Development of enrichment methods for cross-linked peptides to study the dynamic topology of large protein complexes by mass spectrometry

In the cell, most proteins carry out their functions as subunits of larger assemblies. Knowledge about the folding and mutual interactions of composing subunits is crucial to comprehend the dynamics and structures of such protein complexes and the molecular mechanisms underlying biological processes. Unfortunately, large complexes are often not amenable to techniques used to obtain detailed protein structural information like x-ray crystallography and nuclear magnetic resonance spectroscopy. In this thesis chemical protein cross-linking coupled with mass spectrometric analysis (CXMS) has been utilized as a core approach to obtain structural information of proteins. With CXMS the identity of cross-linked amino acids and their position in the protein amino acid sequence is determined, yielding spatial distance restraints, since the linked residues cannot be father away in a cross-linked protein complex than the length of the spacer of the used crosslinker. With this information a topological map of subunit arrangements can be obtained. Although CXMS has been applied for more than a decade, the rareness and low abundance of cross-linked peptides in digests forms a main analytical challenge, since this circumstance hampers mass spectrometric analysis. In this thesis methodologies aimed at enrichment of cross-linked peptides have been developed and applied. These studies were performed both in isolated complexes and in complicated protein mixtures. In Chapter 2, 3 and 4, the development of enrichment approaches intended to isolate azide-containing cross-linked peptides of proteins/complexes for mass spectrometric analysis are described. In Chapter 5, the characterization of novel interaction using the methodology developed in this thesis is shown

A composite filter for low FDR of protein-protein interactions detected by in vivo cross-linking

In vivo chemical cross-linking combined with LCMSMS of digested extracts (in vivo CX-MS) can reveal stable and dynamic protein-protein interactions at proteome-wide scale and at peptide level. In vivo CX-MS requires a membrane permeable and cleavable cross-linker and a fast and sensitive search engine to identify the linked peptides. Here we explore the use of the search engine pLink 2 to identify cross-links induced in exponentially growing Bacillus subtilis cells treated in culture with bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). Cross-linked peptide pairs were identified by pLink 2 in very short time at an overall FDR of <5%. To also obtain a FDR <5% for non-redundant inter-protein cross-linked peptide pairs additional threshold values were applied for matched fragment intensity and for the numbers of unambiguous y and b ions assigned to both composite peptides. Also the mass- and charge-dependent retention times of target peptides purified by diagonal strong cation exchange chromatography were used as a criterion to distinguish true from false positives. After application of the composite filter new protein-protein interactions were revealed among others between the global transcriptional repressor AbrB and elongation factor Tu and between the essential protein YlaN of unknown function and the ferric uptake repressor Fur. SIGNIFICANCE: Important for reliable identification of PPIs by chemical cross-linking in vivo is a low FDR of non-redundant inter-protein peptide pairs. Here we describe how to recognize the presence of spurious interactions in a dataset of cross-linked peptide pairs enriched by 2D strong cation exchange chromatography and identified by LCMSMS by taking into account chromatographic behavior of cross-linked peptide pairs and protein abundance of corresponding peptides. Based on these criteria we assessed that the FDR of the fraction of non-redundant inter-protein cross-linked peptide pairs was approx. 20-25% by interrogating an entire species specific database at an overall FDR of 5% or 0.1% with a search engine that otherwise scores best in sensitivity among other search engines. We have defined a composite filter to decrease this high FDR of inter-protein cross-linked peptide pairs to only about 2%

A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database

A high molecular weight fraction of a HeLa cell nuclear extract containing nearly 1100 identified proteins was cross-linked with bis(succinimidyl)-3-azidomethyl glutarate (BAMG). The azido group in cross-linked peptides can be reduced to an amine group. Reduction enables isolation of cross-linked peptides by diagonal strong cation exchange chromatography. Collision-induced dissociation (CID) of reduced cross-linked peptides shows abundant cleavage of the cross-link amide bonds, along with the cleavage of peptide bonds of the composing peptide pair. A defined relationship exists between the sum of the masses of a pair of cleavage products and the mass of the parent compound. This relationship enables accurate mass determination of the two composing peptides. With this knowledge, the identity of the pair of peptides in a cross-link is revealed at an extremely low false discovery rate by peptide fragment fingerprinting with MS1MS2 data from the entire human sequence databases with a conventional search engine for peptide identification. Our approach resulted in identification of 229 intraprotein and 18 interprotein cross-links. Biological significance Mapping protein-protein interactions in complex samples like digests of in vitro cross-linked extracts, by interrogation of entire species specific sequence database with tandem mass spectrometric data may yield repositories of cross-linked peptides. Results will reveal interactions between proteins, the identity of which may lead to new hypotheses about molecular mechanisms and regulations of biological function, or new targets for drug development. In this paper we describe a new analytical strategy that improves existing approaches of cross-link mapping in complex samples. The cross-linker that we have designed and synthesized for our approach is membrane permeable. This opens avenues for in vivo cross-linking for better understanding of dynamic protein complex topologies involved in many biological processes