Michael T. Sykes


Nucleotide Doublets


Postdoctoral Research

My postdoctoral research focused on mass spectrometry of complex molecular systems. One challenge was to design and implement user-friendly programs to extract as much information as possible from the analysis, in an automated and intuitive fashion. I developed a suite of programs which are currently employed in the Williamson lab for a broad range of proteomic mass spectrometry applications.

Simulated Isotope Distribution Envelope

I also attempted to understand the various factors which complicate in vivo isotope pulse experiments. The incorporation of stable isotopes into ribosomal components provides information on assembly rates, ribosomal intermediates and free protein pool sizes amongst other things, and I did my best to deconvolute the relative contribution of each.

Thesis Research

My thesis research focused on attempting to understand the three-dimensional structure of RNA. Leveraging the database of known RNA structures and simulating RNA molecules we should be able to extract information about what makes an RNA structure stable and why it adopts a particular conformation. Of course this is a task easier said than done.

Size 30 Nucleotide Doublet Library

As part of this research I introduced the concept of a nucleotide doublet, which simply put is any two nucleotides which are close together in space. A library of these doublets selected by clustering doublets extracted from a large set of crystal structures is useful in structure classification, annotation and refinement.

Previous Research

My original interest in computational biology centered around protein dynamics and large conformational changes, including molecular dynamics simulations and comparison to experimental NMR measurements. I have also dabbled in homology modeling and thermodynamics of small molecules.

Before graduate school I was an experimental scientist. As an undergraduate my work included the design of a microchip-based DNA nanosensor, AFM measurements of protein adsorption to modified surfaces (see #1), infrared and NMR spectroscopy, and even a summer spent producing and purifying monoclonal antibodies.

My first taste of "independent" research came in high school as the basis for my Extended Essay, a component of the International Baccalaureate program. I studied the UV absorption properties of commercially available sunscreens, including application methods and skin coverage results from volunteers - 10 years before Procter & Gamble got around to it.