Monthly Archives: December 2015


The Mosquito Net (1912) by John Singer Sargent. Licensed under Public Domain via Wikimedia Commons

The Mosquito Net (1912) by John Singer Sargent. Licensed under Public Domain via Wikimedia Commons


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. 

However, the behaviour is more pronounced among blood-feeding pests (kissing bugs, bedbugs, Ticks, and mosquitoes including Aedes aegypti). Aedes aegypti is a vector for many flaviviral diseases (Dengue fever, Yellow fever, etc.) Until now, it was well established that thermotaxis requires specific thermosensors that activate the sensory signals for a subsequent flight response in a mosquito. However, how exactly they function was not resolved.

ResearchBlogging.orgIn a recent paper by Corfas and Vosshall [1] describe the use of zinc-finger nuclease-mediated genome editing method to identify the role of two receptors TRPA1 and GR19 in Aedes aegypti‘s attraction to heat. It was found that these receptors help the mosquito to identify the host for feeding (in the temperature range of 43-50 deg Celcius), however they avoid surfaces that exhibit above 50 deg Celcius. [Read the recent editorial on genome editing in Genome Biology]

The sequence (923 residues long) of this receptor (Uniprot id: Q0IFQ4) has at least five transmembrane regions that are approximately 20-25 residues long. A cursory glance at homologous sequences shows that it shares 37% sequence identity with the a de novo designed protein (PDB id:2xeh).

The homology modeled structure showing coiled coil region (residues 189-338). Although, the eLife paper does not talk about structure, I felt that this paper deserves a mention here. The reason is the structural biology/bioinformatics possibilities with this novel target. It is a suitable target for designing inhibitors that would potentially act as mosquito repellents.

Also, combined with the method described in my previous post on mutating transmembrane proteins as a method of making them crystallize, I guess the 3D structure of this important protein will come to light sooner!

Homology modeled region of TRPA1, from ModBase

Homology modeled region of TRPA1 (189-338), from ModBase



  1. Corfas RA, & Vosshall LB (2015). The cation channel TRPA1 tunes mosquito thermotaxis to host temperatures. eLife, 4 PMID: 26670734
  2. Greppi, Chloe and Budelli, Gonzalo and Garrity, Paul A (2015). Some like it hot, but not too hot. eLife, 4

I am sharing this guest post of mine that was published in Cell’s Crosstalk: Biology in 3D Blog. Yes, the journal Cell!

Here is the link:


Why Do I Blog about Structural Bioinformatics?:Biology in 3D

When someone says that they have a blog, the stereotypical response would be, “About your travels?” or “Hmmm … Recipes … Must be a delicious blog!” And when one confesses that said blog is about scientific research, the jaw drops. I presume it has to do with the notion that blogging science is not that much fun!

Two things inspired me to become a blogger: (1) an amazing community of scientific bloggers at Research Blogging, who inspired me with their wonderful posts; and (2) my view that structural biology and structural bioinformatics are not getting the exposure they deserve. Thus inspired and motivated, I begun blogging about four years ago, and was able to channel some of my thoughts and energy into my blog, called Getting to Know Structural Bioinformatics.

Guest author and blogger
Raghu Yennamalli

Why do I blog? Blogging is fun! For me, blogging is about sharing with the world recent research and tidbits on structural biology and bioinformatics. Most importantly, it is about sharing the excitement that I feel after reading a paper. In some sense, blogging about research is similar to a journal club, where I am able to share the latest research with my peers. However, unlike a journal club, the audience for my blog is the entire world.

Blogging is also dynamic and interactive, because it allows me to engage in conversation with others (specifically students) when they weigh in with their comments. Below I highlight some of the best practices that I’ve developed over the years that help me with balancing my research, teaching, and personal responsibilities with my blogging.

Selecting the paper

The main way I find articles that I want to blog about is by scouring through the table of contents of the journals I am interested in. Sometimes I also hear about exciting protein structures via friends and other blogs that I follow. I try to have a balanced approach and highlight structural work on systems that are “hot topics” as well as papers that just captured my interest and fancy.

In the early days of my blogging, I was trying to collate and compile tools and techniques that would come in handy for students working with protein structures. I wanted my blog to be a handy place for myself and others to find tips and tricks. Over time, the range of topics and papers I cover has broadened, and although I still cover a lot of method development work, I cover other topics as well. In general, once I make up my mind about the paper I want to blog about, I start reading it, give myself some time to soak in the method and outcome of the paper, and try to think critically as to what possible gaps or methods that the authors could have done to make the paper better. Alternatively, I also analyze the paper’s novelty with respect to structural bioinformatics.

Composing the blog post

I should confess that the monthly posts in Protein Spotlight by Vivienne Baillie Gerritsen are my inspiration while composing posts. I love her writing style and also the manner in which artwork is included in every post, to make it fun to read. Like Protein Spotlight, blogs have the advantage of including other multimedia items, for example using animated gifs and YouTube videos that make the post much easier for the reader. So, I start finding an appropriate image from an art database that best fits the topic (of course, giving credit where it is due). When it is about a tool/software, I figure the best approach is to use said tool/software and include a “first-hand” experience of how I perceived it. Also, I try to include an additional tidbit or information that the authors mention in passing.

Balancing things

With an active teaching and research schedule, finding time to blog does become a challenge. I try to make it a fun process, so that it does not feel cumbersome. If one looks at the frequency of my posts, I try to maintain at least one post per month. Looking at others’ blogs at Research Blogging, I realize that one post a month is a low turnout, and I try to post as frequently as possible. Sometimes, the problem is sheer lack of time or not finding exciting enough material to blog about. However, this does not mean that exciting research is not out there. The key is to find a balance between blogging and other duties. I have had discussions with other bloggers who blog on other nonscience topics, and we observed that the main turnoff in blogging is when one delves deeper and over time a particular post becomes “work.” Maneuvering that roadblock is key to maintaining a successful blog.

In the end, as at the beginning, it all comes down to having fun and sharing with the world my excitement about the type of scientific research I enjoy. I think this is probably the feeling others who blog share as well, and I can see it in some of the blogs I follow, such as the following:

Raghu Yennamalli completed his PhD in Computational Biology and Bioinformatics in 2008 from Jawaharlal Nehru University. He conducted postdoctoral research at Iowa State University, University of Wisconsin-Madison, and Rice University. Currently, he is an Assistant Professor at Jaypee University of Information Technology. He can be contacted at ragothaman AT gmail DOT com.

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”.

Courtesy: Google

Courtesy: Google

This morphing method was also used to analyze changes in protein motions, like in domain rearrangement. A popular webserver, where you can get an animated gif of your protein’s motion (assuming you have two distinct conformations), is the Morph server ( from Gerstein’s Lab. In many cases this gave us insight of how the protein could dynamically change from one form to another.

ResearchBlogging.orgThe change in structural forms of a protein is not a trivial problem. We would need to generate ensembles of protein structures for many purposes. 1) Understand conformational transition paths, 2) Generating more realistic receptors for docking 3) in turn understand the flexible and rigid parts of the protein, and few other applications.

Till now, one could use Normal mode analysis and Molecular Dynamics methods to generate ensemble. It is here that ConTemplate tries to bring in fresh perspective to generate an ensemble of structures.

ConTemplate mines the PDB for existing structures and gives the user a set of possible conformations. The main presumptions are that for any given PDB structure, it has more than one available structure, and there are additional conformations available for proteins that undergo major conformational changes.

For the dataset created for ConTemplate the maximum RMSD between two structures of the same protein is 5 Angstroms. 69.2% of the proteins have less than 1 Angstroms RMSD. Thus, the method uses an interesting three-step process:

  1. using the query it searches for structural equivalents using GESAMT aligner. Here using the structural alignment sequence alignments are generated.
  2. it runs BLAST to identify additional conformations for all structural equivalents obtained in step 1. A representative template is identified
  3. Finally, Modeller is used to build model structures using this template in various conformations.

The advantage of ConTemplate is that it yields a more relevant set of conformations for the query protein. I tried running a query to the server and I would say that I got some interesting results. Screenshot below:


Superposition of models created in ConTemplate for PDB id; 1ECE

Superposition of models created in ConTemplate for PDB id; 1ECE

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