Probing protein surface accessibility with solvent and paramagnetic molecules

The accessibility of molecular surfaces is a dimension of structural biology that needs to be thoroughly investigated in order to increase the ability to predict a large variety of molecular events which are frequently referred to as allosteric effects. Obtaining convergent results on the surface distribution of cold and hot spots by using different techniques can produce important insight about protein surface dynamics. Site directed spin-labeling, that is the semi-synthetic production of protein or nucleic acid analogues incorporating covalently bound spin labels, is a powerful technique used to prepare NMR and EPR samples in order to map the conformational environment of the inserted paramagnetic moiety. Extensive MD sampling in explicit solvent and docking studies into protein-conformation snapshots extracted from such MD simulations should be performed for the interpretation of PRE data, accounting for all the possible interactions.