23 posts · 9,848 views
This blog are about articles in the field of Structural Bioinformatics that I found interesting and wanted to write a short description about them, so that others might find it interesting as well.
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
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 »
Jane S. Richardson and David C. Richardson. (2014) Biophysical Highlights from 54 Years of Macromolecular Crystallography. Biophysical Journal, 106(3), 510-525. DOI: 10.1016/j.bpj.2014.01.001
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 »
Hadas Shema,, Judit Bar-Ilan,, & Mike Thelwal. (2014) Do blog citations correlate with a higher number of future citations? Research blogs as a potential source for alternative metrics. Journal of the Association for Information Science and Technology. DOI: 10.1002/asi.23037
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
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
Jasti J, Furukawa H, Gonzales EB, & Gouaux E. (2007) Structure of acid-sensing ion channel 1 at 1.9 A resolution and low pH. Nature, 449(7160), 316-23. PMID: 17882215
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 »
Torsten Schwede. (2013) Protein Modeling: What Happened to the “Protein Structure Gap”?. Structure, 21(9), 1531-1540. DOI: 10.1016/j.str.2013.08.007
Haas J, Roth S, Arnold K, Kiefer F, Schmidt T, Bordoli L, & Schwede T. (2013) The Protein Model Portal--a comprehensive resource for protein structure and model information. Database : the journal of biological databases and curation. PMID: 23624946
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV.... (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993), 17(2), 151-9. PMID: 19217386
Narasimha Rao Uda, Grégory Upert, Gaetano Angelici, Stefan Nicolet, Tobias Schmidt, Torsten Schwede, & Marc Creus. (2013) Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE: implications of metal heterogeneity for evolution and antibiotic drug design . Metallomics. DOI: 10.1039/c3mt00125c
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
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 »
Whorton, M., & MacKinnon, R. (2013) X-ray structure of the mammalian GIRK2–βγ G-protein complex. Nature. DOI: 10.1038/nature12241
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 »
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
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 »
Butler, D. (2013) Investigating journals: The dark side of publishing. Nature, 495(7442), 433-435. DOI: 10.1038/495433a
... Read more »
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 »
Sanner MF. (1999) Python: a programming language for software integration and development. Journal of molecular graphics , 17(1), 57-61. PMID: 10660911
Sanner MF, Olson AJ, & Spehner JC. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38(3), 305-20. PMID: 8906967
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 »
Weininger, D. (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Modeling, 28(1), 31-36. DOI: 10.1021/ci00057a005
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 »
Sutcliffe, M. (1993) Representing an ensemble of NMR-derived protein structures by a single structure. Protein Science, 2(6), 936-944. DOI: 10.1002/pro.5560020607
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
Laskowski, R., Rullmann, J., MacArthur, M., Kaptein, R., & Thornton, J. (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4). DOI: 10.1007/BF00228148
Gottstein, D., Kirchner, D., & Güntert, P. (2012) Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. Journal of Biomolecular NMR, 52(4), 351-364. DOI: 10.1007/s10858-012-9615-8
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 »
Porollo, A., & Meller, J. (2007) Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics, 8(1), 316. DOI: 10.1186/1471-2105-8-316
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 »
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
post about special feature on protein folding in PNAS, October 2012 issue... Read more »
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
2D representations for protein-ligand interactions... Read more »
Wallace AC, Laskowski RA, & Thornton JM. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein engineering, 8(2), 127-34. PMID: 7630882
Stierand, K., & Rarey, M. (2010) Drawing the PDB: Protein−Ligand Complexes in Two Dimensions. ACS Medicinal Chemistry Letters, 1(9), 540-545. DOI: 10.1021/ml100164p
Durrant, J., & McCammon, J. (2011) BINANA: A novel algorithm for ligand-binding characterization. Journal of Molecular Graphics and Modelling, 29(6), 888-893. DOI: 10.1016/j.jmgm.2011.01.004
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