#PhDaily Day 12 25/08/2015

An update, and an idea…

Hi everyone!

So it does indeed look like I will be processing NMR data for the foreseeable future! I have a lot of data to handle, which is frankly boring to tell you about and after the first day I imagine would be very boring and repetitive to read! This is likely to continue until the 3rd week in September – when I go on work placement for three months. I intend to restart the proper #PhDaily posts once I start on placement, as I hope this will be an interesting part of my PhD with lots to talk about. Just before I start, I will also do a post on what my placement is all about! But until then, I am still going to be giving a brief outline of my day, of course including if I do anything different, but then also throw in some NMR knowledge on some days too.

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#PhDaily Day 11 24/08/2015

Hi everyone,

I’m back for a 3rd week of #PhDaily!

Considering the failure of last weeks ITC experiment, this week (and in the short term at least), I have decided to focus on my NMR experiments, as (fingers crossed) these are still working. I got into work at around 10 am, and set up my computer (a linux system), before being joined by my guide and NMR wizard Andrea.

Previously, I have looked at the backbone structure of the protein i am looking at (essentially a chain of carbon and nitrogen atoms). Now i am looking at the two other parts of the puzzle needed to get a protein structure, the side chains and the spacial analysis. Amino acids – the building blocks of proteins are varied, and some have different side chains which can affect the overall structure of a protein. The spacial analysis allows me to determine where the different amino acids are relative to each other in 3D space, which is crucial to produce a 3D structure of a protein.

There are two stages to each part of the NMR process, running the NMR scans, then processing the data. I am currently processing the side chain data, which like all NMR data, is like a giant confusing jigsaw puzzle!


The NMR data processing screen. Certain peaks (the white circles) have to match up with certain other ones in each of these windows. From that i can tell the amino acid sequence, where all the side chains are, and where each amino acid is in relation to its neighbours.

I worked until 1pm, when i went for lunch and a sit outside, then back at 2pm for more data processing! I get my head around some difficult concepts to do with all of the different types of scan we have done, just in time to go home at 5.

Thanks for reading,

Microbe Stew

#PhDaily Day 8 19/08/2015

Hi everyone,

Well the ‘big experiment’ today turned out to be the ‘big anti-climax’… In work at 8 am to start preparing for the experiment – using a technique called Isothermal Titration Calorimetry (ITC) to look at the change in heat caused by the binding of a protein to another structure or ligand.

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#PhDaily Day 7 18/08/2015

Hi everyone!

An early (well earlier!) start for me today, in the NMR lab for 9.30 to again check on my samples. All looked well and we were good to carry on some further experiments, after the nitrogen fill. The NMR spectrometers are refilled with liquid nitrogen weekly, at which time no experiments can be carried out. Then to the NMR lab meeting at 10 am. No talk from students or staff this week, but a lengthy chat about the general upkeep of the labs, and a few people moving onto new jobs!

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