Computational resources and strategies to construct single-molecule metabolic models of microbial cells

• Type: Article in International Scientific Journal
• Date: 2016

Authors

Denise Gameiro (Author) Other; Martín Pérez-Pérez (Author) Other; Gael Pérez-Rodríguez (Author) Other; Gonçalo Monteiro (Author) Other; Nuno F. Azevedo (Author) FEUP; Anália Lourenço (Author) Other

Journal

Title: Briefings in Bioinformatics

Vol. 17 No. 5

Pages: 863-876

ISSN: 1467-5463

Publisher: Oxford University Press

Indexing

ISI Web of Knowledge

Scopus

Associated Projects

LEPAE/CEFT - RL2 - (Bio) Chemical Engineering: Multi-Scale Approaches for Sustainable Environment and Health

LEPABE - Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia

Other information

DOI: 10.1093/bib/bbv096

Abstract (EN): Recent computational methodologies, such as individual-based modelling, pave the way to the search for explanatory insight into the collective behaviour of molecules. Many reviews offer an up-to-date perspective about such methodologies, but little is discussed about the practical information requirements involved. The biological information used as input should be easily and routinely determined in the laboratory, publicly available and, preferably, organized in programmatically accessible databases. This review is the first to provide a systematic and comprehensive overview of available resources for the modelling of metabolic events at the molecular scale. The glycolysis pathway of Escherichia coli, which is one of the most studied pathways in Microbiology, serves as case study. This curation addressed structural information about E. coli (i.e. defining the simulation environment), the reactions forming the glycolysis pathway including the enzymes and the metabolites (i.e. the molecules to be represented), the kinetics of each reaction (i.e. behavioural logic of the molecules) and diffusion parameters for all enzymes and metabolites (i.e. molecule movement in the environment). Furthermore, the interpretation of relevant biological features, such as molecular diffusion and enzyme kinetics, and the connection of experimental determination and simulation validation are detailed. Notably, the information from classical theories, such as enzymatic rates and diffusion coefficients, is translated to simulation parameters, such as collision efficiency and particle velocity.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 14