Impacts of Different Metabolite Measurement Protocols on Estimating Parameters in Complex Photosynthetic Carbon Metabolism Models Wei Pan 1,2 John Fettig 3 Eric de Sturler 4 Xin-Guang Zhu 1,5, * 1 Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China 2 Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, 230027, China 3 Department of Theoretical and Applied Mechanics, University of Illinois at Urbana Champaign, Urbana, Illinois 61801 4 Department of Mathematics, VirginiaTech, Blacksburg, Virginia, 24601-0123 5 Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China Abstract Obtaining kinetic constants used in rate equations is a key component of building sys- tems model of metabolism. The availability of high throughput metabolomics measurements pro- vides an opportunity to use reverse engineering approach to estimate kinetic parameters such as maximal rate of enzyme V max especially. We presented a method of using two optimization al- gorithms respectively to estimate V max using time series measurements of incomplete metabolites combined with a metabolism model of photosynthetic carbon metabolism. The impact of choosing different experiment protocols on the accuracy of parameter estimation was evaluated. The result showed that using steady state initial condition and multiple measurements at each points can give the best estimates of the estimation results. In addition, the choice of time intervals of time series data does influence the estimation, i.e. focus on transient response or steady state part of time series data will be better for estimation. 1 Introduction Metabolism simulation is important for understanding the function of metabolism in the post-genomic era. Different metabolism models have been built, see review [1, 2]. Metabolism models can be used to testing hypothesis regarding certain dynamic behav- iors, asking “what if”questions, exploring better designs for achieving certain target func- tion, or modification of metabolic pathway for generation of new functions [3]. The model of photosynthetic carbon metabolism is one of such models. The individual steps of photosynthesis process have been studied in great detail, which have been used to build * Corresponding Author. Email: zhuxinguang@picb.ac.cn The Fourth International Conference on Computational Systems Biology (ISB2010) Suzhou, China, September 9–11, 2010 Copyright © 2010 ORSC & APORC, pp. 373–380