Structural proteomics of a bacterial mega membrane protein complex: FtsH-HflK-HflC

Akkulak H., İnce H. K., Goc G., Lebrilla C. B., Kabasakal B. V., Ozcan S.

International Journal of Biological Macromolecules, cilt.269, 2024 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 269
  • Basım Tarihi: 2024
  • Doi Numarası: 10.1016/j.ijbiomac.2024.131923
  • Dergi Adı: International Journal of Biological Macromolecules
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, Chemical Abstracts Core, EMBASE, Food Science & Technology Abstracts, INSPEC, Veterinary Science Database
  • Anahtar Kelimeler: Cross-linking, Mass spectrometry, Membrane protein complexes, Structural proteomics
  • Orta Doğu Teknik Üniversitesi Adresli: Evet

Özet

Recent advances in mass spectrometry (MS) yielding sensitive and accurate measurements along with developments in software tools have enabled the characterization of complex systems routinely. Thus, structural proteomics and cross-linking mass spectrometry (XL-MS) have become a useful method for structural modeling of protein complexes. Here, we utilized commonly used XL-MS software tools to elucidate the protein interactions within a membrane protein complex containing FtsH, HflK, and HflC, over-expressed in E. coli. The MS data were processed using MaxLynx, MeroX, MS Annika, xiSEARCH, and XlinkX software tools. The number of identified inter- and intra-protein cross-links varied among software. Each interaction was manually checked using the raw MS and MS/MS data and distance restraints to verify inter- and intra-protein cross-links. A total of 37 inter-protein and 148 intra-protein cross-links were determined in the FtsH-HflK-HflC complex. The 59 of them were new interactions on the lacking region of recently published structures. These newly identified interactions, when combined with molecular docking and structural modeling, present opportunities for further investigation. The results provide valuable information regarding the complex structure and function to decipher the intricate molecular mechanisms underlying the FtsH-HflK-HflC complex.