To fulfill their biological functions, proteins must interact with their specific binding partners and often function as large assemblies composed of multiple proteins or proteins plus other biomolecules. Structural characterization of these complexes, including identification of all binding partners, their relative binding affinities, and complex topology, is integral for understanding function. Understanding how proteins assemble and how subunits in a complex interact is a cornerstone of structural biology. Here we report a native mass spectrometry (MS)-based method to characterize subunit interactions in globular protein complexes. We demonstrate that dissociation of protein complexes by surface collisions, at the lower end of the typical surface-induced dissociation (SID) collision energy range, consistently cleaves the weakest protein:protein interfaces, producing products that are reflective of the known structure. We present here combined results for multiple complexes as a training set, two validation cases, and four computational models. We show that SID appearance energies can be predicted from structures via a computationally derived expression containing three terms (number of residues in a given interface, unsatisfied hydrogen bonds, and a rigidity factor).protein complex | native mass spectrometry | protein interactions | structural biology | surface-induced dissociation N ative mass spectrometry (MS) has emerged as a powerful structural biology tool. By using "soft" ionization techniques such as nanoelectrospray ionization, noncovalent interactions can be retained, enabling the study of intact protein:protein, protein: ligand, and protein:RNA complexes in the gas phase (1-4). Native MS overcomes many of the barriers associated with traditional protein characterization methods; it requires low sample volumes (3-10 μL) and micromolar or lower concentrations, while also having a broad mass range for analysis, allowing study of small monomeric proteins up to large megadalton assemblies (1,5).Typical MS experiments to study subunit interactions of protein complexes involve first preparing the sample in an aqueous solution at near neutral pH, typically 100-200 mM ammonium acetate. The complex is then introduced intact into the mass spectrometer to measure the mass of the native complex. To obtain subunit connectivity information on the sample, the complex can be disrupted in solution, typically either with small volumes of organic solvent or through alteration of the ionic strength; this destabilizes the protein:protein interfaces and allows measurement of stable subcomplexes (6, 7). This approach, however, targets all species present in solution and can therefore be problematic for heterogeneous samples where it may not be possible to decipher which subcomplex came from which precursor. Alternatively, the complex can be isolated and then dissociated in the gas phase. The most commonly used dissociation method for such studies is collision-induced dissociation (CID). In CID protein ions are accelerated i...

The trimethylamine methyltransferase MttB is the first described member of a superfamily comprising thousands of microbial proteins. Most members of the MttB superfamily are encoded by genes that lack the codon for pyrrolysine characteristic of trimethylamine methyltransferases, raising questions about the activities of these proteins. The superfamily member MtcB is found in the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that can grow by demethylation of L-carnitine. Here, we demonstrate that MtcB catalyzes L-carnitine demethylation. When growing on L-carnitine, E. limosum excreted the unusual biological product norcarnitine as well as acetate, butyrate, and caproate. Cellular extracts of E. limosum grown on L-carnitine, but not lactate, methylated cob(I)alamin or tetrahydrofolate using L-carnitine as methyl donor. MtcB, along with the corrinoid protein MtqC, and the methyl-corrinoid:tetrahydrofolate methyltransferase MtqA were much more abundant in E. limosum cells grown on L-carnitine than on lactate. Recombinant MtcB methylates either cob(I)alamin or Co(I)-MtqC in the presence of L-carnitine, and to a much lesser extent, γ-butyrobetaine. Other quaternary amines were not substrates. Recombinant MtcB, MtqC, and MtqA methylated tetrahydrofolate via L-carnitine, forming a key intermediate in the acetogenic Wood-Ljungdahl pathway. To our knowledge MtcB methylation of cobalamin or Co(I)-MtqC represents the first described mechanism of biological L-carnitine demethylation. The conversion of L-carnitine and its derivative γ-butyrobetaine to trimethylamine by the gut microbiome has been linked to cardiovascular disease. The activities of MtcB and related proteins in E. limosum might demethylate proatherogenic quaternary amines and contribute to the perceived health benefits of this human gut symbiont.

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Salmonella enterica serovar Typhimurium (Salmonella) is one of the most significant food-borne pathogens affecting both humans and agriculture. We have determined that Salmonella encodes an uptake and utilization pathway specific for a novel nutrient, fructose-asparagine (F-Asn), which is essential for Salmonella fitness in the inflamed intestine (modeled using germ-free, streptomycin-treated, ex-germ-free with human microbiota, and IL10−/− mice). The locus encoding F-Asn utilization, fra, provides an advantage only if Salmonella can initiate inflammation and use tetrathionate as a terminal electron acceptor for anaerobic respiration (the fra phenotype is lost in Salmonella SPI1− SPI2− or ttrA mutants, respectively). The severe fitness defect of a Salmonella fra mutant suggests that F-Asn is the primary nutrient utilized by Salmonella in the inflamed intestine and that this system provides a valuable target for novel therapies.

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