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Author(s): Denise Gameiro
Martín Pérez-Pérez
Gael Pérez-Rodríguez
Gonçalo Monteiro
Nuno F. Azevedo
Anália Lourenço
Title: Computational resources and strategies to construct single-molecule metabolic models of microbial cells
Issue Date: 2016
Abstract: Recent computational methodologies, such as individual-based modelling, pave the way to the search for explanatory insightinto the collective behaviour of molecules. Many reviews offer an up-to-date perspective about such methodologies, but little isdiscussed about the practical information requirements involved. The biological information used as input should be easilyand 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 ofmetabolic events at the molecular scale. The glycolysis pathway of Escherichia coli, which is one of the most studied pathwaysin Microbiology, serves as case study. This curation addressed structural information about E. coli (i.e. defining the simulationenvironment), the reactions forming the glycolysis pathway including the enzymes and the metabolites (i.e. the molecules tobe represented), the kinetics of each reaction (i.e. behavioural logic of the molecules) and diffusion parameters for all enzymesand 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 validationare detailed. Notably, the information from classical theories, such as enzymatic rates and diffusion coefficients, is translatedto simulation parameters, such as collision efficiency and particle velocity.
Related Information: info:eu-repo/grantAgreement/Autoriadade de Gestão do Programa Operacional Regional do Norte/Programas Integrados de IC&DT/NORTE-07-0124-FEDER-000025/(Bio) Chemical Engineering: Multi-Scale Approaches for Sustainable Environment and Health/LEPAE/CEFT - RL2
info:eu-repo/grantAgreement/FCT - Fundação para a Ciência e Tecnologia/Projetos Estratégicos/UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939/Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia/LEPABE
Document Type: Artigo em Revista Científica Internacional
Rights: restrictedAccess
Appears in Collections:FEUP - Artigo em Revista Científica Internacional

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