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  • March 16, 2014
  • 06:00 PM

Prions – From Dr. Jekyll to being Mr. Hyde

by ragothamanyennamalli in Getting to know Structural Bioinformatics

The Cellular Prion Protein (PrPc) like Dr. Jekyll converts into PrPSc , a fatal conformational form, like Mr. Hyde, and is responsible for a variety of neurodegenrative disorders. Unlike the use of a potion, this molecular Jekyll and Hyde undergoes conformational change in low pH environment, such as in endosomes. While, there has been many studies done in the past of how this conformational change happens, a recent paper has tried to list the structural and dynamic properties using Molecular D........ Read more »

Chen, W., van der Kamp, M., & Daggett, V. (2014) Structural and Dynamic Properties of the Human Prion Protein. Biophysical Journal, 106(5), 1152-1163. DOI: 10.1016/j.bpj.2013.12.053  

  • February 7, 2014
  • 12:01 AM

Something to Bragg about!

by ragothamanyennamalli in Getting to know Structural Bioinformatics

Yes, the extra “g” was intentional. You see, 2014 is the International Year of Crystallography declared by the United Nations. So, Crystallographers are “Bragg”ing about it! [You see what I did there? :) ]... Read more »

  • February 6, 2014
  • 01:45 PM

Why blogging about research matters more than evah!

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

ResearchBlogging.orgTwo nature news articles make this post. The first one is titled “Scientists may be reading a peak in reading habits”. Read the full news here. With the widespread reading turning towards online rather than the good old library hunting, this is not a shocker. The average time spent on reading is half an hour per article. ... Read more »

  • January 19, 2014
  • 04:00 PM

P212121 – The most frequently seen space group in protein crystals

by ragothamanyennamalli in Getting to know Structural Bioinformatics

t is a fact that there is a non-uniformity with which different space groups occur in protein crystals. For example, the space group P212121 is the most frequent in protein crsytals and occurs almost one-third of the time!!!
Why is this so? This was the question asked by Wukovitz and Yeates in their paper titled “Why protein crystals favour some space-groups over others”... Read more »

Wukovitz SW, & Yeates TO. (1995) Why protein crystals favour some space-groups over others. Nature structural biology, 2(12), 1062-7. PMID: 8846217  

  • October 13, 2013
  • 04:50 PM

Fear factor

by ragothamanyennamalli in Getting to know Structural Bioinformatics

Halloween is right around the corner, and everyone likes to get spooky! I do fear a lot, in the halloween sense. A trip to "Horror forest" few years back ended with my vocal chords getting maximum exercise! :)
It was shown in "Little Albert" that phobias can be conditioned and by conditioning one could trigger the fear response to a stimuli that generally does not induce fear (for example, ringing a bell). While the "Little Albert" experiment is considered as contr........ Read more »

Riccio A, Li Y, Moon J, Kim KS, Smith KS, Rudolph U, Gapon S, Yao GL, Tsvetkov E, Rodig SJ.... (2009) Essential role for TRPC5 in amygdala function and fear-related behavior. Cell, 137(4), 761-72. PMID: 19450521  

Wemmie JA, Taugher RJ, & Kreple CJ. (2013) Acid-sensing ion channels in pain and disease. Nature reviews. Neuroscience, 14(7), 461-71. PMID: 23783197  

  • September 5, 2013
  • 02:35 PM

Where is the model?

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

Wouldn’t it be a great idea to put all these homology modeled structures that were published (of course, in a peer-reviewed journal) in one place? For some researchers, homology models are usually considered with a pinch (sorry a bucket!) of salt. Still, why should I spend time on modeling the protein, if a model exists already?... Read more »

  • August 30, 2013
  • 05:55 PM

SI(c)K1 with jetlag

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

There is a Native American or African belief that when one travels for long distance, the body moves physcially at a faster rate to the new geographic location, but the soul takes its own time to catch up. I am sure traveling to conferences at international venues, or a trip back home (journey from Americas to Asia) can cause severe jet-lag in most of us.

Well, I don’t know about souls, but I do know that being jet lag is the same as getting sick. It is ironic, that the protein responsi........ Read more »

Aarti Jagannath, Rachel Butler, Sofia I.H. Godinho, Yvonne Couch, Laurence A. Brown, Sridhar R. Vasudevan, Kevin C. Flanagan, Daniel Anthony, Grant C. Churchill, Matthew J.A. Wood.... (2013) The CRTC1-SIK1 Pathway Regulates Entrainment of the Circadian Clock. Cell, 154(5), 1100-1111. DOI: 10.1016/j.cell.2013.08.004  

  • June 7, 2013
  • 10:25 AM

Twist, Baby, Yeah Twist

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

If you were born in the 1960′s and if you happen to do The Twist with your partner your heart would of course be racing! Thanks to G protein-coupled inwardly-rectifying potassium channels (GIRKs) your heart can beat back to normal levels. Ironically, the protein does a “twist” to slow down the heart. Go Figure!

GIRK is basically a potassium ion-transporter and found in cardiac cells. It regulates the membrane voltage after the GPCR activated G-beta and G-gamma bind to the tr........ Read more »

  • May 24, 2013
  • 02:50 PM

A mutation leads to phenomenal effect

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

A point mutation in a gene leads to a phenomenal effect on the phenotype. It is a classic Biochemistry textbook case study, Sickle Cell Anemia. The mutant hemoglobin has a Valine instead of the Glutamic acid. The change is highly observable in the form of a debilitating condition. But, not all point mutations in the protein sequence are debilitating, and sometimes they give rise to something spectacular. One such example is the White Tiger, frequently mistaken as an albino. The recent publicatio........ Read more »

Xu, X., Dong, G., Hu, X., Miao, L., Zhang, X., Zhang, D., Yang, H., Zhang, T., Zou, Z., Zhang, T.... (2013) The Genetic Basis of White Tigers. Current Biology. DOI: 10.1016/j.cub.2013.04.054  

  • May 23, 2013
  • 07:15 PM

Molecular visualization tools - Survey and practical tips

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

What would be like to teach a class or describe someone about a protein, without visualizing its structure? Boring is one word that pops in my mind. I vividly remember the professor drawing two blobs touching each other, to describe protein-protein interaction, while explaining it either on the blackboard or on the transparencies of a over-head projector. Those were the days! Tracing back nearly 60 years back, when John Kendrew showed everyone a coiled mess, it has fueled every scientist's ........ Read more »

Craig, P., Michel, L., & Bateman, R. (2013) A survey of educational uses of molecular visualization freeware. Biochemistry and Molecular Biology Education, 41(3), 193-205. DOI: 10.1002/bmb.20693  

  • May 9, 2013
  • 01:00 PM

Resist Thy Temptations

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

This is not a regular research blogging post, but important enough that anyone following this blog should be aware of it. Most of you doing research, I assume being associated with an institute/university, would have an academic email id that does not end with .com. You are vulnerable, my friend. Yes, the subject is "open access publishing scam".... Read more »

  • May 3, 2013
  • 03:40 PM

Why blogging science is rewarding!

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

... Read more »

  • April 30, 2013
  • 05:55 PM

David Goodsell like images

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

Almost all of us visiting PDB would have looked at the image shown below that attract us like moths attracted to a light. I am talking about the aesthetically pleasing protein images created by David Goodsell. In case you didn’t know, he is the author of Molecule of the Month series. Since the images look anything like the ones we usually keep looking at, one is attracted to the level of abstraction the image projects due to which, the reader understands the big picture. And, of course, th........ Read more »

Goodsell, D. (2002) p53. RCSB Protein Data Bank. DOI: 10.2210/rcsb_pdb/mom_2002_7  

  • April 16, 2013
  • 07:15 PM

Say Smiles

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

Recently, Babel (in my system) was not working and I needed to convert my .sdf files to smiles format. I troubleshooted the error was able to run successfully. But, this made me think, what about a web-based application to do this format conversion? That's how I found these three amazing tools based at the National Cancer Institute's CADD Chemoinformatics group.... Read more »

  • March 13, 2013
  • 05:30 PM

What to do with so many models?

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

I have encountered this issue while working with structures in PDB that are solved using Nuclear Magnetic Resonance (NMR). Which model should I choose among the 10 or 20 models? As a general rule of thumb, Model 1 is usually taken for further analysis and consideration. Is that rule universal for all NMR structures? Some studies on this topic makes it interesting to revisit.... Read more »

Furnham, N., Blundell, T., DePristo, M., & Terwilliger, T. (2006) Is one solution good enough?. Nature Structural , 13(3), 184-185. DOI: 10.1038/nsmb0306-184  

MacArthur, M., & Thornton, J. (1993) Conformational analysis of protein structures derived from NMR data. Proteins: Structure, Function, and Genetics, 17(3), 232-251. DOI: 10.1002/prot.340170303  

Sikic K, & Carugo O. (2009) CARON--average RMSD of NMR structure ensembles. Bioinformation, 4(3), 132-3. PMID: 20198187  

  • March 7, 2013
  • 05:10 PM

Quick and easy animated pictures of proteins

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

So, here is an imaginary situation. You have a deadline to achieve and have minimal internet to reach the goal. Few hours before the deadline, your PI asks if you can send him a movie of the protein of interest in PyMOL. He specifies that the movie show the protein rotating, the active site and the ligand bound with it in surface representation, ligands as ball-and-stick, etc. He has a grant review presentation tomorrow and needs it asap.

You finish the movie and realize that to make a good i........ Read more »

  • January 3, 2013
  • 03:45 PM

Multiple Structure Alignment

by RagothamanYennamalli in Getting to know Structural Bioinformatics

Just like Multiple Sequence Alignment (MSA) tools there is a definite need for multiple structure alignment tools. For a long time, I was a big fan of Combinatorial Extension (CE)'s Multiple Structure Alignment (MStA) on their web server. Now, it is no longer maintained and has become a legacy. The good thing about it was you can do pairwise, database search, and MStA by either giving the PDB id or uploading a file.... Read more »

Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne. (2009) Structure Comparison and Alignment. Structural Bioinformatics. DOI: 10.1002/0471721204.ch16  

  • November 29, 2012
  • 02:00 PM

Molecular Dynamics and Pest Control

by RagothamanYennamalli in Getting to know Structural Bioinformatics

How can Molecular Dynamics help in controlling pests? Well, insects have something called resistant to dieldrin receptor or RDL receptors. These are part of a big family of receptors called Cys-loop receptors. Insecticides invariably bind to these receptors and in turn affect the neurotransmission in the pest. So, it becomes imperative to understand these receptors in order to develop and rationally design insecticides that are highly specific.... Read more »

Ashby, J., McGonigle, I., Price, K., Cohen, N., Comitani, F., Dougherty, D., Molteni, C., & Lummis, S. (2012) GABA Binding to an Insect GABA Receptor: A Molecular Dynamics and Mutagenesis Study. Biophysical Journal, 103(10), 2071-2081. DOI: 10.1016/j.bpj.2012.10.016  

  • October 30, 2012
  • 12:00 PM

What’s happening in the area of protein folding?

by RagothamanYennamalli in Getting to know Structural Bioinformatics

post about special feature on protein folding in PNAS, October 2012 issue... Read more »

Service, R. (2008) Problem Solved* (*sort of). Science, 321(5890), 784-786. DOI: 10.1126/science.321.5890.784  

Wolynes, P., Eaton, W., & Fersht, A. (2012) From the Cover: Chemical physics of protein folding. Proceedings of the National Academy of Sciences, 109(44), 17770-17771. DOI: 10.1073/pnas.1215733109  

  • October 30, 2012
  • 05:50 AM

Protein-Ligand Interactions

by RagothamanYennamalli in Getting to know Structural Bioinformatics

2D representations for protein-ligand interactions... Read more »

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