Telomerases, and a Twisty Tale

I saw two talks of interest this week. The first was Michael Stone's job talk on single molecule studies of telomerase, which I mentioned earlier. It was well attended, and he had a lot of data. Much of it was results that were published in a 2007 Nature paper. They were able to FRET label various points on the telomerase RNA, and used the labels to assay structural changes in the RNA upon binding to TERT and p65. He also showed some newer data on an assay they're developing to try to correlate these structural changes with changes in the catalytic efficiency of the telomerase. The data was interesting, but was mostly limited to showing that there were structural changes in the RNA upon binding to TERT and p65, which I don't think would surprise anybody. Trying to correlate those states with functional states of the enzyme seems like it will be the real meat of the work, and that's ongoing. Still, there was a lot of data there, and it was very well put together. I would have liked to have heard more about how how the telomerase RNA pseudoknot, but that just happens to be one of my personal interests (pseudoknots, that is). I asked if they had done any study of it, and he indicated that it was ongoing.


Braulio Gutierrez-Medina also gave a talk yesterday at the Cell and Molecular Biology lunchtime seminar (Hooray! Free pizza!) with the title, "A Twisty Tale Reveals Conformational Properties of Kinesin". There was some debate during his practice talk whether "twisted tale" would have been better, but personally, I think "twisty tale" sounds much cuter. Braulio attached kinesin to beads with flanking fluorescent beads, and was able to use the fluorescence to track rotational motion of kinesin as it was bound to microtubules. He used this to derive information about the torsional flexibility of the kinesin stalk under various conditions. He'll also be presenting a poster on this work at BPS.

Huzzah

I probably should have noticed this earlier, but it wasn't until group meeting this morning that I became aware that Steve is receiving the U.S. Genomics Award for Outstanding Investigator in the Field of Single Molecule Biology at the upcoming Biophysical Society Meeting next week. Apparently, he was nominated for the award for the past two years, but it was deemed unseemly that the society president or president elect should be given an award, so it was put off until this year. In 2006, it was given to Jim Spudich, who was Steve's postdoctoral advisor, and in 2007, it went to Howard Berg, who was Steve's graduate thesis advisor. So, Steve predicts, by this progression, that next year it should go to one of his postdocs. Keep your fingers crossed for me, kids!

Single molecule protein unfolding with optical traps

This paper by Sander Tans is a fascinating study of chaperone contributions to protein folding and stability by looking unfolding and refolding of single maltose binding protein (MBP) molecules in the absence and presence of the SecB chaperone. They use an interesting method to bind the protein to the beads used for optical trapping. The protein is made as a fusion with a quadruple c-myc tag at the C-terminus, allowing them to bind directly to the protein with an antibody-functionalized bead. The N-terminus has a biotin attached, and they grab it using a biotin-streptavidin linkage to a biotinylated DNA handle. The DNA handle is in turn attached to a bead by a digoxigenin-anti-dig linkage. There's a lot of linkages there, and it seems like a lot of potential failure points, but it worked! This is a contrast with this single molecule unfolding paper, by the Bustamante lab, where they used engineered cysteines at the termini to attach to linkers using maleimide chemistry.

The data is very compelling, and shows that SecB essentially binds to the unfolded MBP and stabilizes a non-native conformation, but cannot destabilized natively folded protein.

Dr. Tans is scheduled to discuss this work at the upcoming Biophysical Society Meeting "New and Notable" symposium. Unfortunately, I will not be attending BPS this year due to other pressing engagements (i.e., I have no data to present), so any news from attendees is welcome! If you go, let me know what you saw, and what you thought was cool!

Jobs jobs jobs

Couple interesting tidbits from the CM/AMO rumor mill:

• Ahmet Yildiz is apparently on the short list for a faculty position at Cornell. Ahmet and I worked together in the Selvin lab. He published the extremely influential first paper on FIONA doing single molecule tracking of myosin V. Go Ahmet!
• Tommy Angelini and I were also in grad school together, and though he doesn't do SM biophysics, I thought I'd mention that he's also listed as up for a biophysics job at Colorado. I sent him a Facebook message to confirm (except that he changed his Facebook name to "Manchester Hoboken", because he's a crazy mofo like that. Tommy used to have a band called Shakin' Babies.) Updates as they appear.

Also not from the rumor mill, but Michael Stone from the Zhuang lab is coming here (Stanford) to give a job talk next week, titled Single-molecule studies of telomerase ribonucleoprotein assembly, structure, and function. I'm interested in RNA structure, and did quite a bit of reading about telomerase pseudoknots a while back, so this should be interesting.

Responses

Here is some of the feedback I've received so far to my announcement about the blog:

• "it is a great idea, thanks for the notice!"
• "Nice idea. Good luck!"
• "Dude, this sounds so gay."

As you can see, opinions are highly polarized.

Also, Christian Perez pointed me to the blog Biocurious, which seems to be a pretty good general-interest biophysics blog, with a lot of emphasis on the physics end of things. However, the name makes me wonder.

Here we go!

This is going to be an attempt at professional blogging, we'll see how far I get! I plan to post news, journal articles, and interesting tidbits about single molecule biophysics. Since I have background in both fluorescence and optical trapping, I figure I'm well suited to the task, and I think it will be an interesting way to stay abreast of the current literature!

A few recent papers of note from Science:

• Out of our lab, Will Greenleaf and Kirsten Frieda published a paper about pulling on adenine riboswitches, which looks like a very interesting new application of optical trapping. This was all done with riboswitch fresh of the polymerase, and eventually, as the paper strongly hints, the goal is to look at time-resolved co-transcriptional folding events.
• Yale Goldman's lab has dropped a new paper on single molecule tracking of GFP-kinesin and GFP-dynein interacting with microtubles bound to tau, a microtubule associated protein (MAP) which inhibits kinesin. They find that tau actually makes dynein go backwards!
• Xiaowei Zhuang has graced us with another paper on stochastic optical reconstruction microscopy (STORM), this time for 3D super-resolution imgaing. It looks at first glance to be similar to Eric Betzig's published technique (PALM), but using astigmatism for Z-axis detection instead of sample scanning. Unfortunately, they chose not to cite my SHRImP paper, even though their original STORM paper did.