title: A mathematical approach to molecular organization and proteolytic disintegration of bacterial inclusion bodies.
abstract: The in vivo proteolytic digestion of bacterial inclusion bodies (IBs) and the kinetic analysis of the resulting protein fragments is an interesting approach to investigate the molecular organization of these unconventional protein aggregates. In this work, we describe a set of mathematical instruments useful for such analysis and interpretation of observed data. These methods combine numerical estimation of digestion rate and approximation of its high-order derivatives, modelling of fragmentation events from a mixture of Poisson processes associated with differentiated protein species, differential equations techniques in order to estimate the mixture parameters, an iterative predictor-corrector algorithm for describing the flow diagram along the cascade process, as well as least squares procedures with minimum variance estimates. The models are formulated and compared with data, and successively refined to better match experimental observations. By applying such procedures as well as newer improved algorithms of formerly developed equations, it has been possible to model, for two kinds of bacterially produced aggregation prone recombinant proteins, their cascade digestion process that has revealed intriguing features of the IB-forming polypeptides.
authors.affiliation: Departament de Matemàtica Aplicada IV, Universitat Politècnica de Catalunya, Campus Nord, Jordi Girona, 1-3, E08034 Barcelona, Spain. rcubarsi@mat.upc.es
authors.forename: R
authors.initials: R
authors.lastname: Cubarsi
authors.forename: M M
authors.initials: MM
authors.lastname: Carrió
authors.forename: A
authors.initials: A
authors.lastname: Villaverde
mesh_terms: D000465:Algorithms; D001709:Biotechnology / Q000379:methods*; D002479:Inclusion Bodies / Q000378:metabolism*; D007700:Kinetics; D008954:Models, Biological; D009716:Numerical Analysis, Computer-Assisted; D010446:Peptide Fragments / Q000378:metabolism; D010447:Peptide Hydrolases / Q000378:metabolism*; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000378:metabolism*; D014357:Trypsin / Q000378:metabolism
chemical_list: D010446:Peptide Fragments; D011994:Recombinant Proteins; D010447:Peptide Hydrolases; D014357:Trypsin