| from typing import Optional | |
| from vcutils.vcell_pipeline.citation import getCitation, CitationInfo, getSuggestedProjectName | |
| def test_citation() -> None: | |
| citation: Optional[CitationInfo] = getCitation(pubmedid="35367415") | |
| assert citation is not None | |
| assert citation.author == "Nosbisch, Jamie L" | |
| assert citation.title == ("A kinetic model of phospholipase C-γ1 linking structure-based insights to dynamics of " | |
| "enzyme autoinhibition and activation") | |
| assert citation.year == 2022 | |
| assert citation.journal == "J Biol Chem" | |
| suggestedProjectName = getSuggestedProjectName(bm_key="12345", pub_info=None, citation_info=citation) | |
| assert suggestedProjectName == "VCDB_12345_Nosbisch_JBiolChem_2022" | |
| def test_get_citation(): | |
| pubmdeid = "35367415" | |
| expected_title = ("A kinetic model of phospholipase C-γ1 linking structure-based insights to dynamics of " | |
| "enzyme autoinhibition and activation") | |
| expected_year = 2022 | |
| expected_journal = "J Biol Chem" | |
| expected_author = "Nosbisch, Jamie L" | |
| expected_abstract = ("Phospholipase C-γ1 (PLC-γ1) is a receptor-proximal enzyme that promotes signal transduction " | |
| "through PKC in mammalian cells. Because of the complexity of PLC-γ1 regulation, a two-state " | |
| "(inactive/active) model does not account for the intricacy of activation and inactivation " | |
| "steps at the plasma membrane. Here, we introduce a structure-based kinetic model of PLC-γ1, " | |
| "considering interactions of its regulatory Src homology 2 (SH2) domains and perturbation of " | |
| "those dynamics upon phosphorylation of Tyr783, a hallmark of activation. For PLC-γ1 " | |
| "phosphorylation to dramatically enhance enzyme activation as observed, we found that high " | |
| "intramolecular affinity of the C-terminal SH2 (cSH2) domain-pTyr783 interaction is critical, " | |
| "but this affinity need not outcompete the autoinhibitory interaction of the cSH2 domain. " | |
| "Under conditions for which steady-state PLC-γ1 activity is sensitive to the rate of Tyr783 " | |
| "phosphorylation, maintenance of the active state is surprisingly insensitive to the " | |
| "phosphorylation rate, since pTyr783 is well protected by the cSH2 domain while the enzyme is " | |
| "active. In contrast, maintenance of enzyme activity is sensitive to the rate of PLC-γ1 " | |
| "membrane (re)binding. Accordingly, we found that hypothetical PLC-γ1 mutations that either " | |
| "weaken autoinhibition or strengthen membrane binding influence the activation kinetics " | |
| "differently, which could inform the characterization of oncogenic variants. Finally, we used " | |
| "this newly informed kinetic scheme to refine a spatial model of PLC/PKC polarization during " | |
| "chemotaxis. The refined model showed improved stability of the polarized pattern while " | |
| "corroborating previous qualitative predictions. As demonstrated here for PLC-γ1, this " | |
| "approach may be adapted to model the dynamics of other receptor- and membrane-proximal " | |
| "enzymes.") | |
| citation = getCitation(pubmedid=pubmdeid) | |
| assert citation is not None | |
| assert citation.abstract == expected_abstract | |
| assert citation.author == expected_author | |
| assert citation.title == expected_title | |
| assert citation.year == expected_year | |
| assert citation.journal == expected_journal | |