Back again....

Yet another "quantum effects in photosynthesis" paper.

Waiting for the rampant speculation that can arise from this paper, as well.

Off to troubleshooting the remainder of my afternoon! Read more!

Off the back burner.....

Meant to post about this a while back, but never quite got around to mentioning it.

Lipid Bilayers and Membrane Dynamics: Insight into Thickness Fluctuations.

I suspect anyone reading this post knows that membranes are far from static entities, ranging from lateral diffusion of individual lipids within the bilayer to collective motions of the membrane. Here, the authors report of a thickness fluctuation, which is exactly what it sounds like -

From here.

The authors utilized both small-angle neutron scattering and neutron spin echo spectroscopy on these samples, as neutrons offer remarkable versatility in terms of probing various length and energy scales, as is presented here -

In any case, I thought it was interesting.  They are - based on what I've heard - looking at lipid bilayers with proteins, but I haven't seen it come out yet in the literature.  I think as people become more interested in what is really going on in complex biological systems, we're going to need to look beyond the purely molecular length and energy scales to the mesoscopic regime (however one defines it).

Happy holidays and New Year to all! Read more!

Lit Links

So, in case any were wondering, my area on the East Coast was mostly spared the wrath of Hurricane to Post-Tropical Cyclone Sandy.  Some rain, a bit more wind, but not many power outages in the immediate area.  I am however fairly well prepared for any mystery zombie apocalypses that might arise (from the dead).  I hope that all of you reading who were subject to its furor endured the storm as well as possible.

In any case, some bits of possible interest -

1.) PNAS has a special feature this week on "the Chemical Physics of Protein Folding."  Sadly, it's behind a paywall for the time being.

1.5.) Related to this, I once mentioned a while back in a comment (I believe over at the Inquisitive Ket) about one of the less-important reasons Levinthal's paradox never really bothered me, namely, that proteins aren't really free to sample all possible conformations due to their interactions with other proteins (even indirectly due to crowding), the solvent, and with itself.  In any case, it's always interesting to see people carefully examine these sorts of questions in the recent literature.  

2.) Gaining structural insight occasionally takes a while.  It also reminds me of the utility of neutron science for biochemistry - the ability to use contrast variation using selective deuteration make it possible to probe multicomponent systems.  And let's not forget that one can also use neutrons for spectroscopic measurements. 

Anyway, back to the actual science…..  Read more!

Trust but verify.

The question of how much to trust computational methods is brought up here at Chemiotics II. My answer is that it depends on what one is looking for in the first place.

If one is looking for some sort of completely accurate and precise way to have all biological phenomenona fall out of "first principles," well, I wouldn't hold my breath. Of course, I don't think anyone is really waiting for that. At least I hope not. I believe my feelings on these sorts of issues are best described by personal experiences I've had with computational methods.

In grad school, I had an interest in this one mid-sized protein (somewhere between 40 to 60 kDa) that was known to bind this particular ligand. There was a crystal structure of the protein with and without ligand, although of course it was hardly the entire story (which is why it was the subject of my research attentions). In any case, collaborators did some MD simulations, and it was consistent with what we had found and was known. In their next bit of work, they mentioned that they found something new regarding the mechanism of ligand binding. This was going on the same time as I was doing some work, and as it turned out, my data did not rule it out. And so new research was inspired for those who took up the project after I left.

Currently, I am embroiled in a sordid and complex tale of transmembrane signaling involving the receptor and varying amounts of soluble cytoplasmic proteins that propagate that signal. There was a fairly recent paper detailing MD studies of the signaling process. Well, part of it, I suppose - huge chunks on either end of the transmembrane receptor were not included, and none of the cytoplasmic proteins that bind and are modified by the receptor were included in the study. Certainly a daring attempt, but it's hard to get too worked up over it when it doesn't resemble anything that I actually work with on a daily basis.

In short....I think properly used, it can be a useful way to bridge what is measured experimentally with the metaphors we use to describe processes. (For example - people love using descriptions involving simple machines, but what is actually measured are thermodynamic or spectroscopic quantities. Of course, "force spectroscopy" looks to change this, but when you yank apart a protein, you are no longer just gently playing around at kT or sub-kT conditions to see what kinds of deformations you get naturally or as a response to some stimulus. Anyway....) Certainly, for small enough systems, I am inclined to give them a proper reading, and in cases where the system might be larger but is somewhat well characterized, the same applies. In giant systems where they toss out a number of critical components or oversimplify to the point of absurdity, I am generally far more skeptical.

Merry Christmas to those who celebrate, Happy Hanukkah to those who celebrate, and a delightful winter holiday season to the rest. Read more!