Solvent accessibility profiling in proteins

GÓMEZ, G.E.; BERNAR, E.M. ; ARÁN, M. , SABECKIS, L., GONZÁLEZ LEBRERO, M.C. AND DELFINO, J.M.

Sierra de la Ventana, Buenos Aires

Congreso; XLIII Reunión Anual de SAB; 2014

Topography of proteins and their interactions can be investigated through photochemical mimicry of the aqueous solvent, an approach aimed at estimating the size and nature of the solvent accessible surface area (SASA). After reacting diazirine (DZN, the smallest CNN heterocycle) with proteins, it is possible to measure quantitatively the extent of modification (methylation) by the use of radiotracers (tritiated DZN), by metrics derived from modern mass spectrometry techniques (MALDI-TOF and ESI-MS) or by multidimensional NMR. Maximal resolution of the labeled site is achieved after fragmentation into small peptides or individual amino acids. Interestingly, the NMR approach does not demand cleavage and is potentially rich in conformational information.Predictably, methylation of amino acid side chains rules the DZN modification event. Molecular dynamics simulations highlight the distribution of the reagent onto surface components prior tophotolysis. Thus, the probability of reaction at individual sites along the polypeptide reveals the map of solvent accessibility. Conformations can be distinguished corresponding to native orintermediate states, or the unfolded ensemble. Moreover, a paradigm of a peptide-protein complex (calmodulin-melittin) illustrates the value of this approach as a foot-printing technique able to pinpoint the area of interaction. One cannot overemphasize the worth of these new methods for the benefit of structural proteomics and interactomics.