An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase

Abstract

SHP2 is a protein tyrosine phosphatase (PTP) involved in multiple signaling pathways. Mutations of SHP2 can result in Noonan syndrome or pediatric malignancies. Inhibition of wild-type SHP2 represents a novel strategy against several cancers. SHP2 is activated by binding of a phosphopeptide to the N-SH2 domain of SHP2, thereby favoring dissociation of the N-SH2 domain and exposing the active site on the PTP domain. The conformational transitions controlling ligand affinity and PTP dissociation remain poorly understood. Using molecular simulations, we revealed an allosteric interaction restraining the N-SH2 domain into a SHP2-activating and a stabilizing state. Only ligands selecting for the activating N-SH2 conformation, depending on ligand sequence and binding mode, are effective activators. We validate the model of SHP2 activation by rationalizing modified basal activity and responsiveness to ligand stimulation of several N-SH2 variants. This study provides mechanistic insight into SHP2 activation and may open routes for SHP2 regulation.

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

“…In Figure 5B, the PMF shows a single free energy minimum at ~11 Å corresponding to an open cleft, in line with the 1AYD crystal structure of apo N-SH2 [31]. This finding is further supported by previous MD simulations of isolated N-SH2 [43], thereby clearly confirming that the cleft is open in the isolated N-SH2 domain.…”

“…In particular, Lys 91 side chain in BG loop forms salt bridges with charged residues of another replica, whereas the motion of the Tyr 66 side chain in EF loop is sterically hindered by the presence of other bulky side chains. Even the pY loop, which in absence of a phosphate group is typically modelled in a partially closed conformation, corresponding to an intermediate conformation between the α - and β -state [43], interacts with acidic side chains of Glu 313 and Glu 348 belonging to another protein chain. Therefore, the partially closed loops in the N-SH2 domain might have been stabilized by crystal contacts.…”

“…According to the “allosteric switch” model, the opening and the closure of the N-SH2 binding cleft is coupled with the activation or the stabilization of autoinhibited SHP2 [32, 39]. Considering that the activation of SHP2 presumably involves a free energy difference of several tens of kJ/mol [41, 43], it is mandatory to evaluate the energy required to open the binding cleft in different conditions.…”

“…On the other hand, the energy involved in binding cleft rearrangement is presumably many times smaller than the energy required to destabilize the N-SH2/PTP interface, promoting SHP2 activation. In fact, previous molecular dynamics simulations suggested that the complete displacement of N-SH2 away from the PTP active site requires an energy in the order of 70 kJ/mol [41, 43]. Hence, it is unlikely that rearrangement of the binding cleft are sufficient to drive SHP2 activation.…”

“…Recently, an allosteric interaction in N-SH2 has been proposed as an alternative mechanism of SHP2 activation [43]. Molecular dynamics (MD) simulations have shown that the N-SH2 domain may adopt two distinct conformations, denoted as α - and β -state, which differ primarily in the conformation of the central β -sheet.…”