Biological Physics/Optics and spectroscopy: Protein fluorescence: theory and application
Fluorescence spectroscopy is a powerful tool for the investigation of protein structure, conformations and dynamics since fluorescence properties of tryptophan residues vary widely depending on the tryptophan environment in a given protein. The major goal in the application of tryptophan fluorescence spectroscopy is to interpret the fluorescence properties in terms of structural parameters and to predict of the structural changes in the protein. During the last decade we have developed methods for the mathematical analysis of fluorescence spectra of multitryptophan proteins aimed at revealing the spectral components of individual tryptophans or clusters of tryptophan residues located close to each other. Also, we have created an algorithm for the structural analysis of the tryptophan environment in 3D atomic structures of proteins. The successful design of the methods of spectral and structural analysis opened an opportunity for establishing a relationship between the spectral and structural properties of a protein. A first attempt to analyze fluorescence and structural data gave very good results. We found that tryptophan residues in proteins can be grouped into 5 discrete classes based on their spectral parameters, and that these classes are well correlated with some structural properties. We proposed a model of discrete states of the emitting tryptophan fluorophores in proteins. According to this model, tryptophan fluorophores belonging to various classes have different environment in protein. Therefore, different type of interactions (specific and universal) can occur in the excited state between the atoms of tryptophan fluorophore and surrounding protein or water groups, and as a result, various spectral responses are observed for tryptophan residues of different classes.
The main goals of our research are:
To establish general relation between the protein fluorescence and structural properties by applying novel statistical and bioinformatics approaches;
To provide insights into the nature of discrete classes of tryptophan residues;
To create a web-based toolkit called PFAST (Protein Fluorescence And Structural Toolkit, http://pfast.phys.uri.edu). PFAST contains a database of protein fluorescence and structural properties as well as programs for their analysis. Particularly, it allows the user to: 1) analyze fluorescence data (decomposition algorithms); 2) compute structural properties (algorithms for the calculation of structural parameters of tryptophan environment from atomic structures of proteins from PDB); 3) classify the fluorescence and structural properties and assign the tryptophan residues to spectral and structural classes.
More information could be found in Background section of PFAST: http://pfast.phys.uri.edu
Torrent, M., Cuyás, E., Carreras, E., Navarro, S, López, O., de la Maza, A. Nogués, M. V., Reshetnyak, Ya. K and Boix, E. (2007) Topology studies on the membrane interaction mechanism of the eosinopjil cationic protein. Biochemistry, 46 (3) 720-733.
Reshetnyak Y.K., K.T. Tchedre, M.P. Nair, P.H. Pritchard and A.G. Lacko (2006) Structural differences between wild-type and fish eye disease mutant of Lecithin:cholesterol acyltransferase. , J Biomol. Struct. Dynamics, 24(1), 75-82.
Linke D., Frank J., Pope M.S., Soll J., Ilkavets I., Fromme P., Burstein E.A., Reshetnyak Y.K., Emelyanenko V.I. (2004) Folding Kinetics and Structure of OEP16, Biophys.J., 86(3), 1479-1487.
Reshetnyak Y.K., Yu. Koshevnik, and E.A. Burstein (2001) Decomposition of protein tryptophan fluorescence spectra into log-normal components: III. Correlation between fluorescence and microenvironment parameters of individual tryptophan residues, Biophys. J., 81 (3), 1735-1758.
Reshetnyak Y.K., and E.A. Burstein (2001) Decomposition of protein tryptophan fluorescence spectra into log-normal components: II. The statistical proof of discreteness of tryptophan classes in proteins, Biophys. J., 81 (3), 1710-1734.
Burstein E.A., S.M. Abornev, and Y.K. Reshetnyak (2001) Decomposition of protein tryptophan fluorescence spectra into log-normal components: I. Algorithm of decomposition, Biophys. J., 81 (3), 1699-1709.