Method for the characterization of the three-dimensional structure of proteins employing mass spectrometric analysis and computational feedback modeling

Abstract

A method for characterizing the three-dimensional surface structure of molecules, particularly proteins and protein complexes, employing mass spectrometric analysis, an electrospray ionization (ES) source, a novel data interpretation process that utilizes comparisons of particular binding constants (K B ) and heats of formation (ΔH f ), and computational feedback modeling.

1 . A method for obtaining spectral data, comprising the steps of: 
 (a) mixing a small molecule with a large molecule so that the small molecule binds non-covalently to the large molecule to form a large molecule/small molecule complex; and    (b) performing electrospray ionization mass spectrometry to obtain spectral data relating to the large molecule-small molecule complex.    
   
   
       2 . The method of  claim 1 , wherein the large molecule is selected from the group consisting of one or more of polypeptides, proteins, DNA, RNA, and oligosaccharides.  
   
   
       3 . The method of  claim 1 , wherein the large molecule comprises a protein molecule.  
   
   
       4 . The method of  claim 1 , wherein the small molecule is selected from the group consisting of crown ethers, cryptands, and macrocyclic polyethers.  
   
   
       5 . The method of  claim 1 , wherein the small molecule comprises a crown ether.  
   
   
       6 . A method for obtaining spectral data, comprising the steps of: 
 (a) mixing a crown ether with a large molecule so that the crown ether binds non-covalently to the large molecule to form a large molecule/crown ether complex; and    (b) performing electrospray ionization mass spectrometry to obtain spectral data relating to the large molecule/crown either complex.    
   
   
       7 . The method of  claim 6 , wherein the large molecule is selected from the group consisting of one or more of polypeptides, proteins, DNA, RNA, and oligosaccharides.  
   
   
       8 . The method of  claim 6 , wherein the large molecule comprises a protein molecule.