Monday, December 19, 2011

Weekly RNA News - Week LI - December 2011

Top News of the Year.
According to Chemical and Engineering News

- Spliceosome Assembly Tracking by New Fluorescent Microscopy Technique
Melissa J. Moore at U. Mass. Medical, Jeff Gelles at Brandeis, Virginia Cornish at Columbia.
http://dx.doi.org/10.1126/science.1198830

These researchers use a new spectroscopic technique called Colocalization Single-Molecule Spectroscopy (CoSMOs) to track the dynamics of formation of the spliceosome. They corroborate what has been proposed before where the order of association of the spliceosome on the pre-mRNA is U1 -> U2 -> tri-snRNP (U4/U6.U5) -> NTC (multiprotein Prp 19-complex)
To summarize nothing better than their own mechanistic picture with estimated first order reaction constants.

So. I have been looking for the molecular weight of the Spliceosome for a while now and can't find it. I find that parts of it are around 200kDa, but I don't even know how much the so-called tri-snRNP assembly weighs. If you find it I would appreciate your feedback very much. The prokaryotic ribosome weighs about 2600 kDa.

- Modified Citosine
Guo-Liang Xu from Academy of Science of China and Chuan He from Chicago U.
http://dx.doi.org/10.1126/science.1210944

Evidence for Tighter Wrapping of DNA upon Methylation.
According to Chemical and Engineering News

On the science and technology concentrates from this week on C&EN, work on changes on DNA wrapping around the nucleosome are reported. The work comes from researchers Ju Yeon Lee and Tae-Hee Lee at Penn. State. In the article titled "Effects of DNA Methylation on the Structure of Nucleosome" http://dx.doi.org/10.1021/ja210273w published in the Journal of the American Chemical Society

Monday, December 12, 2011

Weekly RNA News - Week L - December 2011

Is Arsenic-DNA Possible?
A Controversy is Born.

For better or worse Felisa Wolfe-Simon, a research fellow at NASA's Astrobiology unit became a scientific celebrity a year ago. In an express paper to the highest ranked North-American journal, that is, Science,  Dr. Wolfe-Simon (who received her PhD from Rutgers in Oceanography) reported, along with her collaborators that:

"A Bacterium Can Grow by Using Arsenic Instead of Phosphorus"

The bacterium was taken from Mono Lake, California, a  "hypersaline and alkaline environment", as reported in the Science paper http://dx.doi.org/10.1126/science.1197258.
In the time since the express publication a number of papers have been written for, against, and in a neutral tone regarding the reported observations.

I find it interesting that before December 2010, that is, the date of the express report, Dr. Wolfe-Simon was already reporting along with Paul C. W. Davies (why is this name familiar?... ohhh, is the same guy of Superforce, the best-seller layman book on unification theory, a kind of Isaac Asimov guy!) on the Arsenic conjecture in a paper with the very suggestive title "Did Nature Also Choose Arsenic?" in the International Journal of Astrobiology, 2009, 8, 69-74.

Another one of the past collaborators of Dr. Wolfe-Simon and also a researcher at NASA's Astrobiology, but not a coauthor on the Science paper, that is, Steven A. Benner (not to be confused with Steven Brenner @ U.C. Berkeley) wrote a nice commentary  (http://dx.doi.org/10.1126/science.1201304) about the published paper. He highlights how the main problem with an arsenate-diester would be its estimated half-life in water, which, by back-of-the-envelope calculations, leads to a half-life which is too short (About 1 minute) compared to that of the phospho-diester backbone in DNA (About 30 million year). He also proposes and experiment which I'm sure a lot of researchers thought of when eyeing for the first time the Arsenic life report, that is, to use an Arsenic isotope.

One of many papers (http://dx.doi.org/10.4161/adna.2.1.15509) with some criticism is that of Frank-Kamenetskii of B.U published in a new journal named Artificial DNA, whose chief editor is PNA (Peptide Nucleic Acids) main-man Peter E. Nielsen, here it is:

"After all, recent history has taught the scientific community to be very skeptical to any unusual claim, especially appearing in such high-profile journals like Nature and Science. It suffices to  mention the most recent embarrassment with publication in  Science, with loud fanfares, of an article about “arsenic life”.
Once someone reads carefully the article and supporting data, it becomes clear that the data by no means support the claim that arsenic substitutes phosphorus in DNA of a bacterial strain obtained by the authors."

On the other hand theoreticians and modelers have not been shy on jumping right into the problem, two examples are the publications by  Liz Denning at Alex Mackerell group in Maryland (http://pubs.acs.org/doi/abs/10.1021/ja201213b) and Jiri Sponer's group at Brno, Czech Republic (http://dx.doi.org/10.1021/jz200015n).

In conclusion, this story just gets more interesting as it ages. On a personal note I would have to say that on my first read of the paper my thoughts were very close to those of the wise Maxim, but now I'm not so sure and see a window of possibility on this most interesting result. Only time and hopefully Felisa Wolfe-Simon will be able to wrap-up this story on whether she's found a very interesting extremophile, or an alien living among us.


----


An update on my last comment is that there seems to be no results from Wolfe-Simon proving the much publicized article and it's critics are getting some interesting results in the sort of un-asked-for peer-review, as can be see in an article posted to arxiv called "Absence of arsenate in DNA from arsenate-grown GFAJ-1 cells". There is also an iteresting posting of some of the reviewers opinions at Redfield's website.

Monday, November 21, 2011

Weekly RNA News - Week XLIV - November 2011

Meni Wanunu, Swati Bhattacharya, Yun Xie, Yitzhak Tor, Aleksei Aksimentiev, and Marija Drndic
Northeastern, Uni. Illinois and UCSD
Nanopore Analysis of Individual RNA/Antibiotic Complexes.

Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3–3.5 nm diameter pore fabricated in a 8–10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug–RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.

http://dx.doi.org/10.1021/nn203764j

Tuesday, November 15, 2011

Weekly RNA News - Week XLIII - November 2011

Lately I have been late on my weekly posts, so, for now I will only put some brief news until I find the time to write better posts.

- According to experiments carried out by Victoria Jeanne DeRose , Alethia A. Hostetter , and Maire F. Osborn from the University of Oregon, there is more cisplatin acumulation in total RNA in yeast than in total DNA in yeast.
http://pubs.acs.org/doi/abs/10.1021/cb200279p


- Researchers Jeremy E. Wilusz, Joseph M. Whipple, Eric M. Phizicky and Phillip A. Sharp, from the MIT and Uni-Rochester have found that tRNAs marked with CCACCA are targeted for degradation.
http://www.sciencemag.org/content/334/6057/817.abstract


- Antony M Jose, Giancarlo A Garcia and Craig P Hunter.
Harvard and U.Maryland.
Two classes of silencing RNAs move between Caenorhabditis elegans tissues
http://www.nature.com/nsmb/journal/v18/n11/full/nsmb.2134.html


- H. James Tripp, Ian Hewson, Sam Boyarsky, Joshua M. Stuart and Jonathan P. Zehr
UCSC and Cornell
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.
http://nar.oxfordjournals.org/content/39/20/8792.short?rss=1


-Lipfert J, Kerssemakers JJ, Rojer M, Dekker NH.
Delft Uni. Netherlands
A method to track rotational motion for use in single-molecule biophysics
http://www.ncbi.nlm.nih.gov/pubmed/22047303

Monday, October 17, 2011

Weekly RNA News - Week XXXVII - September 2011

New Structures in PDB

A new 70S  ribosomal structure was released to the Nucleic Acid Database this week with PDB_ID:3zvo. The ribosome structure has a release factor protein attached to it. This release factor is called release factor 3. The structure is coming from Ramakrishnan's group and in line with their previous work it's a ribosome extracted from the Thermus Thermophilus extremophile bacteria which lives in hot springs.
The new structure has a 3.8 Angstrom resolution, so perhaps a little bit above the cutoff resolution for the rnasteps database.


From the new structures pouring into the PDB this past week here is a movie of Mss116p (NTE deletion) bound to ssRNA and AMP-PNP.



video

The PDB_ID for this RNA chaperone is 3sqx.pdb.
The chaperone functions in splicing mitochondrial group I and group II introns.
The movie is not very nice since I'm still learning which video format will be preferred by blogger.

Friday, September 23, 2011

Weekly RNA News - Week XXXVI - September 2011

Not One but Two!, Recent Reviews on RNA Structure, Interactions, and Folding Principles.


Two reviews have just come out from the Mondragón group at Northwestern and from the Pyle group at Yale.


Emerging Structural Themes in Large RNA Molecules
Nicholas J. Reiter, Clarence W. Chan and Alfonso Mondragón
Current Opinion in Structural Biology 21, 319-326 (2011)

In line with their previous research (i.e. the RNase P X-Ray structure, PDB_ID:3Q1Q) the authors stick to reviewing what has been learned from intermediate size RNA molecules, that is, RNA molecules larger than a hundred nucleotides, but smaller than say a thousand nucleotides.

The main points argued in this review are:

- RNA's of this size are relatively flat due to tertiary interactions, namely, "extensive" coaxial stacking, loop-loop interactions, and not mentioned in the review side by side helical arrangements.
- The structures of the functional cores of intermediate size RNA's are conserved, not necessarily the sequences.
- The functional cores don't need large conformational arrangements, they are said to be preassembled and usually this happens around a metal ion.
- Molecular recognition of "targets" is accomplished by shape-complementarity and specific atomic interactions (base-pairing, base-stacking, base-sugar, base-backbone). This is a general principle in molecular recognition.
- Adenine's are statistically more abundant than any other base in tertiary interacting regions, they are also the most conserved in all RNase P's.
- Proteins extend the functionality of RNA's and can be essential as in the case of the ribosome and the spliceosome, or non-essential, as in the case of RNase P and Group I and II Introns.

They conclude that the best is yet to come concerning RNA's in line with the promise, highly encouraged by Breaker's Lab. research, that many more RNA structures are to come and then this few empirical facts we've come to know will expand or change accordingly.



For the Group II Intron one can have an image like the above one, showing the helical regions as blue cylinders and the phosphates colored grey connected with a string in red, to illustrate the "flatness" of intermediate sized RNA's.


The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks
Samuel E. Butcher and Anna Marie Pyle
Accounts of Chemical Research X, xxx-xxx (2011)

Interestingly enough the previous paper (the one of Reiter) comes from a whole issue devoted to nucleic acids and edited by Anna Pyle.

In this review Butcher and Pyle take a look at the main interactions and structural elements found in RNA's today.
These seem to be split into:

- Coaxial Stacking of Helical Regions.
- Geometric Organization of Helical Junctions.
- Long-Range Interactions of Watson-Crick Base-Pairs.
    * Kissing-Loops.
    * Pseudoknots.
- Minor Groove Triples and A-Minor Motifs.
- Kink Turns and Other Turn Motifs.
- Tetraloop-Receptor Motifs.
- Intercalation Motifs (T-Loops).
- Triple-stranded RNA's (more like RNA triplets)
- RNA Quadruplexes.

The final remarks on the review concern the nature of the ribose, the 2'-OH interactions (e.g. Ribose Zippers), metal ions (the description of new crystallographic results in accordance to Draper's seminal paper reviewed in this here blog) and non-canonical base-pairs.

In Figure 2 of the article an image of a kissing-loop interaction is shown. The following image reproduces such image with helical regions identified by 3DNA represented as blue cylinders.

Tuesday, September 13, 2011

Weekly RNA News - Week XXXV - September 2011

RNAase P: At Last, the Key Finds its Lock
Benoit Masquida and Eric Westhof
RNA 7, 1615-1618 (2011)

Masquida and Westhof who are both at Strasbourg, France, review the X-ray structure obtained with a resolution of 4.2 Angstroms of RNase P, a ribozyme like the ribosome which has the ability to work as a "multiple turnover" enzyme. The structure of RNase P has PDB_ID's: 3Q1Q and 3Q1R, the difference is that the second one contains the 5'-leader whereas the first comes without, and at 3.8 Angstrom resolution.
The structure was determined by a group of researchers at Northwestern University and the University of Chicago and the main author is Nicolas Reiter who is a post-doctoral researcher at Alfonso Mondragon's Lab at Northwestern. The reason for the review is mainly that Tsai, Masquida, Westhof and others proposed a structure for RNase P in 2003 from secondary structure maps enriched with hydroxyl-radical footprinting data and it's quite close to the final crystal structure. A pymol generated figure showing the full holoenzyme is drawn below:

Notice the 5'-leader is rendered as spheres with carbons in grey color and just in top of the protein part (drawn in black) of the holoenzyme (holoenzyme=enzyme+cofactors). The surface in blue is just given the name P-RNA, and the part rendered as sticks is  pre-tRNAphe. The whole structure has a total of 423 bases coming from the P-RNA and the pre-tRNAphe.

Thursday, September 8, 2011

Weekly RNA News - Week XXXIV - September 2011

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Jan Gorodkin and Ivo L. Hofacker
PLOS Comp. Bio. 7, e1002100 (2011)

This is one of those cases where an article defies the traditional classification. By this I mean that although this article is clearly a review, it is not being published in a review journal, or maybe it's more likely that I don't understand the format of how PLoS works, for example their dislike for the traditional page-numbering scheme.
OK, stop ranting about irrelevancies and stick to the article.
Ohh, well, I can't stop with the "irrelevancies".
I guess it's the model of PLoS which makes articles hard to read, yes, an unfair judgement based on one article which you were expecting to be great (due to the authors) and then you're thoroughly deceived by the many errors and the lack of depth of the content, specially when compared with their much nicer article "De novo prediction of structured RNAs from genomic sequences" published in Trends in Biotechnology, a "regular" type of journal without the PLoS hype.

The article main topic is that of "de novo" discovery of non-coding RNA's. To this end the authors highlight two main strategies.

1) Sequence based alignments.
2) Synteny/Orthology with structure realignment.

Strategy one doesn't need much explanation, just that databases of know RNA sequences are necessary to make comparisons across organisms, for example the Rfam (RNA-families) database.
The second case brings up jargon, and it's not clear what they might mean if one sticks to the wikipedia definition of the term synteny. It would be nice if there was an example of what they mean in practice. What I understand is that perhaps in the second strategy secondary structure alignments are taken into account in the context of distant regions in the same chromosome which might refer to the "same" gene.


BlastR—fast and accurate database searches for non-coding RNAs
Giovanni Bussotti and Emanuele Raineri and Ionas Erb and Matthias Zytnicki and Andreas Wilm and Emmanuel Beaudoing and Philipp Bucher and Cedric Notredame
Nucleic Acids Research, 39, 6886-6895 (2011)

The main idea of this article is to use the already existing techniques for alignments of proteins to the alignment of RNA's. To test the perl script they have implemented to interact with the already existing ncbi-blast package I downloaded the full long-non-coding RNA database from :
http://www.lncrnadb.org/
And then I used it as database to compare, say, one of the sequences existing in such database.
Not surprisingly the result is a 100% score in their similarity measure, and it took a couple of hours to get it all done. Here's a snapshot of the results of running the command:

blastallR.pl -p blastr -i NR_003141.3 -d database/ncbi_blastR_format/db -m 8


Not surprisingly the first score matches as indicated by the 100% score.

Tuesday, August 23, 2011

Weekly RNA News - Week XXXIII - August 2011

It's amazing what a very simple molecule can do. In this case I am talking about 1-Aminoanthracene. I think any chemist, and even non-chemists will be able to draw this simple molecule, yet, very few would be able to tell you that you can make the spinal cord of a tadpole light-up when it has ingested the molecule. Such is the image presented to us in the latest issue of Chemical and Engineering News. Yes, this is where one so easily falls in love with science. Simplicity at its best. This certainly is one beautiful way to obtain powerful insights into nature.

Here's a copy of the image which has been made by Daniel Emerson at Ivan J. Dmochowski's lab at U.Penn in Philly:


The original article was published in the Proceedings of the National Academy of Sciences of the U.S.A.



Carbonaceous Meteorites Contain a Wide Range of Extraterrestrial Nucleobases
Michael P. Callahana and Karen E. Smith and H. James Cleaves II and Josef Ruzicka and Jennifer C. Stern and Daniel P. Glavin and Christopher H. House and Jason P. Dworkin
PNAS, XX, XXX-XXX (2011)

Back to a claim of old, that of finding nucleobases in meteorites. The difference in this study seems to be that of finding some derivatives of purine which are not present in earth nor in the surroundings of the surveyed meteorites. This reminds me of reading the older papers of Dworkin on the possible synthetic routes of this babies in a pre-RNA world.


Monday, July 25, 2011

Weekly RNA News - Week XXIX - July 2011

RNA is back in the front page news of "The New York Times".
A note by some guy called Dennis Overbye is bringing back news on RNA to the front pages. Well, really the news are not so new, but it's good to see that folks are still interested in the origin of life, of course, this is not at all to be unexpected since the main "hot-shot" in the article is Gerald Joyce, and yes, if that name rings a bell it's because is intimately associated with that of the great Leslie Orgel.
Joyce might have been the favorite grad. student of Orgel, and, actually must consider himself quite lucky since Orgel liked to work alone and seldom gave the privilege of coauthorship. Now, what's interesting is that, even though the article is well written and well informed and gives good credit to people like Alex Rich, it also states:

"The first inhabitant of this Eden, chemists suspect, was RNA"

And doesn't even give a small paragraph to say, that chemists also suspect that it could have been a pre-RNA molecule.

Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure
Desirae Leipply and David E. Draper
JACS, XX, xx-xx(2011)
Nice article showing a technique to be able to distinguish two types of association of Mg2+ ions to RNA.
The main idea the article exposes is that Mg2+ ions can interact with RNA's in two ways. In most cases they can form an ion atmosphere (purple haze in image) around the RNA, and in other cases they can get stuck in confined regions (site-bound - brown dot in image) and as such are considered as chelators.

They propose experiments where the free energies of these different ways of binding can be determined.



In the next image the larger green sphere represents a Magnesium site-bound to RNA. The purple, larger sphere is potassium also site-bound, and the surface is the solvent accessible surface mapped with the color of the electrostatic potential. In the right the secondary structure corresponding to structure PDB_ID:1hc8



Effect of Locked Nucleic Acid Modification on Thermal Stability of Non-canonical DNA Structure
Bhattacharyya J, Maiti S, Muhuri S, Nakano SI, Miyoshi D, Sugimoto N
Biochemistry, XX, xx-xx(2011)

A fast look at this paper shows that there are no references whatsoever to the structural work either from modelling studies of Pande and Nilsson, or to the experimental one of Eichert, Forster and collaborators.
Perhaps since they've focused their attention in parallel instead of the more common antiparallel strands, then they didn't worry so much about LNA studies on antiparallel DNA strands.

Thursday, July 21, 2011

Weekly RNA News - Week XXVIII - July 2011

The Endless Subtleties of RNA-Protein Complexes
Eric Westhof and Valerie Fritsch
Structure, 19, 902-903 (2011)

As in other occasions the authors give a good idea of what is to come in the field of RNA, or at least, what would be nice to see coming. In this case they comment on the work done at Juli Feigon's lab at UCLA on the interaction of a protein which binds a double-stranded RNA region of around 14 base-pairs and which contains two G.U wobble base-pairs and is flanked by a tetraloop. Westhof and Fritsch mention two tricks by which proteins can recognize double-stranded RNA helical regions. One is that the helical region per-se is "altered" from a canonical Watson-Crick paired one through bulges in the helical stem or non-canonical pairings modulating it's major groove so that it looks more like a B-DNA conformation one, that is, one which is wider and not as narrow, allowing for sequence recognition. The second trick, and which is the one adopted by the dsRBD (double-stranded RNA Binding Domain) of the reviewed NMR structural work, is that of interacting with the single nucleotides of the loop region. The Feigon lab. work shows how a tetraloop with a different sequence than the "canonical" AGNN one, but which accomplishes a very similar three dimensional fold, can also be bound by the dsRBD showing that not all can be predicted through RNA sequence alone, but that structural data is essential for understanding the details of protein-RNA interactions.
The Structures under PDB_ID: 2LBS have not been released yet.

Tuesday, May 31, 2011

Weekly RNA News - Week XXII - June 2011

Halima Mouhib and Wolfgang Stahl and Monique Luthy and Michelle Buchel and Philip Kraft @ Germany and Switzerland.
Cassis Odor through Microwave Eyes: Olfactory Properties and GasPhase Structures of all the Cassyrane Stereoisomers and its Dihydro Derivatives.
Angewandte Chemie International Edition, 50, 1-6 (2011)

I came across this article while reviewing the Chemical and Engineering News of this week.
What seems interesting about this publication is that such a small conformational change can affect drastically the chemical reactivity, and directly the human sense of smell, also, since these conformational changes in sugars are seen in RNA, then it's just a related story that seems, whatchamacallit, cute.
I can't help but to like that they use correct CPK colors, yes, what do u know, carbon is black, victory!, and also that they seem to be using pymol. Paying attention to the references at the end of the paper perhaps the images were done with Accelerys discovery studio.
But wait, don't be too emotional and pay attention to detail. Actually it is not all a conformational effect. The isomer which has a more fruity character is a DIHYDRO derivative.

Tuesday, April 5, 2011

Weekly RNA News - Week XII - March 2011

A. Vazquez-Mayagoitia and S.R. Horton and B.G. Sumpter and J. Sponer and J.E. Sponer and M. Fuentes-Cabrera
Ab-initio modeling of a possible prebiotic reaction favors ribose over other possible sugars.
Astrobiology, 11, 115-121 (2011)
Many of us like to munch from time to time into the big question. That of the origin of life. Frankly, my guess is that anyone who works with RNA at any level is always tickled, to varying levels, by the big question. The authors of the referenced paper show a detailed quantum mechanical Ab-intio study on a so-called "silicate-mediated formose reaction" which, they show, by energetically favoring arguments, prefers ribose over other sugary options.

Robert V Brown; Laurence H Hurley @ Uni. Arizona
A Review of Cases where DNA might act like RNA
Biochemical Society Transactions, 39, 635-640 (2011)
A fun review mainly concerning the G-quadruplex and how this, and other DNA conformations with loops, for example, might behave in a similar fashion to RNA. It´s interesting to see their reproduced graph of the relation between G-quadruplexes and cancer.

Weekly RNA News - Week XI - March 2011

Jun Feng and Nils G. Walter and Charles L. Brooks, III @ University of Michigan
All-atom Go model study of preQ1 riboswitch aptamer domain folding.
Journal of the American Chemical Society, 133, 4196-4199 (2011)
Feng, Walter and Brooks present interesting results using a Go model for simulating the folding of an RNA sequence into a riboswitch aptamer in the presence of a metabolite called preQ1. The model used seems to favor a description of a funnel shaped free-energy landscape for the folding of this RNA riboswitch. It's interesting to see that what is described as a structure made of two helices called P1 and P2 could also be described as an "irregular" triple-helix:
Some very interesting thoughts come out from reading this article. The folding of this riboswitches must be pretty fast, pico, nano seconds? so, these are good cases for performing MD simulations. In general the folding of parts of mRNA into structured regions seem to be good targets for MD research. I also wonder if the methodology used can take into account the possibility of having a rugged RNA folding landscape and if such case would influence the sequential and cooperative folding mechanism results.
Other things which would be interesting to see are the electrostatics of the A-tract of the folded configuration, for example.

Martin Mann and Konstantin Klemm @ Freiburg & Leipzig
Efficient exploration of discrete energy landscapes
Physical Review E, 83, 1-7 (2011)
The authors use a so-called number partitioning problem, which is common in computer science, to be able to stochasically sample the free energy landscape of RNA secondary structures.

Thursday, March 10, 2011

Weekly RNA News - Week X - March 2011

Scott, Coyle, and Doudna @ Berkeley
Xrn1: Structure of a messenger RNA degrading enzyme in complex with three DNA thymines.
Molecular Cell, 41, 600-608 (2011)

The Doudna lab comes again with another interesting structure related to RNA mechanics. As Scott, Coyle, and Doudna say in their paper, there is only one enzyme with the task of degrading mRNA in the cytoplasm of eukaryotic cells, this enzyme is called Xrn1, which sounds a lot like a sci-fi movie to me. They also say that the enzyme weighs 175 kDa, and is conserved from yeast to mammals. In order to crystallize the structure they used DNA instead of RNA. This you can see in the structure with PDB_ID:2Y35. The idea of the trick is that it takes longer for Xrn1 to degrade DNA than RNA, and the mechanism of degradation is assumed to be similar enough to that of an mRNA since it is based mainly on recognition of an RNA substrate "marked" by a 5'-monophosphate.

In the following image you can clearly see how Histidine 41 and Triptophane 540 kind of make a stacking trap of the three thymines, you can also see in the right part of the image the clear hole where the mRNA must come in and out from, I guess:



Figure four of their article shows the full mechanism they propose for the process of mRNA decay as a four step process of Binding, Hydrolysis, Thermal Breathing, and Translocation.


McCown, Roth and Breaker @ Yale
More glmS ribozymes identified via sequence-structural consensus and with the addition of this ones a new (refined) consensus is suggested.
RNA, 17, 728-736 (2011)
By using the infernal software which looks at sequence consensus and secondary structure consensus they identify more possible candidates for a type of ribozyme. This ribozyme is called glmS, and it's found in prokaryotes.
It seems like this ribozyme is located at the 5' un-translated region (UTR), of mRNA, but, it does assume a 3D-fold. Targeting this ribozyme with antibacterial drugs might result in the control of expression of peptidoglycan and extracellular lipopolysaccharides, which, I'm guessing, must be essential for having a functional prokaryote bacteria.
In general, the article goes along the main proposal or idea of Breaker that there are many 3D structured RNA's that we still don't know much about.

Fang, Yoffe, Gelbart, and Ben-Shaul @ UCLA and Hebrew Uni @ Jerusalem
Another secondary structure folding algorithm where sequential folding starts after locating the duplex (base-pair) which results on the largest possible single stranded loops.
J. Phys. Chem. B, XX, XX-XX (2011)
Perhaps the best way to describe this new algorithm for secondary structure prediction is by using their main figure reproduced here:

Tuesday, March 1, 2011

Weekly RNA News - Week IX - March 2011


Mackay @ U. Sidney, Font and Segal @ UCDavis
The Prospects for Designer Single-stranded RNA-binding Proteins (RBP)
Nature Structure and Molecular Bio., 18, 256-261 (2011)
There are an array of possible uses that RNA-binding proteins could be engineered for. The following figure in their publication makes a nice review of such possibilities.

In their review they show that there are mainly four classes of RBP's. They are called RNA recognition motifs (RRM), Pumilio repeat domains (PUF), human heterogeneous nuclear ribonucleoprotein K homology (KH), and zinc-fingers (ZF). Of these proteins so far the most efficient in recognition are the PUF ones, but the authors point out that this might be due to the infancy of the field.
They also mention the possibility of having proteins that bind to double-stranded RNA's, like the ones present in viruses and in the "new" RNA world of small interfering RNA's and micro RNA's, but focus their attention on single stranded RNA binding, which makes sense if one wants to target mRNA.
I find this review very interesting since in the greater sense it implicitly says that this is a way to bring back the game to proteins. Just by looking at their very neat figure for possible protein-ssRNA interactions one just can't help to wonder that the yellow blob, instead of being a protein, could be an RNA, a DNA, a PNA, or a modified nucleic acid.

Wednesday, February 23, 2011

Weekly RNA News - Week VIII - February 2011

Various authors and N. Ban (ETH) and J. Doudna (UCBerkeley)
Signal Recognition Particle (SRP) in complex with receptor (SR) at 3.9 Angstrom
Science, 331, 881-886 (2011)

Still an unreleased structure in the Protein Data Bank but will be coming out soon.
The Signal Recognition Particle is an RNA-protein complex which delivers at the time of translation (co-translationally) membrane and secretory proteins. The SRP is made of a surprisingly long double stranded RNA, I wonder if it stays "straight" thanks to the aid of the protein, and why would it want to do that?


A. Robbins-Pianka and M. D. Rice and M. P. Weir @ Wesleyan, Connecticut
Translation initiation sites (TIS) are influenced by secondary structure downstream and upstream of this sites in highly expressed genes.
Bioinformatics, 26, 2651-2655 (2011)

The results are clearly explained in their abstract:
"Trends in base composition and base-pairing probabilities suggest that efficient translation initiation and high protein expression are aided by reduced secondary structure upstream and downstream of the TIS. However, the downstream reduction is not observed for sets of TISs with nucleotide sequence contexts unfavorable for translation initiation, consistent with previous suggestions that secondary structure downstream of the ribosome can facilitate TIS recognition."
And in the following figure:

Monday, February 21, 2011

Weekly RNA News - Week VII - February 2011


Bujnicki Lab @ Poznan - Poland
ModeRNA python based software for RNA fold prediction.
NAR Advanced Publication. February 2011

A new software for RNA structure prediction from sequence given the existence of a structure with similar sequence is out, it's called ModeRNA and is somewhat similar to what the MC-Fold MC-Sym pipeline of Major does or the s2s, assemble "pipeline". The article has a nice up to date review on what is out there for RNA structure prediction. Published ahead of print in NAR.
You can find it online at: ModeRNA.
The last update on the software was done in november last year.


Xiao Group @ Hubei - China
Guided manual adjustment of atom clashes and atom stretches on RNA reconstruction.
JBSD 28 675-843 (2011)

Sometimes nice papers, at least from the creative point of view, go to the journals with, perhaps, not such big impact factors but strong traditions behind. I'm liking more and more some of the papers in the journal of biomolecular structure and dynamics, specially if the big shots are not the main authors. I liked the article by Zhao Y, Gong Z and Xiao Y. in JBSD 28 815-26, (2011).


Dill Group @ UCSF - USA
A so called semi-explicit solvation model which aims to be analogous in results to explicit solvation but consuming a much shorter computer time.
PNAS ahead of print February 2011

Not precisely RNA news, but an interesting method that could be applied to RNA's since it's a general solvation method.
The main idea is (coherent with Dill's group work) to think about "partition theory" type ideas, that is, we assume that the total free energy of a process can be split into additive contributions. In this case Fennell, Kehoe, and Dill propose that the free energy of solvation can be split into three components, a non-polar one, and two electrostatic polar components, one due to a first solvation shell, and the second due to the remaining bulk effect. The practical trick to do what they call semi-explicit assembly (SEA) is a four step process as clearly illustrated below:

Thursday, February 10, 2011

Weekly RNA News - Week VI - February 2011


Dekker Lab.
Nano-sized quartz cylinders for force-extension experiments.
ACS Nano. 2011 Jan 31 ahead of time.

In the Dekker lab. in the Netherlands they're now using electron beam litography to make nanometer sized cylinders and truncated cones made of quartz for use in single molecule experiments, for example for use in force extension experiments of DNA or RNA.
Dekker lab. has already provided some nice results on measurement of the persistence length of double-stranded RNA of around 640 Ångström using magnetic tweezers and compliance to the Worm-Like-Chain model.



Sarah Woodson and Eda Koculi
Review on native polyacrlyamide get electrophoresis (PAGE) on RNA.
Methods in Enzymology, Volume 469, 2009, Pages 189-208

My reviews are mainly based on what I get fed to me trough automatic periodic searches for favorite authors and topics in pubmed, and also from periodic flash reviews of the headliners related to RNA of the big journals from the US and GB. Sometimes what pubmed sends is outta sync, that is, this review is a 2009, still valid though.
It actually has some very, very, nice and simple gels which can be read in quite the clean manner. In the gel in the upper part of the image the part marked by P4-P6 refers to a catalytic RNA of the so called group I intron type, the U1 and U2 lines are constructs where the RNA sequence has been modified, that is, these are mutants. We can infer a structural change due to the sequence modification by the difference in the migration on the gel of the mutants and the original. In the lower part of the image a very interesting fact of RNA is shown, that is, RNA while folding can easily be "trapped" into intermediate folds (denoted by I) before getting to the most stable or native (denoted by N) one. We can also see that a mutated RNA (L2L5cP3) can fold faster into an "intermediate-free" lane in comparison to the wild type (wt).



It is interesting to see that in the same journal-book Dave Lilley also has some very nice experiments for what can be learned from RNA helical junctions from gels.
And not only does Sarah Woodson have the previous review but there is another one regarding OH radical footprinting in vivo using X-Ray. While refreshing what I understood of OH radical footprinting I found the following Tom Tullius quotation:

"Because the hydroxyl radical is an extremely reactive and non-discriminating free radical, the site of attack has no dependence on the base sequence of the nucleic acid. Instead, the susceptibility of a particular nucleotide to hydrogen abstraction is governed by its accessibility to solvent. This property makes the hydroxyl radical footprinting method the experimental equivalent of a calculated solvent-accessible surface area of a nucleic acid molecule"

Wednesday, February 9, 2011

Weekly RNA News - Week V - February 2011

Some weeks ago in Chemical and Engineering News there was a story about Roche pulling out of development of RNAi based drug research. Now there is a new article in C&EN talking about progress being made by some companies on RNAi, and the still latent preoccupation by RNAi pharma researchers on such a large move by Roche.
C&EN show a nice table citing the following companies having ongoing RNAi pipelines:

Alnylan
Calando
Marina Biotech
RVi
Silence Therapeutics
Tekmira

What has first impressed me greatly about these companies is the great level of their webpages. I expected older css and perhaps old flash kinda pages. But the majority of these ones look very html5 css3 like, quite stylish IMHO.

It's amazing what "good" publicity can do. If I wasn't a scientist and just wanted to invest some bucks on pharma startups, I would probably not invest in say, tekmira, which has the least "pretty" page on my superfluous 3s judgment.


Not three years have gone by since the publication of the Parisien and Major paper (Nature 1998) which, to my knowledge, is the first fully automated from sequence to 3D structure simulation of RNA, and the RNA structure prediction field sounds as if it was an already consolidated thing. There is a nice paper by Polish researchers on what there is out there and how it compares to protein folding prediction strategies. They have a table with the reviewed software and for RNA they mention RNABuilder, ModeRNA, Vfold, DMD, HiRE-RNA, MC-Fold, SimRNA, and CG. ModeRNA is the one developed by the authors of the review.

Wednesday, January 26, 2011

Weekly RNA News - Week IV - January 2011

Yelena Koldobskaya @ U. Chicago and collaborators propose a new method to crystallize RNA's using chaperones:
NSMB January 2011

There is a protein called Signal Recognition Particle (SRP), it's made of a protein part and a 4.5S RNA. This protein is important in the mechanism of action of the ribosome and Leandro F. Strozi at Grenoble and collaborators have "describe the cryo-EM structure of the E. coli ribosome–SRP–FtsY complex in the early conformation, demonstrating that the ribosome acts as a platform that optimally positions critical SRP regions for receptor recruitment":
NSMB January 2011


The third week of January came with a special issue on surface chemistry in PNAS.
Two interesting articles, one mentions what has been learned using DOS analysis from DFT calculations on surface catalysis, and another a general review on surface processes and the need for taking into account the nucleus, not just electronic structure.
PNAS on Surface Chemistry