AlphaFold2 Insights into c-Abl Transactivation by Adaptor c-Crk or Abi-1: Structural Forms, Active Site Types, and...

This study used AlphaFold2 to investigate allosteric structural changes during c-Abl transactivation. Two structural forms of c-Abl (positions of SH2 and SH3 domains relative to kinase domain) and four active site types (types 0-3) were identified. Key interactions were predicted between the c-Crk SH3 domain (CrkSH3N) and four c-Abl PxxPxK/R motifs, particularly the 612-617 motif, where residue 617R plays a critical role. A residue-level analysis using our developed PAE_json2excel tool supported these findings. The predicted CrkSH3N position relative to c-Abl kinase domain varied. The c-Abl's active site displayed structural flexibility, categorized into four types on the basis of the presence or absence of residues 286E and 381D within the hydrogen-bond distance (3.2 Å) to the side-chain nitrogen of 271K: type 0 (neither 286E nor 381D), type 1 (286E present), type 2 (381D present), and type 3 (both 286E and 381D present). The Abl(SH3W110K) may coincide with the presence of type 1 in the c-Abl mutant alone and may display types 0-3 when complexed. Multiple interactions between CrkSH3N and c-Abl PxxPxK/R motifs may coincide with the presence of type 2. These findings provide new insights into the dynamic flexibility of the c-Abl active site during c-Abl transactivation.