qPIPSA: Relating enzymatic kinetic parameters and interaction fields

Background: The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results: We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for exampl...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Razif R. Gabdoulline, Matthias Stein, Rebecca C. Wade
• Keywords: BMCBI 2007, Enzyme, Kinetic Parameters, Protein