For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.

The reliability and information content of diethylpyrocarbonate (DEPC) as a covalent probe of protein surface structure has been improved when used appropriately with mass spectrometric detection. Using myoglobin, cytochrome c, and β-2-microglobulin as model protein systems, we demonstrate for the first time that DEPC can modify Ser and Thr residues in addition to His and Tyr residues. This result expands the capability of DEPC as a structural probe because about 25% of the sequence of the average protein can now be covered using this covalent labeling reagent. In addition, we establish a new approach based on mass spectrometry to ensure the structural integrity of proteins during amino acid-specific covalent labeling reactions. This approach involves monitoring the extent of modification as a function of reagent concentration and allows any small-scale or local perturbations caused by the covalent label to be readily identified and avoided. Results indicate that these dose-response plots are much more reliable and generally applicable probes of possible protein structural changes than fluorescence or circular dichroism spectroscopies. These dose-response plots also provide a means of quantitatively comparing the reactivity of each modified residue. Based on comparisons to known X-ray crystal structures, we find that the solvent accessibility of the reactive atom in the side chain and the presence of a nearby charged residue most affect modification rates. Finally, this improved surface mapping method has been used to determine the effect of Cu(II) binding on the structure of β-2-microglobulin. Results confirm that Cu(II) binds His31, but not any of the other three His residues, and changes the solvent accessibility of residues near His31 and near the N-terminus.

Abstractβ-2-microglobulin (β2m) self-associates into fibrillar amyloid deposits in the musculoskeletal system of patients undergoing hemodialysis treatment. Previous studies have shown that stoichiometric amounts of Cu(II) at near physiological conditions can cause β2m to organize into native-like dimers prior to forming amyloid fibrils. Here, we report the results from selective covalent labeling reactions combined with mass spectrometry that provide insight into the amino acid residues that mediate dimer formation in the wild-type protein. Using three complementary covalent labeling reagents, we find that the dimer interface is formed by the anti-parallel stacking of ABED β-sheets from two β2m monomers. In addition, our data clearly indicate that a dimer interface involving the interactions of D-D strands from separate protein units as seen in the recent crystal structures of two mutant β2m oligomers is unlikely.β-2-microglobulin (β2m) is the non-covalently bound light chain of the class I major histocompatibility complex (MHC-I) (1). It is a monomeric protein with 99 residues (~12 kDa). It adopts a seven-stranded β-sandwich fold with one β sheet formed by four strands and the other by three strands. A disulfide bond between Cys25 and Cys80 links strands the two sheets in the folded state of the protein. β2m is vital for the correct folding, assembly, and cell-surface expression of the MHC-I complex. As part of normal cell turnover, β2m is released from the MHC-I complex and carried to the kidney where it is degraded. Upon renal failure, serum levels of β2m increase up to ~60 times above the normal level of 0.1 µM, and the protein aggregates into insoluble amyloid fibrils in the joints (2,3). Elevated β2m concentrations alone, however, are not sufficient to trigger fibrillogenesis (4,5). β2m amyloid formation must therefore result from features unique to hemodialysis, but the exact cause in vivo is not known. ®2m amyloid fibrils can be generated in vitro, though, under acidic conditions (pH < 3.6) (6), by removing the first six N-terminal amino acids (7), by mixing the protein with collagen at pH = 6.4 (8), by sonicating the protein in the presence of sodium dodecyl sulfate at pH = *Corresponding author Department of Chemistry, University of Massachusetts, Amherst, rwvachet@chem.umass.edu, Telephone: (413) 545-2733, Fax: (413) . † Department of Chemistry, Universidad Industrial de Santander, AA 678, Bucaramanga, Colombia SUPPORTING INFORMATION AVAILABLEAdditional data can be found in the Supporting Information. These data include (i) plots showing the intensities of unmodified and modified forms of fragment Ile1-Tyr10 for three trials in the absence of Cu; (ii) tables presenting the intensities of unmodified and modified forms of peptide fragments containing residues Asn83, Lys94, and Lys6; (iii) plots illustrating the intensities of unmodified and modified forms of fragment Ile1-Tyr10 in the absence of Cu and 2 hours after addition of Cu; (iv) plots illustrating the extent of NHSA modification of β2m res...

The main pathogenic process underlying dialysis-related amyloidosis (DRA) is the accumulation of β-2-microglobulin (β2m) as amyloid fibrils in the musculoskeletal system, and some evidence suggests that Cu(II) may play a role in β2m amyloid formation. Cu(II)-induced β2m fibril formation is preceded by the formation of discrete, oligomeric intermediates, including dimers, tetramers, and hexamers. In this work, we use selective covalent labeling reactions combined with mass spectrometry to investigate the amino acids responsible for mediating tetramer formation in wild-type β2m. By comparing the labeling patterns of the monomer, dimer, and tetramer, we find evidence that the tetramer interface is formed by the interaction of D strands from one dimer unit and G strands from another dimer unit. This covalent labeling data along with molecular dynamics calculations enable the construction of a tetramer model that indicates how the protein might proceed to form even higher order oligomers.

Abstractβ-2-microglobulin (β2m) deposits as amyloid fibrils in the musculoskeletal system of patients undergoing long-term dialysis treatment as a result of kidney failure. Previous work has shown that Cu(II) binding causes β2m to organize into native-like dimers and tetramers that precede amyloid formation. Cu(II) is then released from higher order oligomers before mature Cu(II)-free amyloid fibrils are formed. While some of the Cu(II)-induced structural changes that enable β2m self assembly are starting to be revealed, the details of how the Cu(II) binding site evolves from the monomer to the dimers and tetramers are not known. Here, we report results from three mass spectrometry (MS) based methods that provide insight into the changing Cu-β2m interactions. We find that monomeric β2m binds Cu(II) via the N-terminal amine, the amide of Gln2, His31, and Asp59. In the dimer and tetramer, Asp59 is no longer bound to Cu(II), but the other residues still comprise a well-defined albeit weaker binding site that is better able to release Cu(II). Consistent with this is the observation that a fraction of the tetrameric species no longer binds Cu(II) at this weakened binding site, which agrees with a previous report that suggested the tetramer as the first Cu(II)-free oligomer. Our results also provide some insight into structural changes caused by Cu(II) binding that facilitate oligomer formation. Specifically, binding by Asp59 in the monomer requires significant movement of this residue, and we propose that this repositioning is important for establishing a pair of dimer-stabilizing salt bridges between this residue and Lys19. We also find evidence that Cu(II) binding in the Nterminal region of the monomer repels Arg3, which likely allows this residue to form a pair of dimerstabilizing salt bridges with Glu16. Overall, our measurements suggest that the previously proposed conformational switch caused by Cu(II) binding includes not only a cis-trans isomerization at Pro32 but also the repositioning of residues that are critical for the formation of new electrostatic interactions.β-2-microglobulin (β2m) is a 12 kDa subunit of the class I major histocompatibility complex and is a structural unit essential for the cell-surface expression of this complex. During normal turnover, β2m is released into serum and is eventually catabolized by the kidney. In patients undergoing hemodialysis as a result of kidney failure, β2m concentrations become elevated in the serum, and after as little as 18 months, β2m amyloids begin to form in the joints of these patients [1]. The cause of β2m amyloid formation in vivo is not precisely known, but several † This material is based upon work supported by the National Institutes of Health Grant RO1 GM 075092 *Department of Chemistry, University of Massachusetts, Amherst, rwvachet@chem.umass.edu, Telephone: (413) 545-2733, Fax: (413) 545-4490. ‡ Current address: Department of Chemistry, U-3060, University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269-3060Supporting Information Ava...