Three Dimensional Structures of Proteins and Protein Complexes from Chemical Cross-Linking and Mass Spectrometry: A Biochemical and Computational Overview

In recent years, protein cross-linking technology using appropriate chemical cross-linking reagents and identification of cross-linked peptides and proteins by mass spectrometry has been used successfully to elucidate the intra- and inter-molecular interactions of protein molecules. Identification of the cross-linking sites within a single polypeptide chain or across polypeptide chains of a protein can provide insight into spatial distance constraints within the molecular structure and hence aid in the prediction of the low resolution three dimensional structure of the protein. In addition, finding cross-linked peptides in a multimeric protein complex is useful for deducing the composition, kinetics, nature of interaction and contact sites of the participating protein molecules in the complex. Here, we describe: (i) commonly used chemical reagents for cross-linking specific amino acid residues in protein molecules, (ii) application of mass spectrometry following digestion of cross-linked proteins with appropriate enzymes of known specificity, (iii) computer software tools for mass spectral data analysis to locate possible sites of intra- and/or inter-molecular cross-linking of protein molecules, and (iv) computational methods for predicting low resolution structure with the help of experimentally identified cross-links. We also discuss various specific examples of the application of the cross-linking technology to the identification of intramolecular and inter-molecular interactions of protein molecules.