The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase

Abstract

Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in the class II complexes. The structures suggest a role of these water molecules in facilitating conformational changes in the SH3 domain to allow the binding of the class I or II peptides. In the third binding pocket these changes modify the cation-π and salt-bridge interactions that determine the affinity of the binding. Comparison of the water molecules involved in the binding of the peptides with previous reported hydration spots suggests a different pattern for the SH3 domains of the Src tyrosine kinase family.

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities

“…In most cases, the PxxP core is flanked by hydrophobic amino acids that improve van der Waals and hydrophobic interactions, and thus optimize the packing geometries of the Pro residues (Lim et al, 1994). Leu is the most prevalent flanking residue (Saraste and , and the representative structure of the class I/II domain FYN-1/1 bound to a peptide containing a À1 LP 0 xL +2 P +3 (+) motif reveals that the tandem repeats in the peptide pack against proximal and distal hydrophobic pockets formed by Y9, W34 and P46,or Y7 and Y49,respectively (Figure 4A) (Camara-Artigas et al, 2016).…”

Involvement of Local, Rapid Conformational Dynamics in Binding of Flexible Recognition Motifs

“…The variation observed among the spectra for the residues in the SH3 complexes generally reflected the three-fold symmetry of the PPII structure that places residues in comparable local environments (Figure b). , To aid comparison, the data are arranged in Figures – to stack the residues according to equivalent locations in the complexes. All of the nonmotif proline residues with side chains expected to point away from the protein surface, P(−1) and P2 of pNS5A and P(−2) and P1 of pPbs2 (Figure b), showed band B contributing ∼70% of the integrated absorbance and approximately equal contributions from bands A and C. The motif residues P0 and P3 of pNS5A, with side chains expected to align and pack within grooves of the SH3 domains, both showed solely bands B and C. However, the spectral subpopulations did not correspond for motif residues of pPbs2 or p­(P­(−2,1)­A)­Pbs2 as expected from the PPII structure.…”

“…MD simulations were performed with the AMBER16 software package and implemented the ff14SB force-field , and TIP3P model for water molecules . The initial coordinates for the protein–peptide complexes were generated using X-ray crystal structures. , Addition or changes to residues in the structural models were introduced using Chimera (UCSF). Following equilibration, one 100 ns production trajectory with 2 fs steps was run for each protein–peptide complex and analyzed with CPPTRAJ from AmberTools16 .…”

Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding

“…Different promiscuous enzymes rely on water-bridged ligand interactions for their differential substrate binding, such as RNAses (Ivanov et al, 2019), N-succinyl-amino-acid racemases (Martı ´nez-Rodrı ´guez et al, 2020) and cytochrome P450 (Madrona et al, 2013). This feature has also been observed for promiscuous solute-binding proteins (Clifton & Jackson, 2016;Matsuoka et al, 2015;Camara-Artigas et al, 2016), and in fact other AP superfamily members present water-mediated ligand interactions, such as the promiscuous ectonucleotidase NPP1 (Namasivayam et al, 2017;Dennis et al, 2020), endo-4S--carrageenan sulfatase (Hettle et al, 2018) and N-acetylgalactosamine-6-O-sulfatase (Ndeh et al, 2020). Our structural models clearly support the involvement of water-mediated interactions assisting choline positioning after hydrolysis, where Lys309, Asp386 and Asn75 might assist in leaving-group stabilization (Figs.…”