A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition
Catherine
Lloyd
Auckland Bioengineering Institute, The University of Auckland
Model Status
This CellML model is known to run in both OpenCell and COR to recreate the results in the published paper. The units have been checked and they are consistent. Please note that many of the figures in the paper are complex and requite special simulation conditions. This particular CellML model represents the basic core model presented in the paper. Initial conditions can be modified to generate more complex results. We thank the model author Prakash Vempati for his assistance in getting this CellML model to run.
Model Structure
ABSTRACT: Matrix metalloproteinases (MMPs) are a class of extracellular and membrane-bound proteases involved in an array of physiological processes including angiogenesis. We present a detailed computational model of MMP9 activation and inhibition. Our model is validated to existing biochemical experimental data. We determine kinetic rate constants for the processes of MMP9 activation by MMP3, MMP10, MMP13, and trypsin, inhibition by the tissue inhibitors of metalloproteinases (TIMPs) TIMP1 and TIMP2, and MMP9 deactivation. This computational approach allows us to investigate discrepancies in our understanding of the MMP9
The original paper reference is cited below:
A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition, Prakash Vempati, Emmanouil D. Karagiannis, and Aleksander S. Popel , 2007, The Journal of Biological Chemistry
, 282, 37585-37596. PubMed ID: 17848556
model diagram
Schematic diagram of the biochemical reaction network for MMP9 activation and inhibition spanning MMP9, MMP3, TIMP1, and TIMP2. pM9, pro-MMP9; M3, MMP3; M9, MMP9; T1, TIMP1; T2, TIMP2; Tr, Trypsin.
trypsin-proMMP9-TIMP1Tr_pM9_T12007-12-28matrix metalloproteinase-3-promatrix metalloproteinase-9 complexMMP3-proMMP9M3_pM9trypsin-proMMP9Tr_pM9The University of Auckland, Bioengineering Institutematrix metalloproteinase-9MMP9M9promatrix metalloproteinase-9-tissue inhibitor of metalloproteinase-1 complexproMMP9-TIMP1pM9_T1This cellML model is known to run in both PCEnv and COR to recreate the results in the published paper. The units have been checked and they are consistent. Please note that many of the figures in the paper are complex and requite special simulation conditions. This particular CellMl model represents the basic core model presented in the paper. Initial conditions can be modified to generate more complex results. We thank the model author Prakash Vempati for his assistance in getting this CellML model to run.matrix metalloproteinase-3MMP3M3MMP9-TIMP1-MMP3M9_T1_M3
Vempati et al.'s 2007 biochemical model of the matrix metalloproteinase 9 activation and inhibition.
trypsinTrAleksanderSPopelCatherineMayLloydThe Journal of Biological Chemistrypromatrix metalloproteinase-9proMMP9pM9TIMP1tissue inhibitor of metalloproteinase-1T117848556100000144000systems biologyMMP9MMP3TIMPangiogenesissignal transductionMMPbiochemical kineticsproMMP9-TIMP1-MMP3pM9_T1_M3c.lloyd@auckland.ac.nzmatrix metalloproteinase-3-promatrix metalloproteinase-9-tissue inhibitor of metalloproteinase-1 complexMMP3-proMMP9-TIMP1M3_pM9_T1MMP3-proMMP9-TIMP1-MMP3M3_pM9_T1_M32008-07-08T00:00:00+00:00PrakashtVempati37596A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition28237585MMP9-TIMP1matrix metalloproteinase-9-tissue inhibitor of metalloproteinase-1 complexM9_T1keywordCatherine LloydMMP3-TIMP1matrix metalloproteinase-3-tissue inhibitor of metalloproteinase-1 complexM3_T1The University of AucklandAuckland Bioengineering Institutetrypsin-proMMP9-TIMP1-MMP3Tr_pM9_T1_M3EmmanouilDKaragiannisinactivated MMP9-TIMP1inactivated matrix metalloproteinase-9-tissue inhibitor of metalloproteinase-1 complexM9_T1_starCatherine LloydThis is the CellML description of Vempati et al.'s 2007 biochemical model of the matrix metalloproteinase 9 activation and inhibition.