Electrospray ionization mass spectrometry was used to investigate the structure of the Escherichia coli chaperone protein SecB. It was determined that the N-terminal methionine of SecB has been removed and that more than half of all SecB monomers are additionally modified, most likely by acetylation of the N-terminus or a lysine. The use of gentle mass spectrometer interface conditions showed that the predominant, oligomeric form of SecB is a tetramer that is stable over a range of solution pH conditions and mass spectrometer interface heating (i.e., inlet capillary temperatures). At very high pH, SecB dimers are observed. SecB contains a region that is hypersensitive to cleavage by proteinase K and is thought to be involved in conformational changes that are crucial to the function of SecB. We identified the primary site of cleavage to be between Leu 141 and Gln 142. Fourteen amino acids are removed, but the truncated form remains a tetramer with stability similar to that of the intact form.Keywords: chaperone; electrospray mass spectrometry; noncovalent interactions; SecB Molecular chaperones are found throughout nature participating in a wide range of processes, including folding, oligomerization, and subcellular localization of polypeptides (Randall & Hardy, 1995). All molecular chaperones selectively bind nonnative polypeptides with no affinity for proteins that have acquired their native state. The mechanism allowing chaperones to recognize a polypeptide as a ligand by virtue of the fact it is nonnative is of great interest. Although detailed structural information would be enormously valuable in understanding how a chaperone works, the structures of only a few chaperones have been determined at high resolution: GroEL (Braig et al., 1994) and Pap D (Holmgren & Braenden, 1989) by X-ray crystallography, and domains of Hsc 70 (Morshauser et al., 1995) and DnaJ (Szyperski et al., 1994) by NMR.We report here the first use of electrospray ionization mass spectrometry (ESI-MS) to investigate the quaternary structure of SecB, a chaperone protein of Escherichia coli. SecB is the only chaperone among the several identified in E. coli that is dedicated to the facilitation of protein export across the cytoplasmic membrane (Randall & Hardy, 1995 promoting the export of a subset of precursor proteins in vivo, SecB has also been shown to bind a number of proteins and peptides that possess nonnative structure even though they are not natural ligands found in E. coli. (Hardy & Randall, 1991). Efforts to crystallize SecB in several laboratories have not produced diffraction-quality crystals (Vrielink et al., 1995; Dodson, Guy G., pers. comm.), thus we have no information related to the 3D structure. SecB has been shown by CD to contain a high percentage of 6 structure, as well as regions with no defined secondary structure (Breukink et al., 1992;Fasman et al., 1995). The initial evidence that SecB is oligomeric came from analysis by size-exclusion chromatography and electrophoresis of the native protein through po...