I promise I’ll get my top level post made soon—I just finished my committee meeting a few hours ago.
The short and dirty version is that Ling seems to completely ignore the entropy contribution to the Gibbs free energy change associated with ATP hydrolysis and throws out about 3⁄4 of the enthalpy contribution on the grounds that it is the energy of solvation of the protons that come off the newly deprotonated middle phosphate rather than the potential energy of the phosphate-phosphate bond itself, when that simply doesn’t matter and you just can’t do that when considering equilibrium and reaction rates and the ability of one reaction coupling to another to drive it. It’s not as if that one bond alone charges up a battery or something, the whole reaction occurs.
I honestly don’t know what to make of the assertion that ATP unwinds proteins just by complexing with unwound backbone. I’ve never seen that claim anywhere else, and I use ATP all the time via standard active-site hydrolysis reactions to drive DNA-building and DNA-modifying reactions as I make the DNA I put into my modified cells.
The simulation I was speaking of about the SNARES was indicating small hydration shells just a molecule or two wide, not large ones. It was interesting though in that it found that when the two membranes were forced into odd geometries and very close proximity by the SNARES forming a tight ring, the hydration shells were forced together to form ordered structures just a few molecules wide between the membranes before suddenly emptying the space. It’s been a while since I’ve seen that paper though, and I’d encourage you to look at the folding@home website and find it if you are curious and you don’t trust my memory (which I do not entirely trust myself, that’s not exactly my field and it’s been a few years).
Odd drug metabolism stuff eh? Want to move that to a PM?
I promise I’ll get my top level post made soon—I just finished my committee meeting a few hours ago.
The short and dirty version is that Ling seems to completely ignore the entropy contribution to the Gibbs free energy change associated with ATP hydrolysis and throws out about 3⁄4 of the enthalpy contribution on the grounds that it is the energy of solvation of the protons that come off the newly deprotonated middle phosphate rather than the potential energy of the phosphate-phosphate bond itself, when that simply doesn’t matter and you just can’t do that when considering equilibrium and reaction rates and the ability of one reaction coupling to another to drive it. It’s not as if that one bond alone charges up a battery or something, the whole reaction occurs.
I honestly don’t know what to make of the assertion that ATP unwinds proteins just by complexing with unwound backbone. I’ve never seen that claim anywhere else, and I use ATP all the time via standard active-site hydrolysis reactions to drive DNA-building and DNA-modifying reactions as I make the DNA I put into my modified cells.
The simulation I was speaking of about the SNARES was indicating small hydration shells just a molecule or two wide, not large ones. It was interesting though in that it found that when the two membranes were forced into odd geometries and very close proximity by the SNARES forming a tight ring, the hydration shells were forced together to form ordered structures just a few molecules wide between the membranes before suddenly emptying the space. It’s been a while since I’ve seen that paper though, and I’d encourage you to look at the folding@home website and find it if you are curious and you don’t trust my memory (which I do not entirely trust myself, that’s not exactly my field and it’s been a few years).
Odd drug metabolism stuff eh? Want to move that to a PM?