Probing Protein Surface Topology by Chemical Surface Labeling, Crosslinking, and Mass Spectrometry

The higher order structural properties of peptides and proteins are commonly investigated in the solid state by X-ray diffraction crystallography (1) or in solution by multidimensional nuclear magnetic resonance (NMR) spectroscopy (2). These techniques can provide detailed structural information; however, they are severely limited by the quantity of protein required for the analyses, difficulties with crystallization of certain proteins (e.g., glycoproteins), and the poor solubility of many macromolecules. Moreover, these methods are generally time consuming and tedious. Computer-based molecular modeling offers an alternative method to obtain information on the three-dimensional spatial arrangement of a protein. The success of this approach, however, is dependent on prior knowledge of the tertiary structure of an homologous protein (3–5). Due to these limitations, there is an increasing demand for an independent method to probe protein structure and/or confirm information obtained by the techniques mentioned above.