4 ms·

No, it converts the proton concentration gradient into mechanical energy. The ATP synthase also works that way. The ADP and Pi are mechanically squeezed agains

by pygy_ 13y ago

No, it converts the proton concentration gradient into mechanical energy. The ATP synthase also works that way. The ADP and Pi are mechanically squeezed against each other in order to create the covalent bound. See the last two videos of [0] for the general process. The first three focus on details. [0] http://www.mrc-mbu.cam.ac.uk/category/slideshows/atpmovies http://www.mrc-mbu.cam.ac.uk/category/slideshows/atpmovies

dekhn 13y ago
"ADP and Pi are mechanically squeezed against each other in order to create the covalent bond." I have a PhD in Biophysics. If I ever said "ADP and Pi were squeezed together", I'd have been laughed out of journal club. The fine details of the reaction coordinate are still being argued about. I'll grant you there are no canonical gears as a mechanical engineer would recognize them. I wasn't talking about the motive coupling. But a number of the physical structures (proteins) that couple the anchoring to the moving body have gear like properties. These are used to orient and clock the moving body in its cycle. OK, I'll up it a notch since you guys are being picky. There are motor proteins which use ATP hydrolysis to do directed (non-random) motion. One of the plausible (IIRC it's passe now) mechanisms involved coupling the ATP hydrolysis free energy to a physical ratchet-like mechanism which, while didn't physically look like a gear when you looked at static crystal structures, seemed to behave like one using various subtle time-resolved mechanisms.
- pygy_ 13y ago
  Doctor of medicine here, with basic notions of chemistry and biochemistry from courses I took 16 years ago. I sure know what I'm talking about! ;-) More seriously, I had inferred the squeezing from the videos I linked to. If I understand properly, the mechanical constrains on the ADP, Pi and AA residuals involved result in the formation of the high energy covalent bound between the two phosphates. Thus mechanical -> chemical energy. I thought that the pressure between the electron clouds of the two molecules caused some superficial electrons to hop, resulting in the new covalent bound (that's what I meant by squeezing), and the dehydration. Is this mostly correct (with possible intermediate steps where either the Pi or the ADP end up in a temporary covalent bound of even higher energy with subunits of the ÀTP synthase), or is this pure hogwash? Also, thanks for the explanations regarding the flagellum, that's very interesting :-) > I'll grant you there are no canonical gears as a mechanical engineer would recognize them. I wasn't talking about the motive coupling. But a number of the physical structures (proteins) that couple the anchoring to the moving body have gear like properties. These are used to orient and clock the moving body in its cycle. Is it mediated by alternating, matching stripes of charged or polar AA residuals?
  - jdgiese 13y ago
    Protein-interaction videos often make molecular reactions seem "deterministic" when in reality everything is quite stochastic; the molecules are "bouncing" around like crazy and each step may go back and forwards several times before completing. That said, I love the videos--its really amazing to think about all these little proteins bending and folding around all the time!
    - pygy_ 13y ago
      The stochastic aspects were also completely neglected in my chemistry courses. We were just taught about macroscopic, aggregate probabilities, and high level descriptions of the reactions, but not the nitty gritty details. I knew that chemical bounds were vibrating (with a frequency proportional to their energy, E=h(nu)), but, for some reason, I had never envisioned macromolecules wiggling and vibrating as a whole. Updating mental model :-)

by pygy_ 13y ago

dekhn 13y ago

"ADP and Pi are mechanically squeezed against each other in order to create the covalent bond." I have a PhD in Biophysics. If I ever said "ADP and Pi were squeezed together", I'd have been laughed out of journal club. The fine details of the reaction coordinate are still being argued about. I'll grant you there are no canonical gears as a mechanical engineer would recognize them. I wasn't talking about the motive coupling. But a number of the physical structures (proteins) that couple the anchoring to the moving body have gear like properties. These are used to orient and clock the moving body in its cycle. OK, I'll up it a notch since you guys are being picky. There are motor proteins which use ATP hydrolysis to do directed (non-random) motion. One of the plausible (IIRC it's passe now) mechanisms involved coupling the ATP hydrolysis free energy to a physical ratchet-like mechanism which, while didn't physically look like a gear when you looked at static crystal structures, seemed to behave like one using various subtle time-resolved mechanisms.

pygy_ 13y ago
Doctor of medicine here, with basic notions of chemistry and biochemistry from courses I took 16 years ago. I sure know what I'm talking about! ;-) More seriously, I had inferred the squeezing from the videos I linked to. If I understand properly, the mechanical constrains on the ADP, Pi and AA residuals involved result in the formation of the high energy covalent bound between the two phosphates. Thus mechanical -> chemical energy. I thought that the pressure between the electron clouds of the two molecules caused some superficial electrons to hop, resulting in the new covalent bound (that's what I meant by squeezing), and the dehydration. Is this mostly correct (with possible intermediate steps where either the Pi or the ADP end up in a temporary covalent bound of even higher energy with subunits of the ÀTP synthase), or is this pure hogwash? Also, thanks for the explanations regarding the flagellum, that's very interesting :-) > I'll grant you there are no canonical gears as a mechanical engineer would recognize them. I wasn't talking about the motive coupling. But a number of the physical structures (proteins) that couple the anchoring to the moving body have gear like properties. These are used to orient and clock the moving body in its cycle. Is it mediated by alternating, matching stripes of charged or polar AA residuals?
- jdgiese 13y ago
  Protein-interaction videos often make molecular reactions seem "deterministic" when in reality everything is quite stochastic; the molecules are "bouncing" around like crazy and each step may go back and forwards several times before completing. That said, I love the videos--its really amazing to think about all these little proteins bending and folding around all the time!
  - pygy_ 13y ago
    The stochastic aspects were also completely neglected in my chemistry courses. We were just taught about macroscopic, aggregate probabilities, and high level descriptions of the reactions, but not the nitty gritty details. I knew that chemical bounds were vibrating (with a frequency proportional to their energy, E=h(nu)), but, for some reason, I had never envisioned macromolecules wiggling and vibrating as a whole. Updating mental model :-)