Biocurious

/ a biophysics blog

Hot off the Press: Single-ribosome translation

Posted 26 March 2008 by PhilipJ under &

While we’ve been watching trippy 70s-era translation videos on YouTube, the Bustamante lab has been busy measuring this process at the single-molecule level, at least indirectly. This was one of those surefire Nature papers, whenever someone figured out how to measure translation at the single molecule level using optical tweezers, it would show up in Nature, and sure enough….

In Following translation by single ribosomes one codon at a time (closed access, PDF), we get to see for the first time the march of the ribosome along mRNA. I don’t think we’re anywhere near the end of single-molecule ribosome work, and part of the reason why is the setup for the experiments outlined in this paper. Reproducing part of Figure 1 from the paper:

single ribosome experiments setup

What’s being measured is not the action of the ribosome itself, but the extension of the RNA/DNA construct as translation occurs. RNA/DNA handles are coupled to mRNA hairpins, and an initially stalled ribosome is then re-activated (by supplying the appropriate tRNAs), and the extension vs time of the entire construct is monitored at very high resolution. Examples of their extension vs time traces look like this:

ribosome steps

The left hand plot shows a typical trace as the ribosome carries out its work, and the right hand side shows what’s called a pairwise difference distribution, or basically the difference between data points. If there is some periodicity in the dynamics, this would show up as a peak in the pairwise differences, and indeed they see peaks at 2.7nm (and multiples thereof). This corresponds to three basepairs being broken in the hairpin, and the ribosome translocating by 3 bases (where three bases form a codon, the unit which specifies for an amino acid). While not a surprising result (despite the authors claiming this was “striking”), this is still significant.

The tricky bit, however, is that this doesn’t really get at the heart of the ribosome’s interesting mechanochemistry. We still know nothing about the force-velocity relationship in single ribosome molecules, and while there are some interesting experiments in this paper involving dwell times at Shine-Dalgarno sequences, and some discussion on changing the ribosome’s reading frame, the paper is a little short on really new measurements.

Technically this is impressive, but the new and interesting data on ribosomes that single-molecule techniques can measure are still to come.

(Hat tip: in singulo)

  Comment [7]

Trippy translation

Posted 25 March 2008 by PhilipJ under

I’m taking a class on the chemistry of biological systems this term (part of the reason why it has been relatively quiet around here recently). A large section of the course was on the details of protein synthesis, or how the ribosome takes mRNA and turns it into protein. Somehow this film was never shown in class, where a (literal) interpretation of the molecular dance is depicted:

Directed in 1971 by Robert Alan Weiss for the Department of Chemistry of Stanford University and imprinted with the “free love” aura of the period, this short film continues to be shown in biology class today. It has since spawn a series of similar funny attempts at vulgarizing protein synthesis. Narrated by Paul Berg, 1980 Nobel prize for Chemistry.

Called “A Protein Primer”, the film is surprisingly accurate given that it was produced in the 70s. The dance starts around the 3:30 mark. Enjoy!

(Hat tip: Kottke)

  Comment

Drew Endy on Engineering Biology

Posted 23 February 2008 by Andre under &

The third part of the Edge series “Life: What a concept!” is now online. This one is a talk with Drew Endy, a bioengineer at MIT. Despite existing for 30 years, we still haven’t realized much of the promise of biotechnology and Endy believes this is because we haven’t invested enough in making versions of biological systems that are easy to engineer.

America, 1860, machinists are building objects, steam engines, what have you. Nuts and bolts that hold together machines are specific to the particular machine shop that manufactures them. What that means is, if you buy some machine from a machine shop in Newark, New Jersey, and it breaks down in Chicago, you have to send it back probably to that specific machine shop, with the machines set to tool things on a particular set of designs in order to get the replacement part or to get the thing fixed.

In April of 1864, somebody says, enough; William Sellers of the Franklin Institute in Philadelphia gives a paper on a system for nuts and bolts. And he proposes the Sellers Screw Thread Standard […].

The consequence of this today is, when I go to the hardware store and get a nut and a bolt, so long as they don’t screw up the English/metric thing, I can take those two objects, and I can put them together. I don’t have to do an experiment. I don’t need to go talk to some Harvard professor to figure this out. I don’t need to do a controlled experiment to see if my first experiment worked. I just get the two objects and put them together.

So, Endy wants to do the same thing with biology. He draws an analogy with the development of computers that might convince you this is exciting. Computers went from large machines run by scientists to personal machines owned by large numbers of non-scientists (not necessarily non-experts!) that are programmable by anyone with time and motivation. Currently, synthetic biology is being done largely by big labs run by scientists, but engineers are also starting to take part, and according to Endy their different approach will yield many more benefits in the long term. I assume this passage is about Craig Venter, but please correct me if I’m wrong:

If you make biology easy to engineer, and you make it accessible, by definition people will learn about it, and write comic strips about it. You can talk to computer programming conferences about it, and it’s a different world. It’s a very different world from going around claiming that you’ve created life. It’s a very different world from going around filing patent applications that say you have invented the idea of a synthetic genome. It’s a very different world from going around and spending $40 billion on a classified biological defense facility, at the site of the past U.S. Offensive Biological Weapons program. And so there’s a cultural mismatch.

Again with the cultural mismatch. One group arguing that intellectual property needs to be controlled to be taken advantage of and the other arguing that new tools need to be open to everyone to be taken advantage of. It will be interesting to see how this plays out. I suspect it won’t be the case that one approach dominates but that we’ll end up with aspects of both coexisting for a long time, as is currently the case with open source and proprietary software.

Regardless of exactly how it develops, expect big changes in our ability to control biological systems and expect significant parts of biology to be reduced to information science, the same way significant parts of electrical engineering have been reduced to information science.

  Comment [1]

Things that biophysicists often do that real biologists never do?

Posted 20 February 2008 by PhilipJ under

Reference Alberts et al‘s Molecular Biology of the Cell in journal articles.

  Comment [9]

Anatomy of a seminar

Posted 22 January 2008 by PhilipJ under &

They don’t all go like this, but the vast majority of seminars I attend seem to follow this general outline.

1. Introduction of Esteemed Speaker by Local Professor with the largest overlap in research interests. Enumeration of every award Esteemed Speaker has ever garnered is standard issue, and if Local Professor and Esteemed Speaker know each other, humorous story from “well, not THAT long ago” is recounted, though chances are you probably had to be there (unless it involves breaking obscenely expensive equipment, in which case everyone has a good laugh).

2. Esteemed Speaker takes over, and begins with a bunch of overly broad introductory slides. Naive audience members might think cancer was about to be cured, or a theory of everything (or at least, everything the speaker is interested in) is near discovery.

3. (For experimental talks, which are the majority I see.) Very brief overview of experimental technique presented, to the point that you have no idea how anything is being measured. Sample prep usually not even mentioned, despite having been years-long labours of love for at least a few graduate students who may or may not have even lasted long enough to see the experiments carried out.

4. A handful of slides on results, culminating with a question, usually from Local Professor, which elicits the following response from Esteemed Speaker: “Well, it’s not QUITE that straightforward” often followed quickly by “We can talk about it after if you like.”

5. A conclusion with extremely specific results, with no cure for cancer or the unification of gravity and quantum mechanics in sight.

6. An acknowledgement slide of all the graduate students and postdocs who actually did the work presented, where the couple of students or postdocs who have since found gainful employment are highlighted. Students in the audience wonder what the other 90% of the former lab members are doing, and then get depressed thinking about their own futures. (Alternatively, this could have been at the very beginning of the talk.)

If nothing else, number 4 is a shoe in. Related to this, I am finding more and more that the kind of talk given in a group meeting environment is more interesting: there’s no grand-standing, there’s no “massaging” of the data, and there is usually good discussion about the real issues faced on data analysis and collection, or the development of simulations, or what have you. Basically all the stuff that is, in number 4 above, brushed over and relegated to a private discussion between Esteemed Speaker and Local Professor after the talk, despite the fact that this is where a lot of the interesting science is found.

I guess I could rephrase my displeasure this way: results are, to first order, presented as though everything fits into a nice little box. But everyone knows that’s rarely the case in research. Also worth reading, YoungFemaleScientist voiced her displeasure with seminars in a slightly different way here (though I don’t agree that most speakers are out to please the old white guys in their field).

  Comment [2]

André on science and blogs

Posted 22 January 2008 by PhilipJ under &

From Matt Agnello’s vimeo page:

The SPARC-ACRL Forum at ALA ’08 entitled “Working with the Facebook generation: Engaging students views on access to scholarship.” Panelists discuss the merits of student activism, patent reform, blogs as a communication medium for scientists, and students as active members of a discussion about the right to access information for scholarly work. Features Andre Brown, Nelson Pavlosky, Stephanie Wang, and Kimberly Douglas as panelists.

I’m embedding Matt’s video here, and André is the third speaker up, at around the 42 minute mark.


SPARC-ACRL Forum ’08 from Matt Agnello on Vimeo.

Hat tip: PhysMath Central.

  Comment [2]

Previous