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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.
Biophysical Journal has created a collection of papers that describe tools and software that can be routinely used in biological research. Editor Prof. Leslie Loew mentions that the full-text of articles in this collection will be freely available until February 25, 2016.... Read more »
Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, & Im W. (2015) CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical journal, 109(10), 2012-22. PMID: 26588561
McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, & Pande VS. (2015) MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical journal, 109(8), 1528-32. PMID: 26488642
Ribeiro AA, & Ortiz V. (2015) MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations. Biophysical journal, 109(6), 1110-6. PMID: 26143656
Hertig S, Goddard TD, Johnson GT, & Ferrin TE. (2015) Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophysical journal, 108(9), 2097-102. PMID: 25954868
Leonarski F, & Trylska J. (2015) RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models. Biophysical journal, 108(8), 1843-7. PMID: 25902423
de Vries SJ, Schindler CE, Chauvot de Beauchêne I, & Zacharias M. (2015) A web interface for easy flexible protein-protein docking with ATTRACT. Biophysical journal, 108(3), 462-5. PMID: 25650913
Biedermann J, Ullrich A, Schöneberg J, & Noé F. (2015) ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units. Biophysical journal, 108(3), 457-61. PMID: 25650912
Holmes WR, Mata MA, & Edelstein-Keshet L. (2015) Local perturbation analysis: a computational tool for biophysical reaction-diffusion models. Biophysical journal, 108(2), 230-6. PMID: 25606671
We all have neighbors who help us in our hour of need. Some go out of the way as well. In enzymes too, it seems, that neighbors play a crucial role. Lafond et al in their recent publication in the Journal of Biological Chemistry report the invovlement of neighboring chains of the same enzyme, lichenase. Apart from the role of stabilizing the quarternary structure (a trimer), they are also invovled in the enzymatic activity.... Read more »
Lafond M, Sulzenbacher G, Freyd T, Henrissat B, Berrin JG, & Garron ML. (2016) the quaternary structure of a glycoside hydrolase dictates specificity towards beta-glucans. The Journal of biological chemistry. PMID: 26755730
We all know how pesky mosquitoes can be. Did you know that the ability of a mosquito to find a suitable host to feed is due to thermotaxis? This behavior, being attracted/repelled due to high/low temperature, is seen in other organisms as well such as Drosophila melanogaster and Caenorhabditis elegans. ... Read more »
Corfas RA, & Vosshall LB. (2015) The cation channel TRPA1 tunes mosquito thermotaxis to host temperatures. eLife. PMID: 26670734
In the 90s morphing of two unrelated images was popular and mostly it was used for entertainment purposes. For example: the famous video of Michael Jackson’s pop hit “Black or White”.... Read more »
Narunsky A, Nepomnyachiy S, Ashkenazy H, Kolodny R, & Ben-Tal N. (2015) ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure. Structure (London, England : 1993), 23(11), 2162-70. PMID: 26455800
Professor Meiering and her colleagues were able to incorporate both structure and function into the design process by using bioinformatics to leverage information from nature. They then analyzed what they made and measured how long it took for the folded, functional protein to unfold and breakdown... Read more »
Broom A, Ma SM, Xia K, Rafalia H, Trainor K, Colón W, Gosavi S, & Meiering EM. (2015) Designed protein reveals structural determinants of extreme kinetic stability. Proceedings of the National Academy of Sciences of the United States of America, 112(47), 14605-10. PMID: 26554002
In protein engineering studies, mutating a residue to increase thermostability without affecting the activity of the protein/enzyme is a major consideration for researchers. The laborious method is list the number of possible mutations and then finding out the stability and activity for each mutant, one after another.... Read more »
Mancusso R, Karpowich NK, Czyzewski BK, & Wang DN. (2011) Simple screening method for improving membrane protein thermostability. Methods (San Diego, Calif.), 55(4), 324-9. PMID: 21840396
Sauer DB, Karpowich NK, Song JM, & Wang DN. (2015) Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical journal, 109(7), 1420-8. PMID: 26445442
Biofuel prodcution involves removing Lignin from the biomass, in fact efficient removal so that Lignin and its by-products do not inhibit the enzymatic process that follows. But, what happens to the Lignin? ... Read more »
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
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