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Various presentations and posters

Published papers

List of software tools and general notes on other software usage

Experimental Notes
Notes on NMR and ATF experiments - data collection and data processing


Cavity Search Program
This project seeks to develop a piece of software that will be able to evaluate environments of ionizable residues. It needs to be able to distinguish between five possible locations: surface, fully buried, interfacial, buried in internal cavity, located in a crevice. Ideally this software will work fast enough to do analysis of the entire PDB database. Probably, it will be too slow for that. I am attempting to write this program in Python.

This project is related to Lys-to-Asp21 project, as V104K is one of the variants that exhibits an interaction with a carboxylic group in the equilibrium thermodynamic experiments. However, as I found, V104K variant does not interact with Asp-21, but it seems to interact weakly with three surface Glu residues: 101, 122, and 129. I am pursuing this as a separate project, as it may nicely complement the T62K project, since this would be evidence for a set of weak one-to-many interactions that an internal Lys is having with surface charges.

D21 Interaction with Internal Lys
This is a sister project to T62K where we investigate other eight variants where internal Lysine probably interacts with Asp-21.

Study of interactions between and internal ionizable group and a surface charge. Titration of an internal lysine in a subset of variants exhibit coupling to another residue, probably Asp-21. This project is a proof of principle for the other 8 variants that behave in this way. The big question here is what are the structural consequences of ionization of Lys-62. We know that protein remains folded but there may be minor conformational changes in the structure.

In this SAXS study, the influence of the pH value on a mutant of the protein staphylococcal nuclease, T62P, which is known to be natively unfolded, was analysed in comparison to the wild type protein.

Domain Swapped Structure
Two of the arginine variants of &Delta+PHS, V66R and T62R, were domain swapped in the crystal structures. Both variants appeared to be monomeric in solution by NMR, Ultra Centrifugation, etc.


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