Computing the functional proteome: recent progress and future prospects for genome-scale models.

TitleComputing the functional proteome: recent progress and future prospects for genome-scale models.
Publication TypeJournal Article
Year of Publication2015
AuthorsO'Brien EJ, Palsson BO
JournalCurr Opin Biotechnol
Volume34
Pagination125-34
Date Published2015 Aug
ISSN1879-0429
KeywordsAnimals, Gene Expression, Genome, Humans, Models, Biological, Phenotype, Proteome
Abstract

Constraint-based models enable the computation of feasible, optimal, and realized biological phenotypes from reaction network reconstructions and constraints on their operation. To date, stoichiometric reconstructions have largely focused on metabolism, resulting in genome-scale metabolic models (M-Models). Recent expansions in network content to encompass proteome synthesis have resulted in models of metabolism and protein expression (ME-Models). ME-Models advance the predictions possible with constraint-based models from network flux states to the spatially resolved molecular composition of a cell. Specifically, ME-Models enable the prediction of transcriptome and proteome allocation and limitations, and basal expression states and regulatory needs. Continued expansion in reconstruction content and constraints will result in an increasingly refined representation of cellular composition and behavior.

DOI10.1016/j.copbio.2014.12.017
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/25576845?dopt=Abstract
Alternate JournalCurr. Opin. Biotechnol.
PubMed ID25576845
PubMed Central IDPMC4495013
Grant ListR01 GM057089 / GM / NIGMS NIH HHS / United States
R01 GM057089 / GM / NIGMS NIH HHS / United States
U01 GM102098 / GM / NIGMS NIH HHS / United States
Track(s): 
Bioinformatics and Systems Biology