Various presentations and posters
List of software tools and general notes on other software usage
Notes on NMR and ATF experiments - data collection and data processing
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.
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.
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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