Src, and distal loops). The binding site is a relatively flat, hydrophobic surface that consists of three shallow pockets. SH3 ligands typically contain the PpP motif (where and p are frequently hydrophobic and proline residues, respectively) and bind in a PPII conformation so that each of the P moieties packs tightly into one hydrophobic pocket formed by highly conserved aromatic residues on the surface of the domain. Additional interactions, which have been proposed to confer increased affinity and specificity, are established between residues flanking the core motif in the ligand and a third pocket delimited by the RT and n-Src loops, whose sequences vary among different SH3 domains (7-9).According to this description, the recognition of proline-rich sequences by SH3 domains, based primarily in the burial of hydrophobic surfaces in the ligand and SH3-binding site (7, 9), would be expected to present a thermodynamic signature dominated by the hydrophobic effect, with the main dr...

A thermodynamic characterization of the interaction of 8‐anilino‐1‐naphthalenesulfonic acid with native globular proteins: the effect of the ligand dimerization in the analysis of the binding isotherms

“…Despite the lack of structural information about the binding site of the ANS to the SH3 domain, our group has large structural information of this domain (Camara-Artigas et al, 2007;Palencia et al, 2010). The ITC experiments indicate one single site of binding and a potential-binding site is the one located at the shallow hydrophobic groove lined with highly conserved aromatic residues.…”

Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl

“…Therefore, the atypical DH and -TDS of nSH3:PRM interaction can be attributed to the water molecules located at the binding interface. Recent studies indicated that the binding interfaces of many SH3:PRM complexes include structured interfacial water molecules (31,72,75). The localization of water molecules was identified in three regions, including the 3 10 -helix, nSrc-loop, and RT-loop regions (75).…”

“…However, nSH3:PRM 758 complex does not contain water molecules at the sites identified in SH3 cAbl :PRM p41 complex. Only one interfacial water molecule in nSH3:PRM 758 is located at a similar site in the nSrc loop region, but this water site is characterized as a transient binding site, and it underwent fast exchange with bulk water in the molecular dynamic simulation of SH3 cAbl :PRM p41 complex (75).…”

“…Recent studies indicated that the binding interfaces of many SH3:PRM complexes include structured interfacial water molecules (31,72,75). The localization of water molecules was identified in three regions, including the 3 10 -helix, nSrc-loop, and RT-loop regions (75). The enthalpy contribution of water molecules in the 3 10 -helix region of SH3 cAbl :PRM p41 complex was estimated to be -4.78 kcal mol À1 (27).…”

G protein-coupled receptor kinase 4-induced cellular senescence and its senescence-associated gene expression profiling

“…In mammals, seven GRKs have been identified so far, which are classified into three main groups: the rhodopsin kinase subfamily (GRKs 1 and 7), the β-adrenergic receptor kinases subfamily (GRKs 2 and 3), and the GRK4 subfamily (GRKs 4, 5 and 6). Besides the role in receptor desensitization, GRKs are also found to be capable of phosphorylating various intracellular proteins including those that potentially modulate cell growth such as insulin receptor substrate 1 and p38MAPK (GRK2 [7,8]), p53 (GRK5 [9]), histone deacetylase 6 (GRK2 [10]) and IκBα (GRK6 [11]). Recently, Johnson et al reported that GRK4 subfamily members (GRK4/5/6) contain a functional nuclear localization sequence which can regulate their nuclear translocation and DNA-binding ability [12].…”