Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B

Abstract

The C-terminus of Protein Tyrosine Phosphatase 1B (PTP1B) includes an α-helix α7), which forms an allosteric binding site 20 å away from the active site. This helix is specific to PTP1B and its truncation decreases the catalytic activity significantly. Here, molecular dynamics (MD) simulations in the presence and absence of α7 were performed to investigate the role played by α7. The highly mobile α7 was found to maintain its contacts with loop 11 (L11)α3 helix throughout the simulations. The interactions of Tyr152 on L11, Tyr176, Thr177 on the catalytically important WPD loop and Ser190 on α3 are important for the conformational stability and the concerted motions of the regions surrounding the WPD loop. In the absence of α7, L11 and WPD loop move away from their crystal structure conformations, resulting in the loss of the interactions in this region, and a decrease in the residue displacement correlations in the vicinity of WPD loop. Therefore, we suggest that one of the functionally important roles of α7 may be to limit the L11 and α3 motions, and, facilitate the WPD loop motions. Truncation of α7 in PTP1B is found to affect distant regions as well, such as the substrate recognition site and the phosphate binding-loop (P-loop), changing the conformations of these regions significantly. Our results show that the PTP1B specific α7 is important for the conformation and dynamics of the WPD loop, and also may play a role in ligand binding.

The Mechanism of Allosteric Inhibition of Protein Tyrosine Phosphatase 1B

“…In our simulation of the apo PTP1B, the three components maintained the triangular frame without allosteric site (Figure 4C), where the N-terminal helix α3 firmly coupled with loop 11 and helix α7 by the dynamical interactions among Tyr152, Tyr153, Ser190, Asn193, Gln288, Ser295 and Glu297. Olmez et al suggested that the stabilization of this structural feature through intensive interactions was closely associated with the physiological conformation of the WPD loop in yersina PTP and PTPL1 [24], and the missing of helix α7 in truncated PTP1B in modeling proposed the significant reduction in the flexibility of the catalytic WPD loop [24]. Consistent with above proposals, our MD simulations showed that upon the binding of compound- 3 , the intrinsic interactions among the triangular interactional region were disrupted and rearranged.…”

“…This finding indicated that the information exchange between helix α7 and C4 community in the allosteric compound- 3 bound state disappeared, with helix α7 departing from the core protein. The betweeness connecting helix α7 with C4 community includes the interactions from the hydrophobic WPD loop environment [19] as well as the triangular interactional region composed of the N-terminal helix α3, helix α7 and loop 11 [24]. Thus, these interactions could contain an allosteric pathway from helix α7 in the allosteric site to the WPD loop in the catalytic site.…”

“…The bi-phosphorylated form of the insulin receptor kinase (IRK), a natural substrate of PTP1B, was taken to model the PTP1B-substatre complex in their catalytically competent state to serve as a negative control for the WPD closed conformation [6]. In a previous study, helix α7 was determined to play a pivotal role in the allosteric regulation of PTP1B [24]. However, helix α7 is not represented in the crystal structures of 2HNP and 1T4J.…”

Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery

“…When benzofuran compounds bind this pocket, the activity of PTP1B is potently inhibited. Although initial molecular dynamics (MD) studies suggested that truncating and/or mutating helix α7 affects WPD loop closure (Li et al, 2014; Olmez and Alakent, 2011; Shinde and Sobhia, 2013), there is still no molecular model that explains how perturbations from the allosteric site are propagated to the active site. Furthermore, the role of dynamics and/or conformational changes in this process remain essential, open questions.…”

Frequency Response of a Protein to Local Conformational Perturbations

“…The target structure in TMD 1 simulation was altered between WPD open and WPD closed structures at 2.5 ns intervals, thus the frequency of the targeting function ( f 0 ) was 0.2 ns −1 (Figure 1A). The highly mobile region comprising residues 281 to 298 (α7 and the loop connecting α6 and α7) was not included in the structural analyses because of the disordered nature of this region [44], [52]. Aligning the C α atoms of Glu2 to Ala278, RMSD from the crystal structure of PTP1B leveled off between 1.5 and 2.0 Å, showing that protein structure was maintained in both simulations (Figure S2A).…”