A novel protein crosslinking reagent for the determination of moderate resolution protein structures by mass spectrometry (MS3-D)

Bioorg Med Chem Lett. 2004 Jan 19;14(2):427-9. doi: 10.1016/j.bmcl.2003.10.043.


A new approach to the determination of moderate resolution protein structures, termed MS3-D-Mass Spectrometry in 3 Dimensions-has recently been disclosed. The method involves the formation of covalent crosslinks between reactive residues on the protein surface, the determination of the location of those crosslinks in primary sequence space by mass spectrometry, and then the imposition of a distance constraint upon the location of the respective side chains during distance geometry calculations of protein structure. MS3-D is rapid, requires small amounts of protein, and works in native biochemical conditions. Therefore, it offers the potential for determination of the structures of all proteins expressed by an organism in a high throughput manner. However, the methodology is completely dependent upon the production of chemical crosslinks and technical limitations of available crosslinkers have proven problematic in generalization and automation of the method for the determination of the structures of complete proteomes. Presented herein is the design, synthesis, and proofing of a novel modular protein crosslinking reagent designed to enhance hydrophilicity, provide an increased effective signal to noise ratio for MS3-D, and allow the sampling of a wider variety of side chains during the process.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cross-Linking Reagents / chemical synthesis*
  • Mass Spectrometry / methods
  • Protein Conformation
  • Ubiquitin / analysis*
  • Ubiquitin / chemistry*


  • Cross-Linking Reagents
  • Ubiquitin