Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The EGF receptor kinase domain is strongly activated by weak dimerization

ABSTRACT: The tyrosine kinase domain (TKD) of the epidermal growth factor receptor (EGFR) activates via a unique mechanism of asymmetric dimerization with a partner EGFR TKD rather than a more typical mechanism of activation loop phosphorylation. There is an EGFR oncogenic variant found in patients in which the TKD region of EGFR has been duplicated, resulting in a construct in which two EGFR kinase domain are linked via a natural peptide linker (KDD). KDD is the best approximation of the natural process of EGFR kinase dimerization and activation as well as an example of bona fide oncogenic activation. We studied the structure, enzyme properties, and structural dynamics of KDD to gather insights into the EGFR kinase activation process and its oncogenicity.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zaritza Petrova

LAB HEAD: Mark Lemmon

PROVIDER: PXD065135 | Pride | 2025-11-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	032222_KDD_exp2.DnX	Other
	201008_EGFR_KDD_0sec_01.raw.zip	Raw
	201008_EGFR_KDD_0sec_01_IA_final_peptide.csv	Csv
	201008_EGFR_KDD_0sec_02.raw.zip	Raw
	201008_EGFR_KDD_0sec_02_IA_final_peptide.csv	Csv

Items per page:

1 - 5 of 64

Similar Datasets

The strutural dynamics of EGFR Exon 19 mutants

Project description:Tyrosine kinase inhibtors are used to treat non-small cell lung cancers (NSCLC) driven by epidermal growth factor receptor (EGFR) mutations in the tyrosine kinase domain (TKD). We characterized the dynamics of purified EGFR exon 19 kinase domain mutants by HDX-MS with or withour erlotinib, one of the first-generation TKIs.

2023-03-11 | PXD037448 | Pride

Biochemical and Structural Basif for Differential Inhibitor Sensitivity of EGFR with Distinct Exon 19 Mutaions

2023-03-11 | PXD037374 | Pride

The structural dynamics of EGFR exon 19 mutants

Project description:Tyrosine kinase inhibitors (TKIs) are used to treat non-small cell lung cancers (NSCLC) driven by epidermal growth factor receptor (EGFR) mutations in the tyrosine kinase domain (TKD). TKI responses vary across tumors driven by the heterogeneous group of exon 19 deletions and mutations, but the molecular basis for these differences is not understood. We characterized the dynamics of the selected EGFR exon 19 mutants by HDX-MS to study the molecular basis of TKI sensitivity and tolerance.

2023-03-11 | PXD037355 | Pride

Molecular mechanism of β-arrestin-2 pre-activation by phosphatidylinositol 4,5-bisphosphate

Project description:Arrestins are a protein family that regulate G protein-coupled receptor (GPCR) signaling, with four distinct members in mammals (arrestin 1–4). Phosphorylated residues of G protein-coupled receptors bind to the N-domain of arrestin, resulting in C-terminus release. This induces further allosteric conformational changes, such as polar core disruption, alteration of interdomain loops, and domain rotation, which transform arrestins into the receptor-activated state. It is widely accepted that arrestin activation occurs by conformational changes propagated from the N- to the C-domain. However, recent studies have revealed that binding of phosphatidylinositol 4,5-bisphosphate (PIP2) to the C-domain transforms arrestins into an active state. In this study, we aimed to elucidate the mechanisms underlying PIP2-induced arrestin activation. We compared the conformational changes of β-arrestin-2 upon binding of PIP2 or phosphorylated C-tail peptide of vasopressin receptor type 2 (V2Rpp) using hydrogen/deuterium exchange mass spectrometry (HDX-MS). Introducing point mutations on the potential routes of the allosteric conformational changes and analyzing these mutant constructs with HDX-MS revealed that PIP2-binding at the C-domain affects the back loop, which destabilizes the gate loop and β-strand XX to transform β-arrestin-2 into the pre-active state.

2024-07-15 | PXD049391 | Pride

Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling

Project description:The structural dynamics of purified wild type and mutant EFR were probed by HDX-MS.

2024-06-27 | PXD049215 | Pride

Structural mechanism underlying primary and secondary coupling between GPCRs and the Gi/o family

Project description:G protein-coupled receptors (GPCRs) are the largest receptor superfamily that can propagate various extracellular stimulus into cells by coupling with heterotrimeric G proteins. G proteins are divided into four families, Gs, Gi/o, Gq/11 and G12/13, which are responsible for the transduction of discrete downstream signaling pathways. Interestingly, one receptor can couple to more than one G protein subtype with different coupling efficiency or kinetics; coupling with the highest efficiency and/or kinetics is known as ‘primary coupling’ whereas the one with lower efficiency and/or slower kinetics is known as ‘secondary coupling’. Due to its significance in human physiology, there has been a great effort to elucidate the precise mechanism of GPCR-G protein coupling, however, the complex nature of GPCR and G protein interaction raises more unanswered questions. Here, we utilized hydrogen/deuterium exchange mass spectrometry (HDX-MS) to understand the molecular mechanism underlying primary and secondary Gi/o coupling using muscarinic acetylcholine receptor type 2 (M2R) and β2-adrenergic receptor (β2AR) as the primary and secondary Gi/o-coupling receptors, respectively. Results showed the engagement of the distal C-terminus of Gi/o with the receptor differentiates primary and secondary Gi/o couplings. In addition, the interaction between the intracellular loop 2 (ICL2) of the receptor and Gi/o in primary Gi/o coupling is not as critical as in primary Gs coupling.

2020-07-02 | PXD019367 | Pride

Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq

Project description:Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets given their involvement in numerous physiological processes and diseases. Although a cryo-electron microscopy study previously defined the structure of the M3-miniGq complex, the lack of information on the intracellular loop 3 (ICL3) of M3 and α-helical domain (AHD) of Gαq has made it difficult to comprehend the molecular mechanism of M3-Gq coupling fully. Here, we present the molecular mechanism underlying the dynamic interactions between the wild-type full-length M3 and heterotrimeric Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. This study suggests potential binding interfaces between M3 and Gq in pre-assembled and fully active nucleotide-free complexes. In addition to well-known binding interfaces, we observed the interaction of long ICL3 with Gβγ. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling. Therefore, we propose a comprehensive molecular mechanism of M3-Gq coupling by analyzing previously well-defined binding interfaces and neglected regions, such as M3 ICL3 and the Gαq AHD.

2024-05-22 | PXD042562 | Pride

Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization

Project description:Upon ligand binding, bone morphogenetic protein (BMP) receptors form active tetrameric complexes, comprised of two type I and two type II receptors, which then transmit signals to SMAD proteins. The link between receptor tetramerization and the mechanism of kinase activation, however, has not been elucidated. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations, combined with analysis of SMAD signaling, we show that the kinase domain of the type I receptor ALK2 and type II receptor BMPR2 form a heterodimeric complex via their C-terminal lobes. Formation of this dimer is essential for ligand-induced receptor signaling and is targeted by mutations in BMPR2 in patients with pulmonary arterial hypertension (PAH). We further show that the type I/type II kinase domain heterodimer serves as the scaffold for assembly of the active tetrameric receptor complexes to enable phosphorylation of the GS domain and activation of SMADs.

2021-08-16 | PXD022944 | Pride

Molecular mechanism of ssDNA-mediated allosteric activation of the WYL-domain containing transcription regulator, DriD

Project description:WYL domain containing transcription factors play critical roles in regulating fundamental processes in bacterial physiology. The Caulobacter crescentus DriD protein is a WYL transcription regulator recently shown to activate a DNA damage response pathway that is independent of the major bacterial SOS repair system. DriD is a 327-residue homodimer and contains a unique fold composed of a N-terminal winged helix-turn-helix DNA binding domain (DNABD), linker region, three-helix bundle (3HB), WYL domain, and WYL C-terminal extension (WCX) dimerization domain. DriD binds ssDNA, which acts as a genotoxic signal that accumulates during double stranded DNA breaks, within its WYL domain. This interaction activates target DNA binding by DriD. However, the molecular mechanism by which ssDNA binding to the WYL domain, which is ~50 Å from the DNABD, activates DriD is unknown. Here, we describe structural and biochemical studies that indicate a novel allosteric mechanism of DriD activation. These data indicate that there is an inhibitory interaction formed between the DNABD and 3HB in the apo form, which is freed upon ssDNA binding. DriD represents the largest class of WYL regulator and thus can serve as a model for understanding activation by WYL activators including those in pathogenic bacteria.

2025-04-14 | PXD056334 | Pride

Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states

Project description:Full-length BTK has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology (PHTH) domain and the long linker that includes proline-rich regions (PRR)) contribute to BTK regulation remains unclear. Here we produce crystals of full-length BTK for the first time. Despite efforts to stabilize the autoinhibited state, the diffraction data still reveals only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. CryoEM data, on the other hand, provides a glimpse of the PHTH domain. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region; the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. Upon disassembly of the SH3-SH2-kinase core, an autoinhibitory site on the kinase domain becomes available for PHTH domain binding. This PHTH/kinase autoinhibitory contact is then lost upon interaction of PHTH with PIP3. Membrane-induced dimerization activates BTK and here we solve a structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural insight into full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.

2024-05-24 | PXD041657 | Pride