Thanks for everyone who voted for me. Follow me on twitter: @xerophytes. You can still keep in touch and ask more questions! I'll be coordinating with Young Crystallographers Group to plan for outreach program to communicate the science of X-ray crystallography! Remember keep askin', keep science in!
Favourite Thing: If I had to choose only one, it’s got to be attending conferences and seminars where I can share my data and results. It’s really fun to discuss this with other people, because not only I can tell them what I do, but sometimes, they also provide me comments and suggestions that I never thought about with my project.
Queen Mary University of London (2008-2012), Cardiff University (2005-2008, De La Salle University (2002-2005), St. Stephen’s High School (1998-2002)
BSc Genetics and BSc Biology
Wales Heart Research Institute
Queen Mary University of London
Me and my work
I am trying to piece together jigsaw puzzle of bacterial proteins. These proteins assemble into a polygon which converts different types of alcohol to use as food by bacteria.
In some bacteria, when they are exposed to environment with alcohol (for example, ethanol and propanediol), they produce an icosahedral (a polygon with 20 faces) organelles. The covering of this icosahedral organelle (think of an egg shell) is made of thousands of seven types of proteins (imagine you smash the egg shell into pieces and you will have thousands of egg shell pieces). Inside this organelle, a number of enzymes convert this alcohol into something more useful for the bacteria like food (now, imagine again – egg – inside you have egg yolk and egg white, where some sort of reaction is happening). In our lab, what we want to know is, how are these proteins assemble together (or how do we piece together a jigsaw puzzle of cracked egg shell pieces) and more importantly, how do these proteins function such that it allows entry of alcohol but also preventing the enzymes inside to get out (or how does egg allow air to go in so the chick will survive but also don’t allow the food to leak out of the egg).
To do this, what I do is take the gene of the protein (DNA sequence) and places it in a “special” bacteria that is able to produce this protein in bulk. Then I get the protein out of the bacterial cell, purify such that I got only my protein of interest, and then use the technique called protein crystallography, where I turn this protein solution into solid microscopic crystal. Next step is to hit this crystal with X-ray beam to produce a pattern of black spots. This will be my data and using complicated mathematics, which mostly the computer does nowadays, I can extra information where each atoms of the protein is situated in a three-dimensional plane, which therefore, could give me information how this protein look like.
My Typical Day
There is no such thing as a typical day.
Everyday is a unique day for me. Although, I do have a research routine, they usually span 3-4 days, rather than a single day. That is why if it did not work on day 1, I can’t proceed to day 2 of experiment.
What I usually deal with:
– Planning of experiment. This includes thinking about what solution should I used, what kind of changes should I do in my method to achieve a better result, what should I continue doing and what I should not.
– Carrying out of experiment. Stuck in the lab. Moving flasks. Watching columns. Using various solutions in the experiment. (See more on me and my work)
– Analysing data and results. This involves identifying amino acid and fitting it into a map; checking if the data makes any sense.
– Publish results. Once I got my data and if it is of reasonable amount to create a story, I make a scientific narrative and send it to publishers.
– I also have to deal with other involvements such as teaching undergraduates, making reports and writing up my thesis.
What I'd do with the money
Outreach for X-ray Crystallography
As one of the committee members of the Young Crystallographer’s Group (http://ycg.crystallography.org.uk/) of the British Crystallographic Association (http://crystallography.org.uk), we can use this money to do more outreach programs around UK.
Two years from now, which is 2014, will be the International Year of Crystallography. This is the celebration, commemoration and looking at back at 100 years of X-ray crystallography, a scientific technique I used for my research. Because of this, we would like to reach out to as many people as possible, letting them know the basic things about crystallography, and letting them know how crystallography helps the society.
How would you describe yourself in 3 words?
geek. hardworking. funny.
Who is your favourite singer or band?
Alex Goot (check him out in youtube!)
What is the most fun thing you've done?
It’s really hard to pinpoint the most fun thing I’ve done, as I enjoyed most of what I’ve done in life. But if I really have to choose one, perhaps, it’s when I successfully did a tightrope walking and intentionally dive down from the tightrope to the river.
If you had 3 wishes for yourself what would they be? - be honest!
(1) Become a well known research scientist, (2) Money to fund my own research and lab, (3) Produce a sci-fi book, movie or TV series
What did you want to be after you left school?
Stay in the world of academia, doing research and teach students
Were you ever in trouble in at school?
Yes (let’s leave it that way)
What's the best thing you've done as a scientist?
The best thing in science is the discovery that happens serendipitously. It’s not really what I’ve done, but what I never expect to happen. Recently, I solved a crystal structure of a protein with glycerol bound to it. This glycerol is used to protect crystal from deteriorating in X-ray beam. And unexpectedly, it is so happen that this protein also interacts with glycerol and was found to be trapped by the protein.
Tell us a joke.
What’s between Iran and Iraq? (IraO and IraP)
Resuspending bacterial cell pellet on a solution where I want my protein to be in.
The bluish column actually contains Nickel beads. We use the Nickel beads to attract the protein containing a chain of Histidine. Histidine is negatively charged and Nickel is positive. So, what happens is my protein gets attached to the Nickel beads so I can isolate it from other contaminants.
This is another type of column we use. We load in the protein sample and gets separated according to its size. Since, I know the size of my protein, I would be able to discern it from other contaminants.
Checking the gel.
This is the gel where we visualise our protein sample. Notice the dark blue stain? That’s a confirmation that is our protein sample.
This is the crystal room and I’m checking via microscope if I got some protein crystals.
Most of the time, I work on a molecular visualisation program called Pymol, where I analyse the protein structure. In here, I am putting together the shell proteins and look if they fit together.
This is how we solve the structure of a protein. The blue wirey blob is the electron density map, which was generated and get from X-ray diffraction. The yellow stick (and some red stick) is the actual amino acid residue. So, in here, I am trying to fit in a residue onto the electron density map and see if that make sense. If it does fit, then that is the correct amino acid residue.
This is what you hope to get when you look at crystal trays using microscope. Crystals can grow in many different shape and form. This is one example.
I solved the crystal structures of two of the shell proteins, which shown on top; then below is a representation of how the bacterial microcompartment process 1,2-propanediol (a type of alcohol).