User talk:TheLarry/Notebook/Larrys Notebook/2009/09/02

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Steve Koch 01:05, 3 September 2009 (EDT): I couldn't exactly follow everything you were saying, but right now I think your initial solution was correct. The on-rate should depend linearly on concentration. You don't need to hard-wire in Michaelis-Menten kinetics...that arises because another step in the process becomes rate limiting when concentration of ATP (or whatever) goes above KM for ATP. I think your first simple assumption was correct.

TheLarry 01:10, 3 September 2009 (EDT): Then I am confused because at first i thought i should make everything linear with concentration. by everything i meant anything that binds to the head. ATP, ADP and P. Then i thought it should be michaelis menten. Then after reading the wiki page I thought it should be only ATP turning into ADP-P which is Michaelis since that is for an enzyme breaking a substrate down to a product. and the enzyme here is ATPase and the substrate ATP, the product being ADP. so that seemed like the only choice. unless that is true and there is a linearity with things binding to the head as well.

I initially thought exactly what you said above that no matter how fast the binding is. in this case the off rate will limit the overall speed.

Steve Koch 01:56, 3 September 2009 (EDT): Well, I'm not exactly sure what you're saying, but I still think you're right ha ha. Maybe it's a lot of terminology that's confusing you (and me). For sure at low [ATP], ATP binding will limit overall reaction rate (aka "turnover"). At very high [ATP] something else will limit reaction rate. In our case it's Pi release, right? But in principle, many other non-concentration dependent things could limit the rate (foot un-binding; ATP hydrolysis; ADP release; etc.). In fact, in the presence of force, one of those other steps will actually become rate limiting and Pi release won't matter. But with everything fixed except [ATP], and with the ATP binding rate linearly proportional to [ATP], I believe you'll see Michaelis Menten, even in your simulation as you have it now. Give it a try and see what happens! The Km maybe will be way off...but I bet it would work.

Steve Koch 01:56, 3 September 2009 (EDT): As for the others: [ADP], [Pi]. Those are product concentrations and I don't know how to describe their effect. I still think, though, that you should have the on-rate proportional their concentrations. In principle, the reverse reaction is the same as the forward. So, there will be some vmax for ATP synthesis. However, in the reverse case, since there are two substrates, it will be a second order reaction. I don't know where you go from there, but I think it doesn't matter in terms of how you program: it's still just on-rates proportional to concentration of species.