Binding peptide

Both the R form or the T form of DnaK are known to have affinity to bind with abnormal peptide and proteins, but the contribution of each form is still unknown. To address this question, we modeled how HSP70 molecular chaperon works with peptide using data from $\sigma ^{32}$-Q132-Q144-C-IAANS , a 12 amino acid residue peptide. This model indicated that when 6000 molecules of this peptide were added to the model system at physiological steady state, about 4000 molecules will bind with DnaK.ATP in less than 1 second on average (Fig 3). And to our surprise that no DnaK.ADP can bind with this peptide. To test whether this was due to the simulation time is not longer enough, we run the model up to 1000 seconds, and still no DnaK.ADP.peptide complex was found (data not shown).

Figure 3: DnaK binds peptide

(a)	(b)
(c)	(d)