This is the first figure our lab has added to FigShare that is new and very likely to be (formally) published soon. It's Andy Maloney's data for microtubule gliding speed on a kinesin-1 surface as he varies the concentration of deuterium or heavy-oxygen in the water. I think his data are exceptionally high-quality and I'm really proud of his work. These two plots are the culmination of a ton of work by him and Larry Herskowitz (image tracking) over the past two years (since we began working on kinesin). I'm not sure but I think there are between 100GB to 1 TB of raw image data associated with these graphs. Not a lot, but not a little data either. It's all open data and we're working on methods for sharing the data. Probably a good page to jump to is Andy's methods in his open dissertation: http://www.openwetware.org/wiki... - Steve Koch

So, now an interesting part about open data: we don't know how to interpret the results yet! And I bet someone out there has some good ideas. We were steered towards these experiments by a collaboration with the Susan Atlas group, who is working on a Charge-Transfer Embedded Atom Model (CT-EAM) force field for molecular dynamics (MD) simulations. We have been thinking about water as a way of tying our experiments and their simulations together at first, since historically the MD force fields for water have been emperical and not necessarily predictive for something like isotope effect. Over the past couple years, my own thinking about how the water isotope will affect the system has changed frequently. First I thought it would be simple, then I thought it would be much too complicated, and now I think it's relatively simple again. But we don't know yet what is going on, or even whether it's a good knob to turn. (A) We notice that the % reduction in speed is very similar to the % increase in viscosity that arises from the two isotopes. Since the data are so clean (thanks to Andy's meticulous technique, and Larry's excellent image tracking software), it's very tempting to investigate a simple viscosity effect. On the one hand, this is disappointing, but on the other hand it probably isn't, because it looks like potential for good physics. (B) Both plots look very linear. This would imply that we are affecting one or some of the rate limiting processing in kinesin-1's kinetic cycle. I think these would be inorganic phosphate release or ADP release. If we were only affecting a rate constant that is not rate-limiting, we would expect the trend to be flat and then roll off as that rate constant became more important. (C) This is really just a foothold. There are a zillion follow-on assays that we can (need) to do. We could see whether this is just viscosity by using other solutes that increase the viscosity but are chemically different from each other. For example betaine and sucrose. We can change the assay so that a different rate constant is rate-limiting...for example by lowering ATP concentration. etc. etc. Is this a good knob to turn and will it give us new information about kinesin and / or the CT-EAM modeling? I can't say right now, but my gut tells me that such clean data from such a fundamental change as water isotope will be useful for something. - Steve Koch

How was the viscosity measured? I'm a bit surprised to see the isotopes make such a difference but that is probably just my ignorance in action. Cytoplasm is very viscous compared to water -- are there any in vivo data available for comparison? Jennifer Lippincott-Schwartz does amazing work on organelle dynamics in living cells, using video and molecular labelling... - Bill Hooker

Hey Bill -- one quick answer: we did NOT measure the viscosity. I just looked it up in primary literature and / or Wikipedia. - Steve Koch

Also, Bill, I am behind on the latest in intracellular studies, though I agree they are fascinating. Without all of the latest information, I'd be shocked if an intracellular measurement could detect the subtle (<25%) effects that we're seeing above. Andy's method is more suited for biophysical study of the isolated motor system, as a way of probing the solvent effect on the system. No doubt, in vivo the solvent is critically important as well--especially fascinating is intracellular osmotic pressure. But of course, there's a bunch of other stuff going on inside the cell--crowding (running into stuff) and a whole slew of other proteins that can modulate kinesin's speed, processivity, cargo binding, etc. etc. - Steve Koch

http://www.articlesofbusiness.com - Carri Shabi

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I'll be sure to fix those error bars. - Andy Maloney

Yeah I know you will. And I know they won't be much different, so didn't want to wait to publish to FigShare. - Steve Koch

Very nice work, Andy! - Steve Koch

Yeah, I forgot to say so, but nice work deserves recognition and this is nice work. Good data are hard to come by and it warms an old experimentalist's heart to see such attention to detail. - Bill Hooker

Something else you've probably already thought of -- the Pi exchange/ADP release is a good idea, so I wonder if there are other well characterised systems which include a similar step that would be amenable to study in your setup. I got there from here: what do seeds (Lewis) and tumors (PubMed search for DDW) have in common? Rapid growth and proliferation, which requires rapid DNA synthesis, which involves the sorts of phosphotransactions we are talking about... probably bullshit but thought I'd dump it here anyway. - Bill Hooker