Use of Proteinase K Nonspecific Digestion for Selective and Comprehensive Identification of Interpeptide Cross-links: Application to Prion Proteins

Abstract

Chemical cross-linking combined with mass spectrometry is a rapidly developing technique for structural proteomics. Cross-linked proteins are usually digested with trypsin to generate cross-linked peptides, which are then analyzed by mass spectrometry. The most informative cross-links, the interpeptide cross-links, are often large in size, because they consist of two peptides that are connected by a cross-linker. In addition, trypsin targets the same residues as amino-reactive cross-linkers, and cleavage will not occur at these cross-linker-modified residues. This produces high molecular weight crosslinked peptides, which complicates their mass spectrometric analysis and identification. In this paper, we examine a nonspecific protease, proteinase K, as an alternative to trypsin for cross-linking studies. Initial tests on a model peptide that was digested by proteinase K resulted in a "family" of related cross-linked peptides, all of which contained the same cross-linking sites, thus providing additional verification of the cross-linking results, as was previously noted for other post-translational modification studies. The procedure was next applied to the native (PrP C ) and oligomeric form of prion protein (PrP␤). Using proteinase K, the affinity-purifiable CID-cleavable and isotopically coded cross-linker cyanurbiotindipropionylsuccinimide and MALDI-MS cross-links were found for all of the possible cross-linking sites. After digestion with proteinase K, we obtained a mass distribution of the crosslinked peptides that is very suitable for MALDI-MS analysis. Using this new method, we were able to detect over 60 interpeptide cross-links in the native PrP Structural proteomics, which combines protein chemistry methods with modern mass spectrometry techniques for protein and peptides, is an emerging technology in structural biology. One of the tools for modern structural proteomics is chemical cross-linking combined with mass spectrometry (1-5). Cross-linking analysis provides the distance between two cross-linked amino acid residues, whereas mass spectrometry provides information on which residues are connected. The basis of this method is a chemical reaction of the crosslinking reagent with functional groups on a protein, leading to the formation of a covalent bond between each end of the reagent and the protein. The distance between two crosslinked sites is determined by the length of the spacer in the cross-linking reagent. Thus, identification of the cross-linked sites on a protein or a protein complex provides spatial information and distance constraints for the two amino acid residues that are connected by the cross-linker.The use of chemical cross-linking combined with mass spectrometry is a rapidly developing technique for structural proteomics (4, 6 -8). In recent years, we and others have been developing an array of cross-linking and modification reagents, software, and methods specifically designed for protein cross-linking experiments combined with MS analysis (9 -18). For mass spectrometric determina...

Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure

“…20 Other researchers used different cross-linking reagents and PK digestion to study the structural differences between rPrP and rPrPβ. 21 These approaches used recombinant PrP or regions of PrP Sc that were not glycosylated. Mass spectrometry-based study of PrP Sc structure has mainly focused on the non-glycosylated N-terminal region of PrP Sc .…”

Use of proteomics in the study of microbial diseases of small ruminants

“…Other studies have contributed in the elucidation of the structure of prion protein, by using proteinase K for protein digestion in the process of molecule identification (Petrotchenko et al, 2012).…”

Blind testing cross-linking/mass spectrometry under the auspices of the 11thcritical assessment of methods of protein structure prediction (CASP11)

“…Numerous factors have led to this dominance, but essentially reliance on trypsin means that peptide identifications depend on good sequence coverage of tryptic cleavage residues, Arg and Lys. Cross-linking via amine-reactive NHS-ester based cross-linkers (DSS/BS3/sulfo-SDA) targets Lys residues, which subsequently become non-cleavable by trypsin following cross-linking reaction, the prevalence of Lys and Arg residues becomes even more important (42). It has been shown that cross-linked residue pair identification can be boosted by the use of alternative proteases to trypsin, including proteinase K, Asp-N, Glu-C, Lys-C and Lys-N (18,42,43).…”

“…Cross-linking via amine-reactive NHS-ester based cross-linkers (DSS/BS3/sulfo-SDA) targets Lys residues, which subsequently become non-cleavable by trypsin following cross-linking reaction, the prevalence of Lys and Arg residues becomes even more important (42). It has been shown that cross-linked residue pair identification can be boosted by the use of alternative proteases to trypsin, including proteinase K, Asp-N, Glu-C, Lys-C and Lys-N (18,42,43). We decided to employ Glu-C to target acidic residues for cleavage for all targets alongside standard trypsin digestion.…”