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Diedrichs2018 - A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response

ABSTRACT: A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response This model is described in the article: A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response. Diedrichs DR, Gomez JA, Huang CS, Rutkowski DT, Curtu R. Mol. Biol. Cell 2018 Apr; : mbcE17090565 Abstract: The vertebrate unfolded protein response (UPR) is characterized by multiple interacting nodes among its three pathways, yet the logic underlying this regulatory complexity is unclear. To begin to address this issue, we created a computational model of the vertebrate UPR that was entrained upon and then validated against experimental data. As part of this validation, the model successfully predicted the phenotypes of cells with lesions in UPR signaling, including a surprising and previously unreported differential role for the eIF2? phosphatase GADD34 in exacerbating severe stress but ameliorating mild stress. We then used the model to test the functional importance of a feed-forward circuit within the PERK/CHOP axis, and of cross-regulatory control of BiP and CHOP expression. We found that the wiring structure of the UPR appears to balance the ability of the response to remain sensitive to ER stress yet also to be rapidly deactivated by improved protein folding conditions. This model should serve as a valuable resource for further exploring the regulatory logic of the UPR. This model is hosted on BioModels Database and identified by: MODEL1803300000. To cite BioModels Database, please use: Chelliah V et al. BioModels: ten-year anniversary. Nucl. Acids Res. 2015, 43(Database issue):D542-8. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Danilo R. Diedrichs

PROVIDER: BIOMD0000000703 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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			Action	DRS
	BIOMD0000000703?filename=BIOMD0000000703-biopax2.owl	Owl
	BIOMD0000000703?filename=BIOMD0000000703-biopax3.owl	Owl
	BIOMD0000000703?filename=BIOMD0000000703-matlab.m	Other
	BIOMD0000000703?filename=BIOMD0000000703-octave.m	Other
	BIOMD0000000703?filename=BIOMD0000000703.m	Other

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A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response.

Diedrichs Danilo R DR Gomez Javier A JA Huang Chun-Sing CS Rutkowski D Thomas DT Curtu Rodica R

Molecular biology of the cell 20180418 12

The vertebrate unfolded protein response (UPR) is characterized by multiple interacting nodes among its three pathways, yet the logic underlying this regulatory complexity is unclear. To begin to address this issue, we created a computational model of the vertebrate UPR that was entrained upon and then validated against experimental data. As part of this validation, the model successfully predicted the phenotypes of cells with lesions in UPR signaling, including a surprising and previously unrep ...[more]

PMID: 29668363

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