Friday, December 21, 2012

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!

Monday, November 19, 2012

Speak of the devil....

...and the devil, he shall appear.

A recent discussion at the Curious Wavefunction briefly touched upon the role of (macro)molecular crowding in biochemical studies.  I am presently preparing to see whether a certain set of experiments are feasible, and in some of the potential tests, I am adding a fair amount of crowding agents to my samples. 

The samples that have those crowding agents are presently the only ones that exhibit any enzymatic activity.  The other samples are dead, biochemically speaking.  One of the "dead" samples does exhibit complex formation in one of my alternate tests, but that's it.  Further tests are needed, of course, and it's certainly possible that I can retain enzymatic activity in the other samples upon logically adjusting my current protocols.  But perhaps there's a lesson here to be learned.

Read more!

Wednesday, October 31, 2012

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!

Friday, October 26, 2012

Chiming in with a #ChemCoach entry

Here's my contribution to the ChemCoach Carnival, for what it's worth.

Your current job.

I am a postdoc in an actual chemistry department on the East Coast (USA) doing a mix of physical chemistry, biochemistry, and spectroscopy, along with dashes of molecular biology, computation, and misery. 

What you do in a standard "work day."

No such thing as a standard work day for me -  I'm presently slogging through heaps of molecular biology in order to validate a protocol for producing uniformly 13C/15N labeled protein (mostly since my PI isn't yet comfortable with how we do things in the 21st century).  Earlier this year, for example, I was doing everything from NMR on inorganic solids (after effecting some probe repairs on my own) as well as some p. chem. of lipid mixtures, in addition to protein NMR (solution and solid state). 

What kind of schooling / training / experience helped you get there?

 I was a biochem/chem undergrad (did my undergrad research in a biophysics lab - lasers and magnets, what more could one wish for?) and did my Ph.D. in an honest-to-Buddha chemistry department, doing biophysical chemistry.  I was briefly diverted into a year at a cancer research institute doing biophysics/soft matter-oriented work (that was a trip, let me tell you), but returned to my chemical roots. 

How does chemistry inform your work?

Just the other day I was trying to get this horrendous mix of inorganic chemicals to go into and stay in solution, actually - and people say there is no chemistry in biochemistry!  Heh.   My perspective on many of my scientific interests is rooted in my chemical background - for example, signal transduction could be translated as essentially controlling the rates of chemical reactions across interfaces, after all.  It's a rather essential component of what I do on a daily basis.

Finally, a unique, interesting, or funny anecdote about your career

I was at a conference where I spoke to the colleague of this scientist who had written a paper I had read and digested multiple times, as it was extremely germane to my interests.  He noted that said scientist had never followed up on this particular aspect since they found that obtaining reproducible data was far too tricky.  I should have realized then that my project might have been a bit ambitious, but I persevered and did manage to get reproducible data.  It just took another 2.5 years on top of the 2 years I had spent working on said project.....  Read more!

Tuesday, October 16, 2012

Some minor notes.

The reason they're making your son take chemistry?  Because they're mean.  Or perhaps because they hold to some archaic notion that education is about broadening one's horizons and tempering the intellect, not just about preparing one for any particular career path.  I haven't decided. 

Small-molecule synthetic chemistry in the NY Times?   A pleasant surprise to see in the national newspaper of record, at least last I checked. 

Microbial physiology via NMR.  So cool.   Also, kind of jealous.  I really need to get some awesome stuff done sooner rather than later.

I think that will be all for the evening.

Read more!

Thursday, October 11, 2012

Prize ponderings

There have been some particularly interesting and worthwhile points made on the blogosphere over the last two days in the wake of the Nobel announcements.

1.) The success of small/investigator-driven/table-top science.  Actually, this applies to more than just the Chemistry Prize - see here for some comments regarding this year's Physics Prize. 

2.) Are we doing ourselves a disservice by discussing and debating the Nobel ad infinitum?  Is trying to find one to three people to recognize for a certain (set of) accomplishments really the best option?  How much of this is a holdover from how science used to be conducted pre-1900?  I happen to especially like Paul's Chemical Hall of Fame idea, and am willing to participate.  (I may want to nominate a physicist or two, though.*)

3.) Chemjobber brings up the interesting point as to whether the "mix" of chemistry that gets highlighted due to the Prize announcements is the one the community wants to present to the public. 

4.) There seems to be a sense that we need to circle the wagons a bit before the central science withers away.  I can't entirely disagree with this one.  I've been told multiple times that some of the questions I've stumbled over while doing biological chemistry regarding underlying questions of (mostly) physical and inorganic chemistry aren't really fundable, at least relative to the biological question with which I'm engaged.  You can only try and spin questions into applications for so long and so far before it gets tedious.

5.) I would read this post over at Everyday Scientist if you haven't already.  I'm in the same sort of boat as a bio/physical chemist.  I look at the Physiology/Medicine Prize and see work like in vitro fertilization and the H. pylori work recognized, and vast amounts of cell biology and systems physiology in their ranks (immunology, olfaction, neurobiology, and so on).  I view biochemistry as something which is securely rooted within the realm of chemistry.  Of course, this makes me wonder - while the issue of communicating chemistry to the public has been a discussion topic in various contexts over the years, maybe we also need to open up the lines of communications between chemists.  I'm not entirely sure how to go about doing this right at the moment, but I am definitely open to ideas.  

Of course, perhaps this is all just colored by my spectroscopic tendencies - if I can fit it into a coil,  cuvette, or beamline, consider my interest piqued.  Biological, chemical, geological, material, or physical. 

As always, the comment section is open. 

*: Erwin Hahn and Albert Overhauser.  Spin echoes and the Overhauser effect.  You know you want to agree with me! Read more!

Wednesday, October 10, 2012

A perhaps idiosyncratic view.

So, as it turned out, I called this year's Nobel Prize for Chemistry.  While I am now curious if I have any Elven ancestry (Elrond had that gift of foresight, right?), I feel I should note the following for those feeling that biochemistry isn't really chemistry.

I like biological chemistry since, in my view, it allows me to explore so many areas of chemistry.  I've synthesized isotopically enriched small molecules, I've purified proteins, I've been able to work with multiple spectroscopic and physical measurement methods in detail, I've examined paramagnetic inorganic solids with both success and failure, I've spectroscopically dissected multicomponent organic solids, I've had to explore certain types of self-assembling systems, I've cranked through theoretical treatments of metalloenzyme catalysis as well as polymer chemistry to make sense of my data over the's been a good time.

Extending from that, I like chemistry since it is perfectly situated to go hopping over boundaries.  I don't see why I shouldn't be able to figure out signal transduction pathways just because I'm a chemist.  I don't see why I should humbly hand over fundamental questions about the theoretical basis for spectroscopic methods to the physicists.   

Although right now biochemistry is giving me a headache.  Speaking of which, back to it.....

P.S. - A hearty congratulations to both Serge Haroche & David Wineland as well as, of course, Robert Lefkowitz & Brian Kobilka! Read more!

Monday, October 8, 2012

To The Classroom!

A recent post at Chemiotics sparked some old, dimly remembered memories from my grad school days as a gen. chem. TA leading weekly discussion sections.

Now, general chemistry is, from what I can figure, is a slightly different beast than organic chemistry.  At the universities I attended, the class was also a requirement for physical science and engineering majors, and could make up a substantial fraction of the class given the strength of the engineering programs at my alma maters.  Organic chemistry tended to draw from a smaller student pool - outside of the legion of premeds, it was populated by those with chemistry & biological science majors, as well as the expected chemical/materials engineering students. 

Back to general chemistry - this situation leads to walking an incredibly tricky path so as to keep the material interesting, relevant, and not too off-putting to anyone in the audience.  In short, no one is entirely happy with things, but one might consider that a sign that everyone is getting what they need in the final accounting, although not necessarily what they'd prefer. I'll be a bit obnoxious as usual here and suggest that gen. chem. can be an opportunity to demonstrate chemistry's status as the central science to a diverse audience, if done well. 

Back to the premed issue, though - I think what perturbed many of us is the attitude that arises in a class with a significant premed population.  I won't belabor this point with various horror stories (as we all have them), but, for example, the majority of the "point lawyering" I experienced was from premedical students.  In all of those cases I can still remember/wrote down for the record, none of them involved an actual grade breakpoint (e.g., they were nowhere near the boundary that would have resulted in a different overall final grade).

Of course, perhaps what we need is a different model for medical education.   Or maybe not.  Perhaps what we need is to be reminded of the difference between education and training.  Learning about something that may not be transparently applicable to your post-university career plans is not the end of the world.  A radical idea, I know. 

Obligatory mention - congratulations to the new Nobel laureates

P.S. - If anyone wants to share their horror stories teaching undergraduates, please share in the comments.  Read more!

Tuesday, September 25, 2012

Stuck in the middle with you.....

So, due to recent research efforts, the path to enlightenment - well, at least, reasonable progress on a project - has become clearer.  Of course, it entails going back and preparing otherwise identical samples, albeit with a different labeling scheme.  Naturally, this will require some optimization.

In other news, I've recently been inspired to think about how to characterize extremely nasty and messy mixtures of appallingly complex and egregiously sensitive molecules.  My initial thought was that I should just let other people do this sort of thing.  However, I had a number of uncharitable thoughts about certain areas of the research community and realized that I should think more carefully about this situation.   I then had the notion that I need to do what my blog name suggests and think about things with less than precise site-specific chemical resolution for a bit.  I can layer on some perfectly reasonable physical parameters and other particular measures of interest.   Some people will complain, but then again, there are always those sorts.

Another unrelated topic I've been pondering - just how "open source" is chemistry?  How many of us have data trapped in proprietary formats in backup discs or external hard drives?  How often have you had to grudgingly use readily available software in ways it should never be used since more appropriate software doesn't exist or is egregiously expensive for the extent one needs it? Any information, griping personal anecdotes,  or interesting reads on the topic would be appreciated.

That will be all for tonight, I'd say.

Read more!

Wednesday, September 19, 2012

Nobel Notes (Pt. II)

Upon request.....

Molecular Dynamics

So if we skip over the entire Monte Carlo simulation work, the first proper MD work was Berni Alder and Tom Wainwright in the late 1950s on hard-sphere systems.  Wainwright, as I noted last year, passed away a few years ago.  George Vineyard (Brookhaven National Lab) used MD to study radiation damage right around 1959/1960, and Aneesur Rahman did the first MD simulations of an actual liquid (for the pedants - yes, I know it was argon) in the mid 1960s.  Unfortunately, neither Vineyard and Rahman are still with us.

Here it gets more complicated, as the move to more "chemical" systems involved a number of people (David Chandler and Bruce Berne among others).  And then there's developments like ab initio MD (Car & Parrinello in the mid-1980s) which have been more on the fundamental side, in terms of bridging MD to DFT in this case, and has found plenty of application (Car & Parrinello were jointly awarded the APS's Rahman Prize for Computational Physics a while back).  

Magnetic Resonance/NMR

So, I really do think solid state NMR has a prize with its name written on it.  It's obviously been a while in the making, but it is finding great use in multiple areas of application (chemistry, structural biology, polymers & materials, and various subfields and intersections branching off from these).  My general feeling is that it would be tricky to award a Nobel for solids NMR without including Alex Pines (Berkeley), as he's had his hand in the development of cross polarization (which basically everyone uses, whether you're doing static solids NMR or magic angle spinning solids NMR), as well as contributing to multiple-quantum NMR spectroscopy, quadrupolar NMR methods, and various other proofs of principle and applications (investigations of the Berry phase by NMR to his more recent efforts in combining optical pumping and hyperpolarization for imaging purposes).  There are other names here, but it gets tricky.  I suppose Pines' former graduate advisor, John Waugh, could be here as well.  And there's always the risk I'm forgetting someone, since I'm sure there's some paper from 1975 that I haven't read (or whenever). 

I think I've brought up Harden McConnell before, not only for his contributions to NMR but also for his work in EPR and its applications to understanding biomembranes, including early work in spin labels.  Of course, I'm sure people will gripe about the fact that his more recent work was biochemistry and immunology-oriented.  Heh.

I wouldn't object to Ad Bax being included, but I can see where it might be hard to convey the Nobel-quality novelty after Wuthrich's prize 10 years ago or so now.   I know he's tremendously well-cited - heck, I've cited him! - and always places very highly on those h-index rankings, but I could see this being an uphill battle to some extent.

So that's that, at least for now, I'd say.

Read more!

Wednesday, September 12, 2012

Nobel Notes

I am not even going to try and offer up any predictions or suggestions given last year's surprise.  I will, however, make a few comments, some of which I've mentioned in the past.

Molecular Dynamics

Martin Karplus is usually mentioned here.  Chembark has this folded into a more general computational chemistry prize with other scientists who have contributed greatly in other areas of comp. chem., as has the listing over at the Curious Wavefunction.  Not to take anything away from Prof. Karplus and his extraordinary career, but as was brought up last year, this position betrays a lack of appreciation for the development of MD.  I'm not sure how one could reward Karplus without snubbing the early accomplishments under the rug that showed the power of computational methods to ask questions and provide answers to physical problems.  Of course, it's also entirely possible that an MD prize would be one in Physics, which would be entirely acceptable as well.


While some have noted that a Prize for the recent structural accomplishments might seem premature, I can envision a slightly different scenario.  Kobilka's former mentor, Robert Lefkowitz, did receive the National Medal of Science a few years ago for his pioneering work in GPCRs, and has earned various other accolades over the years.  It's possible that there might be some sort of Prize that involves more on the biochemical side of things, but with an eye (and inclusion of) the structural work.

Magnetic Resonance

Not even going to try since I'll just keep babbling on for a while.

The Kavli Question

Will we ever see a dual Nobel/Kavli Prize laureate?  Or is the work that the Kavli Prizes recognize too interdisciplinary to make it through the Nobel process?  (Cue the whining of chemists who want to eliminate biochemistry from eligibility for the Nobel Prize.  Heh.)

P.S. - Really kind of hoping a physician wins the Nobel for chemistry, a chemist wins the Nobel for physics, and a physicist wins the Nobel for physiology/medicine.  It would be a tremendously hilarious week.

Read more!

Sunday, August 19, 2012

Generality and Contingency.

There's an interesting post over at In the Pipeline regarding the nature of how enzymes work, and it has inspired excellent comments (as is par for the course at ItP).  One notion comes up that if so-called generalized mechanisms can't be devised, it's a failure of sorts for chemists.

My question - the photosynthetic reaction center is an enzyme (oxidoreductase).  Dinky soluble proteins that do isomerizations are enzymes.  Metalloproteins that rip apart chemical bonds are enzymes.  Some proteins float around in the cytoplasm.  Others are embedded are in a membrane of some sort or another.  Others exist at a membrane/solution interface.  Others are extruded from the cell to go do their thing in the cell's environment.  So, how general can a mechanism be for an enzyme? 

One of the things that is often brought up is that there's an element of historical contingency to consider when examining the history of life on this planet.   While we obviously can't just throw up our hands in defeat to try and understand the mechanistic details of biological chemistry, neither can we truck along without acknowledging that context and history are important aspects of the grander scheme.

If that is still not comforting, perhaps one can find some solace in Kornberg's reminder to trust in the universality of biochemistry.  Consider it a tradeoff - while your one enzyme might not shed light on all enzymes, it can shed light on the same enzyme (or similar ones) across many organisms, from the modestly-scaled unicellular beasties to the gargantuan eukaryotes that now populate the Earth.  Read more!

Monday, July 30, 2012

Additional indications of decline.

Along with many others, I too had my obligatory weekly dose of rage the other day when I read Is Algebra Necessary? by Andrew Hacker. 

Now, I'm not going to pretend that there isn't room for improvement in the U.S. educational system.   But I think calling to teach "citizen statistics" without teaching algebra is rather silly.  I can't imagine trying to teach statistics without some significant exposure to algebra.  (Truth be told, calculus is also immensely helpful in learning/understanding statistics as well, but I won't even try and deal with that at the moment.)   Ultimately, I think the point that many others have made regarding education versus training is germane here.   They are not the same, and if we deem algebra unnnecessary, soon enough we will be dropping literature classes for courses in how to compose PowerPoint presentations and reading Twitter updates.

In other news, I've been busy.  Will attempt to get back to semi-regular blogging in the near future, I hope. Read more!

Tuesday, June 19, 2012

The Eternal Struggles

I managed to wrap up some experiments for a paper (sent back the revised version just the other day), While doing all of that over the last two weeks and change, I was stimulated to contemplate some long-standing issues off and on.  I figured they might be of mild interest.

The first - I'd like insight and numbers.

There's a fairly famous quote attributed to the late theoretical chemist Charles Coulson on obtaining insight versus just numbers.  My question - why can't we have both?  My  purely anecdotal experiences have suggested that chemists tend to be really ambivalent on this topic - on the one hand, we tend to be annoyed if we can't intuit everything from just a glance at the periodic table and a smattering of semiclassical physics (as I once vaguely alluded to recently), but on the other hand, we're quite quick to complain about things not being rigorous and how it's all just a model.  Other fields tend to be a bit less gripey about this sort of thing in my experience - they've either learned to deal with the indeterminacy or uncertainty, and/or come to grips with the ups and downs of toy models. 

The second - the perpetual translation that goes on in the head of anyone working at an interface.

A long time ago, I had gotten myself into a little back-and-forth because, in short, I was reading with my physics filter on when I should have been reading it with my chemistry filter.  This is hardly new, and it's certainly happened since then, for that matter.  It usually manifests in turns of phrase or underlying assumptions that - for example - aren't anything unusual in one setting but might be a bit odd or worse in another setting.  I'm not sure how to resolve this recurring situation, except to try and be more careful.   Suggestions would be welcomed.     

The third - is biochemistry really just "applied organic chemistry," as I was once informed as an undergraduate and have heard off and on since then?

Please.  One is only fooling the innocent undergraduates with that pompous bit of nonsense.  There's a reason it's called biochemistry - one needs to appreciate and understand how to navigate through the entirety of chemistry.  Once one casts aside the self-completing fantasies of some deluded chemists, it's rather straightforward to see interesting chemistry of all stripes manifest in biological systems.  There are incredible metalloenzymes that can fix nitrogen (nitrogenase), we have a chromophore bound to a membrane protein which experiences a photochemically induced conformational change (bacteriorhodopsin), and of course there's all of the multiple feedback and regulatory pathways that all seem to tie into one another in ever-increasingly labyrinthe but beautiful ways that seem to be well-attacked (to some extent, at least) with the mathematical formalisms of physical chemistry.  And all of that is just the tip of the iceberg.  Read more!

Friday, May 25, 2012


Chiming in late on the Toxic Carnival, but I can't help but mention one of the most historically significant chemical threats to life on this planet.

My chosen chemical is arguably responsible for one of the greatest environmental catastrophes in history, whose effect was global in its reach and certainly changed the biological face of the planet.  Said chemical is still produced in vast amounts to this very day, and no one seems inclined to do anything about it.

The culprit, of course, is dioxygen (O2).

Billions of years ago (a bit over 2 billion of them, in fact), the Earth's atmosphere became significantly more oxygenated due to the increasing extent of oxygenic photosynthesis. I can't even begin to fathom how many otherwise innocent anaerobic bacterial species must have been driven to extinction. Of course, it was perhaps just a matter of time once oxygenic photosynthesis evolved from its anoxygenic roots. 

The worst part is that oxygen still wreaks havoc among organisms to this very day.  Exposure to higher-than-normal partial pressures of oxygen can be toxic, and - in fact - many animals have elaborate mechanisms of oxygen transport that serve to protect the organism from unfettered oxidative damage, including specific "oxygen chaperones" (in essentially all vertebrates, this role is filled by hemoglobin).   Of course, anaerobic organisms are still susceptible to the threat of dioxygen in their environment to this very day.  The reasons for this can range from insufficient amounts of enzymes capable of metabolizing reactive oxygen species (catalase, peroxidase, and others) to oxygen poisoning their (frequently novel) catalysts  - err, metalloenzymes - that are specific for anaerobic metabolism. 

At a more molecular level, dioxygen is critical for the function of cytochromes P450, which has been termed "nature's blowtorch."  That doesn't sound very soothing, now does it?  One of the oxygen atoms is doubly reduced and scoots off as water, leaving behind a vicious biological oxidant which will insert the remaining oxygen atom even into fairly unreactive C-H bonds.  Reactive oxygen species such as superoxide and peroxide are produced as a result of oxidative phosphorylation, due to incomplete reduction of dioxygen by the cytochrome c oxidase complex.

When you take a deep oxygen-rich breath one of these days, think of the poor anaerobes who can't. You should feel a twinge of guilt. Read more!

Saturday, May 19, 2012

Quantum biology - A Rose By Any Other Name?

I believe I may have off-handedly mentioned some of this work somewhere in a blog comment semi-recently, but I suppose some further thoughts would not be out of place at this time.  I bring it up because of this preprint and this article about said preprint.

Clearly, on one level, quantum mechanics - via chemistry - underlies biology.  This is, I suspect, a fairly unoffensive statement.  Chemical reactions are quantitatively studied in a quantum mechanical framework, and I don't see biochemical reactions being much different. 

On another level, direct appeal to quantum mechanical behavior to explain biology can seem kind of silly.  Biology is slow, wet, messy, and takes place at a whole bunch of time and length scales.  I imagine many of us recall the exercise - likely done in an introductory general chemistry course, at least in my experience - where one calculates the de Broglie wavelength for an electron and then, say, a baseball. 

Of course, when one looks at table 1 in the preprint, a light goes on.  Long-range electron transfer in proteins?  The role of tunneling in enzyme catalysis?  Vision - which involves the photochemistry of a protein-immobilized chromophore?  Photosynthesis?  A proposed radical spin mechanism for avian magnetoreception? 

This all reeks of physical(ly predisposed) chemists trying to get their dirty mitts onto a whole lot of funding.  Not that there's anything wrong with that, mind you - I'm presently trying to work "quantum biology" into my CV/resume as we speak. 

But for sake of argument, let's take a look at the Fenna-Matthews-Olsen (FMO) protein from a green sulfur bacterium where quantum effects were observed via 2D electronic spectroscopy.

Yep, definitely a protein.  But what's all of that inside the protein?

Why, it looks like the protein is the wrapping for a photochemically delicious filling of chlorophyll molecules!  I could envision that this is the sort of environment which would be conducive for maintaining some sort of quantum mechanical excitation. 

But what about - for instance - microtubules, which some have suggested play a role in consciousness via quantum mechanical effects?  Why, there's even GTP (GDP) known to associate with tubulin in the structure!  Let's take a look -

Hmmm.  Let's focus on the GTP and GDP, so how about….

Well, that was kind of anticlimactic.  That's it?  That is somehow supposed to sustain and nurture our very consciousness from the harsh decoherent world out there?  I find myself skeptical. 

I suppose that is as good a place to end as any.  I may or may not have more to say in the future after I've had a chance to properly consume and digest the preprint.  While I do find the idea of nature exploiting exciton transport, radical spin pair chemistry, proton tunneling, and so on incredibly exciting - I don't think taking that and wantonly speculating is the best route.   

FYI - This was also mostly a chance to play around some more with UCSF Chimera.  Just started using it a bit earlier this year, so if anyone has any tips or list of useful tricks, please share!  The structures were generated with this program using PDB ID 3ENI (FMO protein) and 1JFF (tubulin).  Read more!

Friday, May 18, 2012

Black boxes and rigor.

There was a thought-provoking post over at the Curious Wavefunction regarding a Nature op/ed piece on the increasing "black boxification" of modern biological research.  While it is both concerning and makes for an easy bit of mockery, I have to sometimes wonder where one can draw a line.  For example, it's been fairly typical (in my experience) for some specific physical/spectroscopic method to be introduced in a manner consistent with one's expected minimum physical chemistry background.  It's not uncommon for there to be a step or two which is essentially "and we take this result from classical mechanics/electrodynamics" or "this is actually a result of a certain mathematical theorem/relation" in such an introduction.   Some might claim that there's a huge difference between not knowing a technique relies upon a particular mechanism versus (for example) not having worked out a laborious series expansion for a particular term that yields the desired form in that case.  But I would view it as a caution - what happens if you stumble across a case where, in fact, you need to go back and rederive the expression for a term since some parameter or limiting case has changed?  Naturally, you find that if you end up relying upon that method in your research to any significant extent, you are going to dig in deeper.  You will figure out what the limiting cases are, and where any approximations are likely to break down. 

Of course, here I'm reminded that there is a difference between being able to contend with the formalisms of an argument and being able to develop a more physically rooted intuition for said argument.  I suspect many of us have encountered the "it's not rigorous enough" student somewhere along the line - they're the ones who find the experimental nature of scientific research a bit troubling and are worried that we're not careful enough with our mathematics.  We don't want to go in that direction either, of course.  Well, those of us who are scientists and not just frustrated mathematicians, at least.  I'd like to think that there can be a fruitful synergy between the two - when one is able to invoke physical intuition is a good time to develop one's mathematical skills and understanding, and then later on apply that mathematical expertise to a new problem where intuition is lacking at the start. 

I have more stuff to blather about, as it distracts me from extremely unfortunate technical difficulties in my own research.  Stay tuned. Read more!

Saturday, May 12, 2012

Trifling Observations

The major issue with working at interfaces is that when you need to return to a place of stability, said place of stability often needs quite a bit of attention. You've left it abandoned and unattended, and it will suck up all of your effort until you've returned it to a state of steady reliability. Of course, one never lingers for long, as there either is a new avenue to wander down in one's research or to bring a different project off the back burner.

This tangentially ties into some discussion last month (at a couple of blogs, by my recollection) about how the academic sector does not adequately prepare one for positions in the private sector, at least insofar in chemistry. While numerous wry remarks can be made about the state of the chemistry job market in response to this, it relates - broadly - to the breadth of modern chemistry. Even if you were to organize a curriculum solely for aspiring chemists (here in the US, aspiring engineers and biologists & medical students make up a non-trivial fraction of the general and organic chemistry student populace), you still have to figure out how to make a course palatable for those who may end up working in any number of fields and subspecialties, and will likely end up switching and moving about in any case. The idea (naive as it might be) is that one develops the foundation to pursue anything from synthetic organic chemistry to ultrafast chemical dynamics to chemical biology. Or even all three, if you're feeling adventurous.

Anyway. Read more!

Monday, May 7, 2012

Cultural Differences

There was an interesting post over at In The Pipeline last week about the differences between chemists and biologists, in particular the nature of how chemists and biologists conduct research presentations in mixed company. As the vast majority of my experience is in academic environments, I will not claim that any of the following observations necessarily extends beyond the weed-ridden walls of academe.

1.) Biochemists do aspire to make details of individual preparations something that can be avoided. Certainly, for those of us who are not working with wretchedly ill-behaved proteins (at least on occasion), we can basically just describe the protocol in broad terms (overexpression, cell lysis, clarifying the lysate, and the chromatographic methods/other procedures). I've done that without specifying buffer compositions in exacting detail before. Also, we are trying to make things as routine and unexciting as possible - preparing protein constructs with cleavable affinity tags; expressing eukaryotic in bacterial cell strains that compensate in various ways for not having all of the innate eukaryotic metabolic machinery; using multi-well plates for spectrophotometric assays of various sorts. We would like for things to be boringly reliable, rest assured.

2.) One fundamental problem with presenting material to mixed audiences is that your own people are in attendance waiting to pick your stuff apart. Not necessarily in a malicious manner, of course - well, at least not always. In short, you might decide to go light on the detailed mechanistic enzymology (say, for sake of example, you are an enzymologist) in your latest talk, but what then happens in the Q&A session? Your fellow enzymologists pepper you with a dozen intricate mechanistically oriented questions in no time at all. Six months later, you present again in front of this mixed audience. You have included adequate enzymological detail in your talk and slides. The cell biologists and analytical chemists yawn, and the synthetic chemists wonder why you're boring them with this information. And now you'll never break the chain.

3.) Biology fundamentally means working with living organisms. I sometimes have the impression that chemists who haven't ever done any substantive biochemistry or biology research don't fully appreciate this distinction in the visceral way that those of us who have fallen to the Dark Side do. If it takes a week for something to grow up, then that is what we do. We can't just toss it on a hot plate to speed things up. Conversely, not everything can be stashed in a freezer to wait until tomorrow (although when it can, we do appreciate it). There's also the price of doing interesting biology/biochemistry, where the efforts to make things boringly reliable in point 1 are nowhere near being implemented.

There's certainly more I could eventually think of, but these were the major points I wished to mention. I, personally, do my level best to make my points as understandable and transparent as possible when giving a talk. Of course, given that some of my ideas involve slaughter by spin Hamiltonian, it can be easier said than done...... Read more!

Sunday, April 29, 2012

Sunday Contemplations

It's been a lively time on the chemical interwebs.

The entire chiral space dinosaur story is kind of getting tedious at this point. While the allegations of plagiarism certainly needs to be investigated, adjudicated, and resolved, I was most intrigued by the post here at the Curious Wavefunction. I find it convenient that he brings up the famed geologist Charles Lyell - there is a personally beloved example of what might be termed geological/geochemical contingency that I perpetually bring up at these moments.

Xanthine oxidase. You may or may not remember this enzyme from undergraduate biochemistry (well, for those of you took such a class). I mention it since it is a fairly well-known example of an enzyme which uses molybdenum as a cofactor. There are a number of molybdenum-utilizing enzymes that organisms use. However, it has been observed that certain organisms prefer to use tungsten. These are usually so-called "extremophiles" (deep-sea hydrothermal vents, in particular), where tungsten is more abundant than molybdenum, as well as needing to do chemistry at higher temperatures and under far more anoxic conditions. Perhaps it is not as dramatic as the sorts of substitutions that have been bandied about by some (hello, #arseniclife!), I will admit. But it bears consideration - how might multiple perturbations along these lines shape and remodel biochemistry?

(For anyone who wants more info on the above, I'd suggest first checking out the work of Michael Adams at the University of Georgia. If you are just curious about a point I bring up, let me know so I can reference you properly.)

The other interesting point that was brought up, IMO, was the idea of convergent evolution. This relates broadly to the idea that there are going to be certain physical "boundary conditions" one has to consider. My latest book of interest on this is Living at Micro Scale - the Unexpected Physics of Being Small by David Dusenbery. Here, the focus is on microorganisms and - to recall Edward Purcell - life at low Reynolds numbers.

I don't have anything interesting to note about DHFR since I neither deal with drug discovery nor with the biochemistry of DHFRs. Although I wonder - what if that paper hadn't shown up in J. Med. Chem.? What if it had ended up in a more general-audience biochemistry journal? Would there have been the same response? Would anyone have even noticed it on the chemistry blogosphere? I wonder.

Anyway, I'm going to contemplate lipid bilayers, detergents, and how they are clearly conspiring to make my life difficult. Read more!

Tuesday, April 24, 2012

Something to read.....

Check it out -  a recent article by Nobel laureate Steve Weinberg on the problems facing big science.  It might be noted that the article is very US-oriented, which is only fair as Prof. Weinberg is here in the US.  Still, something that we all should read.

Try to think of the major scientific efforts that have been started or completed in the last 10 years here in the US.  OK, there is that entire NSLS-II project presently going on at Brookhaven which is supposed to run not quite a full $1 billion dollars.  OK, there was also the LCLS at SLAC (the free electron laser which came online a few years ago).  Well, just so no one accuses me of a totally horrible memory, the SNS at Oak Ridge was just shy of $1.4 billion and started up a couple of years back (and they're still building the full complement of instruments to go with the source). 

Hmm.  Maybe we're not neglecting "big science" after all.   If anyone has thoughts as to how to resolve this conundrum, they would be welcomed! Read more!

Friday, April 20, 2012

Quantum Chemistry on the Cheap.

I am not liking this new Blogger interface.  I suppose it will become more familiar with time, which I might take as a reason to post more.  In any case.....

The main reason for this post is to alert those who haven't heard/seen - the January 2012 issue of Chemical Reviews is the free sample issue available to non-subscribers, and contains the (near) latest in quantum chemistry.  I know there's a tiny bit of interest in what can actually be done with these methods by some, and - at least from my POV - yet another delightful article from Pekka Pyykkö, whose material I always find interesting and readable. 

Anyway, the rest of the month, I will be mired in tremendous experimental effort.  Not going off the grid, but more "locked in an NMR room until I finally keel over in exhaustion."  Wish me luck. Read more!

Saturday, March 24, 2012

Lit Post.

A few interesting-looking papers that I have stumbled across lately:

- Cellular solid-state nuclear magnetic resonance spectroscopy. Clearly, analyzing membrane proteins that are still in the native intact cell membrane is what we'd all like to see.

- Red wine, iron telluride, and superconductivity. Sadly, I do not think that soaking any of my biological samples in a preferred alcoholic beverage will facilitate noteworthy results. Although perhaps I should try, just in case.....

- The Next Big(ger) Thing. Actually not a research article, it's a news item on mesoscale science.

As I've had to suppress a fair amount of sarcasm while writing this post, I will end things here. Read more!

Thursday, March 8, 2012

Break On Through To the Other Side

I was reminded to share this page in light of some recent conversations elsewhere. I would also encourage interested readers to check out the rest of Prof. Sethna's web site - there's a whole lot of great material on numerous interesting topics in physics and "complex systems," as well as what seems to be a nice, modern introduction to statistical mechanics for a wider audience than for whom most texts are intended. (I've only skimmed over it here and there so far - your mileage may vary.) Disclaimer - I am not affiliated with the lab. In fact, my only affiliation with Cornell is that I once dated a girl who lived in Ithaca, and her father worked at the university. Heh.

I will say that many physicists I've known - at least publicly - aren't convinced that they are after finding 3 laws to explain 99% of the behavior in the known universe. Most have far less ambitious goals (like being able to explain superconductivity for non-BCS systems), although I suppose this is their PR problem - they clearly need more Philip Andersons and Robert Laughlins to champion what most physicists are actually interested in, and not just what the very prolific high energy theorists and astrophysicists are putting on the book shelves. Of course, it's not to say that there can't be some excellent synergy going on - there's plenty of fundamental physics going on at neutron sources worldwide, and many groups are interested in using the tools of AMO physics as increasingly powerful probes of fundamental physics.

We can all recount anecdotes from our personal experiences - I met a bio grad student who clearly thought of their project in terms of cartoon diagrams without a number or semi-quantitative thought in mind, the theoretical physicist who thought that explaining his ideas to the experimentalists (or anyone who wasn't actually a frustrated mathematician) was the role of the phenomenology folks, and the chemists who complain about lack of rigor yet still seem desperate to explain everything in terms a first-year chemistry student would recognize. What we should focus on is trying to understand what is useful in such diverse approaches and work from there.

Biophysical chemists such as myself do not suffer from such faults, as we have all of their strengths and none of their weaknesses. We're also very modest. :) Read more!

Sunday, February 12, 2012

A Note on "Pure" Chemistry

Over at the Curious Wavefunction, a recent post touched upon the idea of "pure" chemistry not being well-recognized as of late by the Nobel Committee. I of course find the entire notion to be rather silly - if one can't see the chemistry in those Prizes, then you have my condolences - but I thought it would be interesting to do the following exercise.

The American Chemical Society has a yearly "Award in Pure Chemistry" that is intended to recognize fundamental research in chemistry by a young researcher. Just to see what the ACS has considered "pure chemistry" since the 1990s, shall we?

Hmmm. This is a bit unusual. It seems that amongst the fairly obvious "traditional" chemistry researchers that are being recognized, there are a bunch of interdisciplinary scientists who are undermining the sanctity of chemistry! And some of them - dear Odin! - even have biological interests. Even if you go further back, I recognize a number of names who have become rather renowned for their interdisciplinary research.

Clearly, there is a mismatch between what the chemical community officially considers "pure" chemistry versus what the unofficial position tends to be, if one considers the chemical blogosphere to be representative. Hmmmm. Read more!

Wednesday, February 8, 2012

Random Interfacial Griping

To no one in particular.....

1.) We teach a lot of very handwavy material in introductory general chemistry at the university level here in the US. It does not mean that such material never gets a proper treatment. One thing to keep in mind is that such a course is generally intended to appeal to a wide audience, frequently to no one's complete satisfaction. (Especially the premeds.)

2.) Who the frak wrote this Wikipedia entry? I emphasize the following:

Nitrogen-15 is frequently used in nuclear magnetic resonance spectroscopy (NMR), because unlike the more abundant splinless nitrogen-14, it has a fractional nuclear spin of one-half, which makes it observable by NMR.

Just so we are all clear - you can do 14N NMR. See, for example, the excellent webpage here for a bunch of references on exactly that. It's just that 14N is a quadrupolar nucleus (I = 1), which makes life a little more interesting, but is not everyone's cup of tea.

3.) Inverse problems can be challenging. Obviously.

And with that, I'm done. At least until next time! Read more!

Wednesday, January 18, 2012

A Modest Update

Point the first -

- It was remarked to me that my occasional overindulgence for parenthetical remarks in my writing suggests that I am secretly a Lisp programmer at heart. I snickered. It does look like an interesting language to learn, though…

Point the second -

- I was reminded of a thoroughly snarky point I had made to some friends a while back. String theory (or whatever your preferred scheme for quantizing gravity and unifying the fundamental forces) can explain physics. But the really interesting stuff will require using physics to explain the laundry list of actual phenomenona that we have on our platter. So learn your statistical mechanics, as you can then do everything from analyze (to one degree or another) magnetic samples, ion channel clusters in membranes, and socioeconomic behavior.

So love your stat mech and cherish the partition function!

Point the third -

- A recent blog post over at Just Like Cooking sparked a comment, harkening back to a brief digression elsewhere last year. I was of course led astray for a bit, and dug up some earlier papers on the topic. Not that my to-do list is by any means feeling underweight, but I feel it could be edifying (and potentially interesting) to try and work through the idea in a manner that would be fairly accessible to a (more) general audience. So less "death by Hamiltonian," and more "spiced up with Hamiltonians," if one will permit that metaphor. Read more!

Sunday, January 8, 2012

You Shall Pass!

I saw this paper, and it was just asking be blogged about here. I figured I’d give it a shot.

Disclaimer – Not my work, never met any of the authors (although I’m sure they’re all within six degrees of me scientifically). The paper is open access, which I think is a good policy for me to adhere to in any future efforts along these lines.

Citation: L.A. Clifton, et al. “Low Resolution Structure and Dynamics of a Colicin-Receptor Complex Determined by Neutron Scattering.” The Journal of Biological Chemistry. Vol. 287, No. 1, pp. 337-346; January 2, 2012.

Among the many things that bacteria can do, one of them is knocking off other bacteria. There are a number of ways to go about this critical task, not surprisingly, and one of them involves proteins known as bacteriocins. These are proteins that the bacterium uses to kill off potential competitors, as they typically go after closely related bacteria. In this paper, the authors are focusing on Colicin N (ColN), a bacteriocin produced by E. coli. ColN depolarizes the inner membrane of Gram-negative bacteria by forming pores in the inner membrane, resulting in cell death.

The question the authors address is a fundamental one – how does ColN get past the lipopolysaccarhide-decorated outer membrane of a bacterium? It is ~ 40 kDa in size - so, clearly, not going to be able to easily masquerade as an ion or small molecule and pass unhindered through a pore in the outer membrane. The authors note that past research on ColN demonstrated that it is dependent on the presence of an outer membrane protein, OmpF (or related porins), to be effective. Cells that are OmpF-deficient will not be killed off by ColN. I should note that OmpF is a trimeric porin that permits the passage of ions and small molecules through the outer membrane. It was suggested that ColN could pass through the OmpF pore, but would need to be completely unfolded to do so. So there is clearly something going on here that is interesting.

The paper describes a multipronged approach to this question – the authors integrate microscopy, neutron reflectivity, and small angle neutron scattering (SANS). The authors step through their case – they first present the thin film imaging (Brewster’s angle microscopy) and neutron reflection data for their model of the OmpF/phospholipid monolayer. The microscopy suggests similar stability for the OmpF/phospholipid monolayer, although different topography and compression behavior (the formation of domains appears less evenly distributed in the OmpF/phospholipid monolayer, and there are “kinks” in the isotherm for the phospholipid-only monolayer compared to the OmpF-containing one). The neutron reflection data also seems to support the existence of an OmpF/phospholipid bilayer, despite Fig. 3B being mislabeled by my eye. Normally the neutron “refractive index” - neutron scattering length density, aka nSLD – is plotted as a distance away from some reference (e.g., an easily determined interface or a metal layer on which your sample is ultimately deposited). It seems that is what they intended to write (the x-axis seems to be labeled as such) but is mislabeled with the “Q/A-1” tag.

In any case, much of biologically-oriented neutron scattering is dependent on the existence of contrast variation in the nSLD. You can purchase deuterated compounds (such as lipids), prepare buffers in deuterium oxide, and even express & purify deuterated proteins. You then mix and match your deuterated and protonated components to see what each component looks like when in complex with everything else. It is a low-resolution means of doing so, but the benefits can outweigh the disadvantages.

The authors move onto the ColN portion of their work, showing the microscopy and neutron reflection data for ColN interacting with the OmpF/lipid monolayer. The time-lapse microscopy of ColN with the pure lipid monolayer and the OmpF/lipid monolayer shows increased image intensity, but appears to “smear” homogeneously with the pure lipid monolayer while forming larger, brighter spots with the OmpF/lipid monolayer. Their analysis of the neutron reflectivity data indicates the presence of the ColN in the same layer with the OmpF, and not just interacting with its surface, as they see in the ColN + pure lipid monolayer sample. Given the contrast variation matching, they state that they are able to see ColN extend as it inserts into the lipid region, suggesting that it is unfolding to some extent. The increase in surface pressure would suggest that it is not going through the OmpF pore but is, instead, inserting into the lipid region next to the OmpF. If it was inserting through the pore channel, the surface pressure might be expected to level off and not keep increasing.

The SANS data round out the story – they’re looking at the ColN/OmpF complex in detergent. (I know, I know.) Anyway, their data-derived model has one of the ColN domains slithering down between the cleft between OmpF monomers, while the remainder of ColN remains protruding outward. If you look at Fig. 6C, the blue distance distribution (where you are only looking at scattering from ColN) has two peaks, one that overlaps with the red trace (where one is only looking at OmpF) and a separate peak. So this at least makes sense. They do discuss the potential for translocation via the pore, and some recent literature on that possibility.

Mostly, I thought that this was a really interesting bit of research – while there is the obligatory mention of potential application to antibiotic development, it’s pretty obvious that the fundamental scientific question of “how does a largish protein get across a cell membrane where the cell has no interest in letting it inside?” I think that the experiments were reasonable, were carefully done, and did not set off too many massive alarms in my brain while reading. I would like to think that you could use something like nanodiscs or bicelles for the SANS studies so you could at least approximate a native membrane environment – clearly, sample homogeneity is a concern, as scattering methods can be notoriously sensitive. (Did I ever tell you about the time I spent a good afternoon into evening washing banjo cells for SANS experiments since said cells were just disgusting?) I haven’t worked with nanodiscs – although I’ve heard and read more than I can shake a stick at - and my experience with bicelles hasn’t been quite so detail-oriented, so maybe it would require sublime experimental mastery beyond the typical.*

Anyway. That was kind of fun. Also, how many of you saw Ohm’s Law Survives to the Atomic Scale? I imagine people will want to confirm this, as it is definitely seems really cool. Clearly, it was custom-made by “hand” (well, scanning tunneling microscope), so no immediate applications to large-scale mass production any week soon, but that isn’t why we do science.

Now, off to think about thermodynamics for a while. I need to come up with a reasonable explanation of some data today….. Read more!