The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT

Abstract

RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains—the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling proteins. To prepare a structural basis for the characterization of the interactions of KIT with its signalling proteins (KIT INTERACTOME), we generated the 3D model of the full-length CD attached to the transmembrane helix. This generic model of KIT in inactive state was studied by molecular dynamics simulation under conditions mimicking the natural environment of KIT. With the accurate atomistic description of the multidomain KIT dynamics, we explained its intrinsic (intra-domain) and extrinsic (inter-domain) disorder and represented the conformational assemble of KIT through free energy landscapes. Strongly coupled movements within each domain and between distant domains of KIT prove the functional interdependence of these regions, described as allosteric regulation, a phenomenon widely observed in many proteins. We suggested that KIT, in its inactive state, encodes all properties of the active protein and its post-transduction events.

Does Generic Cyclic Kinase Insert Domain of Receptor Tyrosine Kinase KIT Clone Its Native Homologue?

“…In general, this analysis supports the secondary structure interpretation in KID assessed in the previous works by the DSSP, which was described as a helical fold composed of the α- and 3 10 -helices [ 29 , 38 , 39 ]. Identifying helicity is in good agreement between the two methods, DSSP and Ramachandran plot.…”

“…The conformational diversity of IDP KID can also be assessed via the Gibbs free energy ( ) landscape as it was applied in [ 29 , 38 ] for KID D and KID C . The representation provides a statistical overview of the KID conformational ensemble as a function of two reaction coordinates.…”

“…Similar to all RTKs, KIT contains a tyrosine kinase domain (TKD) crowned by several IDRs–juxtamembrane region (JMR), kinase insert domain (KID), and C-tail [ 28 ], which are inherently coupled [ 29 ]. In turn, the TKD of KIT is also composed of two sub-domains–N- and C-lobes—enriched by an IDR called activation (A-) loop, tightly collaborating in the activation/deactivation process [ 30 ].…”

“…The characterisation in terms of structural and biophysically related metrics of the conformational spaces generated by the large-scale MD simulations of KID which was considered to be (I) a generic macrocycle (KID GC ), (II) a cleaved isolated polypeptide (KID C ), and (III) a natively TKD-fused domain (KID D ) [ 29 , 39 ] ( Figure 1 ), inspired us to examine the crucial question: how does a KID evolve when studied in isolation compared to more complex architectures? While the allostery of a multidomain protein and the role of quaternary structure in modulating affinity is well established in many proteins [ 40 ], we asked whether the folding of the KID GC and its binding sites are in correct position for its functioning.…”

Receptor Tyrosine Kinase KIT: A New Look for an Old Receptor

“…We present the first structural model of the full-length cytoplasmic domain of KIT, which contains all regions involved in post-transduction processes, phosphorylation and binding of intracellular protein [5] (Figure 1). Rigorous analysis of the structure and dynamics of KIT, carried out using advanced mathematical methods, has led to a new vision of KIT as a multidomain protein made up of structurally ordered and disordered regions which together constitute a mutually and tightly driven engine [6,7]. This atomistic model of an allosterically regulated KIT is the first step for the reconstruction of its INTERACTOME, which consists of a set of KIT complexes with its signalling proteins, and DYNASOME, which constitutes an ensemble of intermediate conformations of KIT before, over and after the post-transduction processes.…”