PYK2 senses calcium through a disordered dimerization and calmodulin-binding element

Momin, Afaque Ahmad Imtiyaz; Mendes, Tiago; Barthe, Philippe; Faure, Camille; Hong, Seungbeom; Yu, Pengpeng; Kadaré, Gress; Jaremko, Mariusz; Girault, Jean‐Antoine; Jaremko, Łukasz; Arold, Stefan T.

doi:10.1038/s42003-022-03760-8

Cited by 9 publications

(11 citation statements)

References 85 publications

(95 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Proteins can interact in several ways, including stable or defined associations such as domain‐domain, domain‐linear peptide, and coiled‐coil interactions, as well as fuzzy interactions where partners associate without forming stable complexes, as in membrane‐less condensates (Alberts, 2015; Momin et al., 2022). Strong interactions resemble those that stabilize protein 3D structures and are affected by mutations in the same way.…”

Section: Guidelines For Understanding Resultsmentioning

confidence: 99%

Leveraging AI Advances and Online Tools for Structure‐Based Variant Analysis

et al. 2023

Self Cite

View full text Add to dashboard Cite

Understanding how a gene variant affects protein function is important in life science, as it helps explain traits or dysfunctions in organisms. In a clinical setting, this understanding makes it possible to improve and personalize patient care. Bioinformatic tools often only assign a pathogenicity score, rather than providing information about the molecular basis for phenotypes. Experimental testing can furnish this information, but this is slow and costly and requires expertise and equipment not available in a clinical setting. Conversely, mapping a gene variant onto the three‐dimensional (3D) protein structure provides a fast molecular assessment free of charge. Before 2021, this type of analysis was severely limited by the availability of experimentally determined 3D protein structures. Advances in artificial intelligence algorithms now allow confident prediction of protein structural features from sequence alone. The aim of the protocols presented here is to enable non‐experts to use databases and online tools to investigate the molecular effect of a genetic variant. The Basic Protocol relies only on the online resources AlphaFold, Protein Structure Database, and UniProt. Alternate Protocols document the usage of the Protein Data Bank, SWISS‐MODEL, ColabFold, and PyMOL for structure‐based variant analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol: 3D Mapping based on UniProt and AlphaFoldAlternate Protocol 1: Using experimental models from the PDBAlternate Protocol 2: Using information from homology modeling with SWISS‐MODELAlternate Protocol 3: Predicting 3D structures with ColabFoldAlternate Protocol 4: Structure visualization and analysis with PyMOL

show abstract

Section: Guidelines For Understanding Resultsmentioning

confidence: 99%

Leveraging AI Advances and Online Tools for Structure‐Based Variant Analysis

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…31 Indeed, the recently reported Ca 2+ /calmodulin-induced dimerization of Pyk2 via the intrinsically disordered kinase—FAT linker is likely a critical factor in outcompeting the activity of cellular phosphatases for robust activation in vivo . 19…”

Section: Discussionmentioning

confidence: 99%

“…31 Indeed, the recently reported Ca 2+ /calmodulin-induced dimerization of Pyk2 via the intrinsically disordered kinase-FAT linker is likely a critical factor in outcompeting the activity of cellular phosphatases for robust activation in vivo. 19 We capitalized on the reconstitution of Pyk2 with defined phosphorylation states by exploring the conformational dynamics associated with nucleotide substrate binding and activation loop phosphorylation. Reported high-resolution structures of Pyk2 and FAK kinase domains are invaluable resources, but static snapshots may obscure the dynamics responsible for activation.…”

Section: Discussionmentioning

confidence: 99%

“…Whereas FAK is canonically activated by membrane lipid interactions and clustering at focal adhesions, 17,18 Pyk2 has adopted Ca 2+ sensitivity in neuronal cells. [19][20][21] However, the mechanistic details of activation remain unclear, especially in Pyk2. 22 Ultimately, activation involves autophosphorylation of a key tyrosine (FAK Y397, Pyk2 Y402) in the FERM-kinase linker.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation

Zanela

Woudenberg

Bello

et al. 2022

Preprint

View full text Add to dashboard Cite

Pyk2 is a multidomain non-receptor tyrosine kinase that undergoes a multistage activation mechanism. Activation is instigated by conformational rearrangements relieving autoinhibitory FERM domain interactions. The kinase autophosphorylates a central linker residue to recruit Src kinase. Pyk2 and Src mutually phosphorylate activation loops to confer full activation. While the mechanisms of autoinhibition are established, the conformational dynamics associated with autophosphorylation and Src recruitment remain unclear. We employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) and kinase activity profiling to map the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation. Nucleotide engagement stabilizes the autoinhibitory interface, while phosphorylation deprotects both FERM and kinase regulatory surfaces. Phosphorylation organizes active site motifs linking catalytic loop with activation segment. Dynamics of the activation segment anchor propagate to EF/G-helices to prevent reversion of the autoinhibitory FERM interaction. We employ targeted mutagenesis to dissect how phosphorylation-induced conformational rearrangements elevate kinase activity above the basal autophosphorylation rate.

show abstract

“…PyK2 phosphorylation is also modulated by the signaling messenger, intracellular Ca 2+ . PyK2 senses Ca 2+ signaling through calmodulin (CaM), and PyK2 has a CaM-binding motif [ 110 ]. In hypoxia, increases in the intracellular Ca 2+ concentration ([Ca 2+ ] i ) induced PyK2 phosphorylation [ 111 ].…”

Section: Pyk2-associated Molecules In Cancermentioning

confidence: 99%

Activated PyK2 and Its Associated Molecules Transduce Cellular Signaling from the Cancerous Milieu for Cancer Metastasis

Lee

Hong

2022

IJMS

View full text Add to dashboard Cite

PyK2 is a member of the proline-rich tyrosine kinase and focal adhesion kinase families and is ubiquitously expressed. PyK2 is mainly activated by stimuli, such as activated Src kinases and intracellular acidic pH. The mechanism of PyK2 activation in cancer cells has been addressed extensively. The up-regulation of PyK2 through overexpression and enhanced phosphorylation is a key feature of tumorigenesis and cancer migration. In this review, we summarized the cancer milieu, including acidification and cancer-associated molecules, such as chemical reagents, interactive proteins, chemokine-related molecules, calcium channels/transporters, and oxidative molecules that affect the fate of PyK2. The inhibition of PyK2 leads to a beneficial strategy to attenuate cancer cell development, including metastasis. Thus, we highlighted the effect of PyK2 on various cancer cell types and the distribution of molecules that affect PyK2 activation. In particular, we underlined the relationship between PyK2 and cancer metastasis and its potential to treat cancer cells.

show abstract

PYK2 senses calcium through a disordered dimerization and calmodulin-binding element

Cited by 9 publications

References 85 publications

Leveraging AI Advances and Online Tools for Structure‐Based Variant Analysis

Leveraging AI Advances and Online Tools for Structure‐Based Variant Analysis

Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation

Activated PyK2 and Its Associated Molecules Transduce Cellular Signaling from the Cancerous Milieu for Cancer Metastasis

Contact Info

Product

Resources

About