XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues

Author(s)

Fioramonte, Mariana ^[1] ; Ramos de Jesus, Hugo Cesar ^[1] ; Ramos Ferrari, Allan Jhonathan ^[1] ; Lima, Diogo Borges ^[2] ; Drekener, Roberta Lopes ^[1] ; Duarte Correia, Carlos Roque ^[1] ; Oliveira, Luciana Gonzaga ^[1] ; da Costa Neves-Ferreira, Ana Gisele ^[3] ; Carvalho, Paulo Costa ^[4] ; Gozzo, Fabio Cesar ^[1]

Affiliation

^[1] Univ Estadual Campinas, Inst Chem, CP 6154, BR-13083970 Campinas, SP - Brazil

^[2] Inst Pasteu, CNRS USR 2000, Mass Spectrometry Biol Unit, Paris - France

^[3] Fiocruz MS, Oswaldo Cruz Inst, Lab Toxinol, Rio De Janeiro - Brazil

^[4] Fiocruz MS, Carlos Chagas Inst, Lab Prote & Prot Engn, Curitiba, Parana - Brazil

• Document type: Journal article
• Source: Analytical Chemistry; v. 90, n. 10, p. 6043-6050, MAY 15 2018.
• Web of Science Citations: 6

Abstract

Cross-linking/Mass spectrometry (XLMS) is a consolidated technique for structural characterization of proteins and protein complexes. Despite its success, the cross-linking chemistry currently used is mostly based on N-hydroxysuccinimide (NHS) esters, which react primarily with lysine residues. One way to expand the current applicability of XLMS into several new areas is to increase the number of cross-links obtainable for a target protein. We introduce a multiplex chemistry (denoted XPlex) that targets Asp, Glu, Lys, and Ser residues. XPlex can generate significantly more cross-links with reactions occurring at lower temperatures and enables targeting proteins that are not possible with NHS ester-based cross-linkers. We demonstrate the effectiveness of our approach in model proteins as well as a target Lys-poor protein, SalBIII. Identification of XPlex spectra requires a search engine capable of simultaneously considering multiple cross-linkers on the same run; to achieve this, we updated the SIM-XL search algorithm with a search mode tailored toward XPlex. In summary, we present a complete chemistry/computational solution for significantly increasing the number of possible distance constraints by mass spectrometry experiments, and thus, we are convinced that XPlex poses as a real complementary approach for structural proteomics studies. (AU)

• FAPESP's process: 14/50249-8 - Green chemistry: sustainable synthetic methods employing benign solvents, safer reagents, and bio-renewable feedstock
• Grantee: Arlene Gonçalves Corrêa
• Support Opportunities: Research Grants - Research Centers in Engineering Program
• FAPESP's process: 16/13195-2 - Modeling of protein structure and protein complexes using mass spectrometry data
• Grantee: Allan Jhonathan Ramos Ferrari
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 14/17264-3 - New frontiers in structural proteomics: characterizing protein and protein complex structures by mass spectrometry
• Grantee: Fabio Cesar Gozzo
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 12/10862-7 - Structural Proteomics by Chemical Cross-linking Coupled to Mass Spectrometry: Development, Fundamental Studies and Applications.
• Grantee: Mariana Fioramonte
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 14/12727-5 - Genome mining in Streptomyces
• Grantee: Luciana Gonzaga de Oliveira
• Support Opportunities: Regular Research Grants