Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis

Computer Methods and Programs in Biomedicine

Volumn 104, Issue 2, 2011, Pages 70-80

  Hattersley, J G ^a   Perez Velazquez J ^a   Chappell, M J ^a   Bearup, D ^a   Roper, D ^a   Dowson, C ^a   Bugg, T ^a   Evans, N D ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Biomedical systems; Experiment design; Identifiability; Indistinguishability; MurC; Parameter identification

Indexed keywords

BIOMEDICAL SYSTEMS; EXPERIMENT DESIGN; IDENTIFIABILITY; INDISTINGUISHABILITY; MURC;

BIOCHEMISTRY; BIOSYNTHESIS; DESIGN OF EXPERIMENTS; EXPERIMENTS; RATE CONSTANTS;

STRUCTURAL ANALYSIS;

PEPTIDOGLYCAN;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CELL CYCLE PHASE; CHEMICAL REACTION KINETICS; CLINICAL EFFECTIVENESS; ENZYME SUBSTRATE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR MODEL; MURC REACTION; NONHUMAN; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; STRUCTURE ANALYSIS;

KINETICS; MODELS, THEORETICAL; PEPTIDOGLYCAN; SYSTEMS BIOLOGY;

EID: 80054123848     PISSN: 01692607     EISSN: 18727565     Source Type: Journal    
DOI: 10.1016/j.cmpb.2010.07.009     Document Type: Article

References (34)

1. Anderson M.S., Eveland S.S., Onishi H.R., Pompliano D.L. Kinetic mechanism of the Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme: use of a glutathione S-transferase fusion. Biochemistry 1996, 35:16264-16269.
2. Brown E.D., Marquardt J.L., Lee J.P., Walsh C.T., Anderson K.S. Detection and characterization of a phospholactoyl-enzyme adduct in the reaction catalyzed by udp-n-acetylglucosamine enolpyruvoyl transferase, murz. Biochemistry 1994, 33(September (35)):10638-10645.
3. Bellu G., Saccomani M., Audoly S., D'Angiò L. Daisy: a new software tool to test global identifiability of biological and physiological systems. Comp. Methods Prog. Biomed. Oct 2007, 88(1):52-61.
4. Chappell M.J., Godfrey K.R., Vajda S. Global identifiability of the parameters of nonlinear systems with specified inputs: a comparison of methods. Math. Biosci. Nov 1990, 102(1):41-73.
5. Cobelli C., Salvan A. Parameter estimation in a biological two compartment model-ii: a computer experimental study of the influence of the initial estimate in the parameter space, of some sampling protocols and of weighting factors. Math. Biosci. 1977, 37(3-4):267-274.
6. Franco R., Gavaldà M.T., Canela E.I. A computer program for enzyme kinetics that combines model discrimination, parameter refinement and sequential experimental design. Biochem. J. Sep 1986, 238(3):855-862.
7. El Zoeiby A., Sanschagrin F., Havugimana P.C., Garnier A., Levesque R.C. In vitro reconstruction of the biosynthetic pathway of peptidoglycan cytoplasmic precursor in Pseudomonas aeruginosa. FEMS Microbiol. Lett. 2001, 201:229-235.
8. Emanuele J.J., Jin H., Yanchunas J., Villafranca J.J. Evaluation of the kinetic mechanism of Escherichia coli uridine diphosphate-N-acetylmuramate:l-alanine ligase. Biochemistry 1997, 36:7264-7271.
9. érdi P., Tóth J. Mathematical Models of Chemical Reactions 1989, Princeton University Press.
10. Espenson J.H. Chemical Kinetics and Reaction Mechanisms 1995, McGraw-Hill, Singapore.
11. Evans N., Hattersley J., Hutchison C., Hu Y., Godfrey K., Bradwell A., Mead G., Chappell M. Modelling of haemodialysis in limiting serum free light chains in patients with renal failure. Proceedings of the 6th IFAC Symposium on Modelling and Control in Biomedical Systems 2006, 75-80. Elsevier. D. Feng, O. Dubois, J. Zaytoon, E. Carson (Eds.).
12. Evans N.D., Chapman M.J., Chappell M.J., Godfrey K.R. Identifiability of uncontrolled nonlinear rational systems. Automatica 2002, 38:1799-1805.
13. Evans N.D., Chappell M.J., Chapman M.J., Godfrey K.R. Structural indistinguishability between uncontrolled (autonomous) nonlinear analytic systems. Automatica 2004, 40:1947-1953.
14. Fersht A.R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding 1999, Freeman, New York.
15. Fisher F.M. Generalization of the rank and order conditions for identifiability. Econometrica 1959, 27(3):431-447.
16. Godfrey K.R., Chapman M.J. Identifiability and indistinguishability of linear compartmental models. Math. Comput. Simul. 1990, 32:273-295.
17. Godfrey K.R., DiStefano J.J. Identifiability of model parameters. Identifiability of Parametric Models 1987, 1-20. Pergamon Press, Ch. 1. E. Walter (Ed.).
18. Jacquez J.A. Red blood cell as glucose carrier: significance for placental and cerebral glucose transfer. Am. J. Physiol. 1984, 246(March (3 Pt 2)):R289-R298.
19. Kholodenko B.N., Bruggeman F.J., Sauro H.M. Mechanistic and modular approaches to modeling and inference of cellular regulatory networks. Systems Biology: Definitions and Perspectives 2005, Springer-Verlag. L. Alberghina, H. Westerhoff (Eds.).
20. Ljung L., Glad T. On global identifiability for arbitrary model parametrizations. Automatica 1994, 30:265-276.
21. Marmor S., Petersen C.P., Reck F., Yang W., Gao N., Fisher S.L. Biochemical characterization of a phosphinate inhibitor of Escherichia coli MurC. Biochemistry 2001, 40:12207-12214.
22. Nölting B. Protein Folding Kinetics: Biophysical Methods 1999, Springer, Berlin.
23. Pohjanpalo H. System identifiability based on the power series expansion of the solution. Math. Biosci. 1978, 41:21-33.
24. H. Pohjanpalo, Identifiability of deterministic differential models in state space, research report no. 56, Tech. rep., Technical Research Centre of Finland, Espoo, 1982.
25. Saccomani M., Audoly S., Bellu G., D'Angio L. A new differential algebra algorithm to test identifiability of nonlinear systems with given initial conditions. IEEE Conf. Decis. Control 2001, 4:3108-3113.
26. Saccomani M.P., Audoly S., D'Angio L. Parameter identifiability of nonlinear systems: the role of initial conditions. Automatica 2003, 39:619-632.
27. Sauer U., Heinemann M., Zamboni N. GENETICS: getting closer to the whole picture. Science 2007, 316(5824):550-551.
28. Schnell S., Chappell M.J., Evans N.D., Roussel M.R. The mechanism distinguishability problem in biochemical kinetics: the single-enzyme, single-substrate reaction as a case study. C. R. Biol. 2006, 329:51-61.
29. Segel I.H. Enzyme Kinetics 1993, Wiley Classics.
30. Snoep J.L., Westerhoff H.V. From isolation to integration, a systems biology approach for building the Silicon Cell. Systems Biology: Definitions and Perspectives 2005, Springer-Verlag. L. Alberghina, H. Westerhoff (Eds.).
31. Tunali E.T., Tarn T.J. New results for identifiability of nonlinear systems. IEEE T. Automat. Contr. 1987, 32:146-154.
32. Vajda S., Godfrey K.R., Rabitz R. Similarity transformation approach to identifiability analysis of nonlinear compartmental models. Math. Biosci. 1989, 93:217-248.
33. Walsh C. Molecular mechanisms that confer antibacterial drug resistance. Nature 2000, 406:775-781.
34. Walter E. Identifiability of State Space Models 1982, Springer-Verlag.