Alternate conformations

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

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 (http://www2.molmovdb.org/) from Gerstein’s Lab. In many cases this gave us insight of how the protein could dynamically change from one form to another.

The 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

References:
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

Designer proteins helping biomedicine

Reblogging this blog post

http://loonylabs.org/2015/11/24/protein-structure-biotechnology-personalized-medicines/

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.

Using a combination of biophysical and computational analyses, the team discovered this kinetic stability can be successfully modeled based on the extent to which the protein chain loops back on itself in the folded structure. Because their approach to stability is also quantitative, the protein’s stability can be adjusted to naturally break down when it is no longer needed.

Reference:

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

Mutations that identify Thermostability

 

Fire, by Giuseppe Arcimboldo.
1566
Oil on wood, 67 x 51 cm
Kunsthistorisches Museum, Vienna
The allegory of Fire combines objects that are more or less directly related to fire in a bizarre profile head. The cheek is formed by a large firestone, the neck and chin are formed by a burning candle and an oil lamp, the nose and ear are contoured by firesteels; a blond moustache is formed by a crossed bundle of wood shavings for kindling, the eye is an extinguished candle stub, the forehead area is a wound-up fuse, the hair of the head forms a crown of blazing logs. The breast is composed of fire weapons: mortar and canon barrels together with the respective gunpowder shovel and a pistol barrel.

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.

This method becomes more time consuming if the protein is a membrane proteins and especially determining their 3D structure. I like to call membrane proteins as “diva” proteins. The reason being that they are high maintenance and tend to be picky about what conditions require for them to crystallize. It has been reported that when thermostability is introduced in membrane proteins, their solubility increases, thus increasing the chances of getting a good crystal for diffraction. [1]

Not everyone could avail high-throughput mutation experiments to screen for thermostable membrane proteins. Here is where Bioinformatics based analysis comes to help in faster screening and selecting a few mutants among the hundreds that can be tested experimentally. In the recent issue of Biophysical Journal, Sauer et al have come up with two methods to identify potential “thermoadaptive” sequences. [2]

The first method or global method, involves generating a heatmap of amino acid frequency differences between the thermophilic and mesophilic sequences. So, residues that are either most represented or less represented are identified.

The second method or pairwise method, involves pairwise comparison of thermophilic and mesophilic sequences and identify the differences.

A unique observation was that the the selected list of amino acids did not overlap from either of the methods and the global method identified potential mutants in the N-terminal domain of the test case and the pairwise method identified the potential C-terminal mutants only. This could be a case of thermostabilization for the protein tested, i.e., BsTetL – Tetracycline transporter from Bacillus subtilis.

The caveat is that there should be enough available sequences for identification of potential mutants, in any protein family. This does not, on the outset, seem like a limitation. Since, we have abundant protein sequences available and steadily increasing.

The main selling point is the speed of identifying the mutations given a particular target sequence, and its applicability in membrane protein crystallization. However, their success rate was 26-30%. Here, success indicates both thermostable mutant and maintaining the tetracycline resistance activity.

References:

1. 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
2. Sauer DB, Karpowich NK, Song JM, & Wang DN (2015). Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical journal, 109 (7), 1420-8 PMID: 26445442

What about Lignin?

Image Courtesy: i.bnet.com

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? Well, it can used in laying roads and thus creating bioasphalt.

Usually, after the sugars, cellulose, and other more useful materials have been extracted from plant matter to make biofuels or paper, the leftover lignin is tossed aside and burned. In principle, the economics are therefore promising: Paper companies could profit from what had been a waste product, and biofuel makers could similarly use the proceeds of selling lignin to bring down fuel production costs.

FYI, Lignin looks something like this.

Lignin. Image Courtesy: Wikimedia Commons

Read more here

 R. Chris Williams, a materials engineer at the Iowa State University Institute for Transportation, has developed a way to turn lignin-rich stover, leftover from biofuel production, into bioasphalt. The Iowa team uses a process called fast pyrolysis that turns plant waste into a charcoal-like fertilizer, natural gas, and an oily mixture that can be made into bioasphalt.

If you live in Iowa, you could see the bioasphalt paved bike path in Des Moines as the article mentions.

Update: My friend Ethy, pointed out that the bike trail (~1 mile long) between University Avenue and Franklin Avenue, on the west side of Glendale Cemetery has this bioasphalt bike path. See map below. Link: http://www.news.iastate.edu/news/2010/oct/bioasphalt

Google Maps

Bourzac, K. (2015). Inner Workings: Paving with plants Proceedings of the National Academy of Sciences, 112 (38), 11743-11744 DOI: 10.1073/pnas.1509010112

Science blogging

Reading one paper in a decent way takes a lot of time, which I realized in the past few months where I am strapped for time! Hopefully the dry phase ends sooner.

Came across this “Science blogging” article/podcast in Nature newsletter and thought of sharing it here. Enjoy!

The challenges of science blogging for established professors and young PhD students.

Whether you’re a PhD student or an established professor, being able to communicate your research is an important part of your career development. You will, at some point, have to persuade that funding body to give you some money, or that supervisory committee to grant you that PhD. Other times, you might have to work with politicians and the media to help them access your research. All these conversations, whether oral or in writing, require good communication skills.

Many of these will be done in a written format and blogging can be a great way to practice those writing skills.

Suzi Gage is writing up her PhD thesis. Three years ago, this was a gargantuan challenge that she was unsure of how to tackle. To prepare, she started blogging. “I really feel like the blogging has helped so much. When I sit down at a blank page, I know that I can write 1000 words. They might not be good words, but I know that I can turn them into something better.” Now she’s a well-established, award-winning science blogger, writing about epidemiology on Sifting the evidence, hosted by the Guardian.

Professor Jon Butterworth is an established experimental physicist, splitting his time between the Large Hadron Collider in Geneva and teaching at UCL. He blogs at Life and physics, also hosted by the Guardian. “We wanted to share the excitement of the thing [LHC].”

Science blogging challenges for young scientists

Audience

Your audience could include fellow students, potential employers and your supervisors. Therefore, think carefully about how you portray and express yourself, “particularly if you’re blogging under your own name,” says Suzi. There is a fine line between voicing your opinion and becoming a trouble maker, so it’s worth understanding where that line is. Our advice: don’t cross it.

Evidence

“My blogs came under a lot of attention from those who disagreed with what I was saying… everything I said I had to back up,” says Suzi. This is the case for anyone who is blogging about science, really, but it’s especially true for young scientists as they don’t have a decade-long research career and reputation to back them up. Do your research, interview scientists in the field and be 100% positive that what you are saying is correct, or can be backed up if it is opinion.

Bosses

Suzi is fortunate in that she has had supportive bosses who understand and agree with what she is doing. “But I don’t take the micky,” she says. As a young scientist, your priority should be your research, so don’t let your hobby take over. Suzi suggests combining the two: if you have to read a paper for your literature review, why not write up a lay summary for it at the same time? This is a good test to see if you have really understood it: if your audiences understand what you’ve written, you’re off to a flying start.

Goals

Are your science communication efforts a hobby, or are they something more? “This is a question that might come up in a job interview,” says Jon, and one that you should be prepared to answer. If you’re interviewing for a postdoc position, make sure that your potential employer understands that this is a hobby, that you’re organised and that your blogging won’t interfere with your work. If it isn’t a hobby, and you’re considering becoming a journalist, think carefully about applying for a postdoc, it might not be the right thing for you.

Sounding boards

“Two heads are better than one.” Wise words that apply to science blogging (as well as many other things!) When you run dry on ideas, or you’re not sure if one will work, use a friend or colleague as a sounding board. They’ll be able to help you think through your ideas, or maybe even give you new ones. It’s always useful to get another set of eyes on your work, just to check for grammatical and spelling errors.

Networks

“If you don’t think you have time to do a blog entirely by yourself….” approach a network that is already on the go, says Suzi. “That’s a great way to practice writing and see if it’s the kind of thing that you want to do,” she says. Setting up a blog for your lab can also be an option. “You don’t just have to cover the science, you can also talk about the PhD life.” Some good examples are The Mental Elf (mental health research, policy and guidance), Speakers of Science (science communication), Naturejobs (science careers), Climate Snack (environmental science) and others.

Science blogging challenges for an established scientist

Audience

The audience of an established researcher will be mixed. It might include your students and others that work for you, colleagues or “directors of labs in the US and Switzerland, leaders in the field and within government departments,” says Jon. They will each be judging your written words with their role in mind. You can never keep everyone happy, but try not to upset the same group of people two posts in a row!

Impact

What you say not only affects you, but it could also impact on your colleagues, policy, funding bodies and research decisions. Consider what you write, and how you write it, very carefully. “It does cramp your style a little bit,” says Jon, but don’t let that take all the enjoyment out of it.

Trust

Maintain the trust of your colleagues. As a senior scientist, you’ll be privy to meetings and experimental results that are not to be shared with the media. So don’t share them. Simple. If you do, you’ll risk being blacklisted from those meetings. Jon, as a researcher at the LHC, was part of several meetings that discussed confidential results, and he had to make sure that his colleagues trusted him not to spill the beans. “I don’t want to be shut out of the room for those [meetings],” says Jon.

Location

Don’t write a corporate blog, that’s Jon’s advice. Jon feels that a blog is a space where you can express your own personality and views (in a sensible way). If you have to walk a corporate tight-rope, he says it might not be worth it.

Responsibility

“You have a position of influence that you have to be conscious of when you’re writing,” says Jon. Accept your responsibility as a professor and a blogger: be polite, considerate of colleagues and your science, and a nice person!

Schrödinger’s Protein Design Webinar

Register and join us next week for a seminar on protein design using the Biologics Suite! This seminar is free of charge and our speaker, Dr. David Pearlman, will take questions from the audience in a Q&A session.

---

Recent Advances in Protein Design using the Biologics Suite – Featuring BioLuminate  Tuesday, June 24 10 am and 1 pm EDT  Schrödinger’s structure-based design platform for biologics – the Biologics Suite, featuring BioLuminate – includes a number of important tools for modeling biologics, antibodies, and proteins. In this presentation, we discuss recent applications of the Suite to protein and antibody design, including:
Alanine scanning to identify mutational hot spots A new approach to identify residue mutations favorable for forming a cysteine disulfide Dramatic success using Prime de novo loop prediction to model antibody H3 loop structures, including first-place performance in the Second Blinded Antibody Modeling Assessment (AMA-II) Incorporating residue mutation affinity calculations into workflows to facilitate enzyme design Register

Confession of a Scientist

Today, I saw this blogpost by Dr.Adam Ruben in social media via a researcher. It was very funny, yet nailed the truth quite strong. Reading through the long list, I kept saying “Yes, that true!”. So, here I am sharing the list with you, those highlighted in bold are mine. Those in italics are not completely true to me. Mea Culpa! 🙂

I don’t sit at home reading journals on the weekend.

I have skipped talks at scientific conferences for social purposes.

I remember about 1% of the organic chemistry I learned in college. Multivariable calculus? Even less.

I have felt certain that the 22-year-old intern knows more about certain subjects than I do.

I have avoided eye contact with eager grad students while walking past their poster sessions.

When someone describes research as “exciting,” I often don’t agree. Interesting, maybe, but it’s a big jump from interest to excitement.

Sometimes I see sunshine on the lawn outside the lab window and realize that I’d rather be outside in the sun. [TOTALLY!!!]

I have gone home at 5 p.m.

I have asked questions at seminars not because I wanted to know the answers but because I wanted to demonstrate that I was paying attention.

I have never fabricated data or intentionally misled, but I have endeavored to present data more compellingly rather than more accurately.

I have pretended to know what I’m talking about.

I sometimes make superstitious choices but disguise them as tradition or unassailable preference.

I like the liberal arts. [No, I LOVE them!]

When a visiting scientist gives a colloquium, more often than not I don’t understand what he or she is saying. This even happens sometimes with research I really should be familiar with.

I have enjoyed the fruits of grade inflation.

I have called myself “doctor” because it sounds impressive.

I dread applying for grants. I resent the fact that scientists need to bow and scrape for funding in the first place, but even more than that, I hate seeking the balance of cherry-picked data, baseless boasts, and exaggerations of real-world applications that funding sources seem to require.

I have performed research I didn’t think was important.

In grad school, I once stopped writing in my lab notebook for a month. I told myself I could easily recreate the missing data from Post-it notes, paper scraps, and half-dry protein gels, but I never did.

I do not believe every scientific consensus.

I do not fully trust peer review.

When I ask scientists to tell me about their research, I nod and tell them it’s interesting even if I don’t understand it at all.

I never was never interested in Star Wars. [I don’t know why Scientists = Star Wars Fan!]

I have openly lamented my ignorance of certain scientific subtopics, yet I have not remedied this.

I have identified steps in lab protocols that can be optimized, yet I have not optimized them.

I have worried more about accolades than about content.

If I could hand over my lab work to a robot, I’d do it in a second. Then I’d resent having to maintain the robot.

During my graduate-board oral exam, I blanked on a question I would have found easy in high school.

I can’t name four papers my grad-school lab published, but I can describe the details of our entry every year into the Biology Department Holiday Party Dessert Competition.

I have feigned familiarity with scientific publications I haven’t read.

I have told other people my convictions, with certainty, then later reversed those convictions.

I have killed 261 lab mice, including one by accident. In doing so, I have learned nothing that would save a human life. [No, not 261. About 20 in high school.]

I can’t get excited about the research to which some of my friends and colleagues have devoted their lives.

I can’t read most scientific papers unless I devote my full attention, usually with a browser window open to look up terms on Wikipedia.

I allow the Internet to distract me.

I have read multiple Michael Crichton novels.

I have taken food from events I did not attend and mooched swag from vendors I did not talk to.

I have used big science words to sound important to colleagues.

I have used big science words to sound important to students.

I have used big science words to sound important to my 3-year-old daughter.

I sometimes avoid foods containing ingredients science has proved harmless, just because the label for an alternative has a drawing of a tree.

I have miserably failed exams in the exact field I chose to study.

I own large science textbooks I have scarcely used. I have kept them “for reference” even though I know I’ll never use them again. I intend to keep them “for reference” until I die.

I have abandoned experiments because they did not yield results right away.

I own no wacky science ties.

I want everyone to like me.

I have known professors who celebrate milestone birthdays by organizing daylong seminars about their field of study. To me, no way of spending a birthday sounds less appealing.

Sometimes science feels like it’s made of the same politics, pettiness, and ridiculousness that underlie any other job. [Absolutely!]

I decry the portrayal of scientists in films, then pay money to go see more films with scientists in them.

I have worked as a teaching assistant for classes in which I did not understand the material.

I have taught facts and techniques to students that I only myself learned the day before.

I find science difficult.

I have delusions that people will read this confession and applaud my bravery for identifying a universal fear.

I am afraid that people will read this confession and angrily oust me from science, which I love. [Yes, Maybe.]

27 confessions!!!! So, what about you? 🙂

Prions – From Dr. Jekyll to being Mr. Hyde

Image reproduced under Creative Commons licence. Source: Wikimedia commons

The Cellular Prion Protein (PrP^c) like Dr. Jekyll converts into PrP^Sc , 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 Dynamics.

To list these properties,three structures were taken into consideration; one NMR structure (PDB id: 1QLX) and two X-ray structures (PDB id: 2W9E and 3HAK). Interestingly the 3HAK structure is from a SNP variant of human PrPc, where the Met129 is replaced by Val129. Furthermore, those who genetically have this variant are less susceptible to Prion diseases!

Structural alignment of 1QLX (blue), 2W9E (red), and 3HAK (orange) with Met129/Val129 shown as sticks. Image made using PyMOL

Using an in-house MD package called in lucem molecular mechanics, ilmm for short, Chen et al simulated the three structures under two different pH conditions (pH 5 and pH 7) and under two different temperatures (298K/25C and 310K/37C), totaling for about 3.6 microseconds of simulation. (For each structure under each condition the MD simulation was performed in triplicates.)

Analyzing the MD results they found that at 37C and low pH the C-terminal globular domain had significant destabilization effects.

• The helix HA and its neighboring loop S1-HA for the SNP variant was higher compared to other two structures at 37C and low pH. It is interesting to note that the S1-HA loop becomes a strand during the prion’s conversion.
• At low pH, another helix HB destabilizes, where the His187 becomes solvent exposed, leading to partial unfolding of the C-terminus.
• Two residues, Phe198 and Met134, converting from being part of the hydrophobic core to being exposed to the solvent may be involved in partial unfolding and might possibly provide aggregation sites.
• The X-loop in the Val129 SNP variant’s structure took a different conformation that was not populated by the other two structures.
• Formation of new secondary structures of the N-terminus region to either alpha and beta strands is spontaneous. While, in all two structures both alpha and beta strands formation was seen, in the SNP variant alpha strands were rarely formed. (This N-terminus region is missing from the solved structures and hence was modeled and in each starting structure this region was unstructured.)

These results give more insights into the conversion of the benign form of human Prion to the infectious form.

References:

1. 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

PDBx format!

I am sure this blog’s readers are aware of the PDB format. This format, created in the 1970s, is a standardized format for data derived from X-ray diffraction and NMR studies [1]. Until 2006, homology/theoretical models were also accepted for deposition, but not any more [2]. [See previous post on Protein Model Portal for submitting homology/theoretical models]

The current limit of PDB format is that a coordinate file with more than 62 chains and 99,999 atoms cannot be uploaded as a single file and hence was split into three or four separate PDB depositions. To overcome this limitation, a new format has been on the works and recently the working group announced the new format recommendations. [3, 4]

Not that I warned you. The first FAQ [4] on this link says:

What should every PDB user know about PDBx/mmCIF?
The PDB file format will be phased out in 2016.
PDBx/mmCIF will become the standard PDB archive format in 2014.

What is this new format?
To illustrate the changes, the first image is the ATOM records in the current PDB format. And, the second image is the PDBx format of the same information.

The new PDBx format:
Did you observe any changes? Here is a comparative image below that has the ATOM records aligned one below the other.
The first thing that caught my eye was the order of the columns the new format is using. Also, the extra decimal positions for occupancy and B-factor columns. Now, if you look at the second image, we saw some extra lines before the ATOM records. These are the list of things in the “atom_site” category. The new format has the following categories and under each category, there is a detailed description of what goes into it. For example, the ATOM records is what is called as the ATOM_SITE category. Under this, there is information describing atomic positions.

PDB to PDBx correspondences

This link describes what items in PDB correspond to the new PDBx format

The website (http://mmcif.wwpdb.org/) and the FAQ have tons of information. Check it out, and get familiar with the new format of PDB! You have two years to learn it. 🙂

References:

1. http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html. Accessed: 2014-03-07. (Archived by WebCite^® at http://www.webcitation.org/6NtpuqkvU)
2. http://deposit.rcsb.org/depoinfo/depofaq.html. Accessed: 2014-03-07. (Archived by WebCite^® at http://www.webcitation.org/6NtpzBByw)
3. http://www.emdatabank.org/lrg_strct_dpstn.html. Accessed: 2014-03-07. (Archived by WebCite^® at http://www.webcitation.org/6Ntq1KxKY)
4. http://www.wwpdb.org/workshop/wgroup.html. Accessed: 2014-03-07. (Archived by WebCite^® at http://www.webcitation.org/6Ntq3BY5u)
5. http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html. Accessed: 2014-03-07. (Archived by WebCite^® at http://www.webcitation.org/6Ntq56e1O)

Know any high schoolers?

Structural View of HIV/AIDS:

A Video Challenge for High School Students

http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/educational_resources/videochallenge/video_challenge_2014.html