||The last step in the synthesis of functional enzymes is the stochiometric formation of 155 macromolecular complexes. Macromolecular complexation is kinetically fast, and energetically favorable. Consequently, the model assumes that complexation is limited only by subunit availability, and proceeds to completion rapidly. In addition, we assume that each complex forms with the same specific rate. First, we use mass-action kinetics to compute the relative formation rate of each complex. Second we stochastically form complexes according the computed formation rates. This is repeated until no further complexes can form.
Forms macromolecular complexes are formed assuming
Complexation is highly energetically favorable and
Complexation is fast, and thus
Macromolecular complexes are formed to completion; that is until there are insufficient free monomers to form additional complexes.
Complexes are formed according to Monte Carlo simulation for each independent protein complex network. Outside this function the complete protein complex network is broken up into smaller networks
which share nxsDNA complexes or monomers (edu.stanford.covertlab.util.ComputationUtil.findNonInteractingRowsAndColumns).
The rate of building each complex is motivated by collision theory, and is equal to the product of the concentration of all monomers raised to the power of their stoichiometries within the complex. These rates are then normalized and used to select the next complex to form.
Typical k=105-106 M-1s-1 [PUB_0612]
k>109 have been measured [PUB_0612]
ΔGbind=ΔGpositional + ΔGintegration [PUB_0613]
ΔGpositional=15 kcal/mol [PUB_0613]
ΔGintegration=-17 kcal/mol [PUB_0613]