The transcription factor NF-kappa B is a protein complex which comprises a DNA-binding subunit and an associated transactivation protein (of relative molecular masses 50,000 (50K) and 65K, respectively). Both the 50K and 65K subunits have similarity with the rel oncogene and the Drosophila maternal effect gene dorsal. The 50K DNA-binding subunit was previously thought to be a unique protein, derived from the 105K gene product (p105). We now report the isolation of a complementary DNA that encodes an alternative DNA-binding subunit of NF-kappa B. It is more similar to p105 NF-kappa B than other family members and defines a new subset of rel-related genes. It is synthesized as approximately 100K protein (p100) that is expressed in different cell types, contains cell cycle motifs and, like p105, must be processed to generate a 50K form. A 49K product (p49) can be generated independently from an alternatively spliced transcript; it has specific kappa B DNA-binding activity and can form heterodimers with other rel proteins. In contrast to the approximately 50K protein derived from p105, p49 acts in synergy with p65 to stimulate the human immunodeficiency virus (HIV) enhancer in transiently transfected Jurkat cells. p49/p100 NF-kappa B could therefore be important in the regulation of HIV and other kappa B-containing genes.

Electrospray ionization mass spectrometry (ESI-MS) has proven to be a useful tool for examining noncovalent complexes between proteins and a variety of ligands. It has also been used to distinguish between denatured and refolded forms of proteins. Surfactants are frequently employed to enhance solubilization or to modify the tertiary or quaternary structure of proteins, but are usually considered incompatible with mass spectrometry. A broad range of ionic, nonionic, and zwitterionic surfactants was examined to characterize their effects on ESI-MS and on protein structure under ESI-MS conditions. Solution conditions studied include 4% acetic acid/50% acetonitrile/46% H 2 0 and 100% aqueous. Of the surfactants examined, the nonionic saccharides, such as n-dodecyl-P-D-glucopyranoside, at 0.1 Vo to 0.01% (w/v) concentrations, performed best, with limited interference from chemical background and adduct formation. Under the experimental conditions used, ESI-MS performance in the presence of surfactants was found to be unrelated to critical micelle concentration. It is demonstrated that surfactants can affect both the tertiary and quaternary structures of proteins under conditions used for ESI-MS. However, several of the surfactants caused significant shifts in the charge-state distributions, which appeared to be independent of conformational effects. These observations suggest that surfactants, used in conjunction with ESI-MS, can be useful for protein structure studies, if care is used in the interpretation of the results.Keywords: conformation; denaturation; detergent; electrospray; mass spectrometry; surfactant Surfactants play a significant role in protein chemistry with primary applications ranging from solubilization and stabilization of proteins to disaggregation of protein complexes and denaturation (Neugebauer, 1990(Neugebauer, , 1992Bollag & Edelstein, 1991). Some surfactants can disrupt protein higher order structure, whereas others are used as aids in protein refolding. They are employed in both gel and capillary electrophoresis and enhance protein and peptide recoveries from synthetic membranes employed in electroblotting and in electroelution of proteins from gels (Fernandez et al., 1994). Membrane-bound proteins, in particular, require surfactant treatment for solubilization. Abbreviotiom: CMC, critical micelle concentration; ESI, electrospray ionization; ESI-MS, electrospray ionization mass spectrometry; MALDI, matrix-assisted laser desorption/ionization; NP40, Nonidet P a , CHAPS, 3-(3-cholamidopropyl)dimethylammonio-I-propane sulfonate; CTAB, cetyl trimethylammonium bromide; LDAO, laurel dimethylamine oxide; n-dodecyl glucoside, n-dodecyl-0-D-glucopyranoside; n-hexylglucoside, n-hexyl-0-D-glucopyranoside; octyl glucoside, octyl-fl-D-glucopyranoside; octyl thioglucoside, I-S-octyl-fi-~-thioglucopyranoside.Matrix-assisted laser desorption/ionization or electrospray ionization have demonstrated molecular weight determinations for proteins greater than 100 kDa (Fenn et al., 1989;Smith et al., 19...

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