Poster Presentation 29th Annual Lorne Proteomics Symposium 2024

Defining the 3D Structures of the Human Platelet Proteome using Alphafold2 and Chemical Crosslinking (#145)

Benjamin Eberand 1 , Michelle Cielesh 1 , Ashleigh Dale 1 , Yvonne Kong 1 , Harry Tjondro 1 , Jemma Fenwick 1 , Freda H Passam 1 , Mark Larance 1
  1. University of Sydney, Camperdown, NSW, Australia

Platelet-derived proteins are essential in the modulation of essential haemostasis and coagulation processes. However, our understanding of the regulation and function of these proteins has been obstructed by a lack of protein 3D structure information and limited knowledge of protein-protein interactions. Here, we provide the first chemical crosslinking analysis of the platelet lysate and secretome using DSSO and nanoLC-FAIMS-MS2 analysis with stepped-HCD fragmentation. Platelets from 7 different patients were isolated and fractionated into resting lysate and thrombin-activated secretome samples. These protein samples were crosslinked with optimised DSSO concentrations (0.1-1mM). After trypsin digestion, peptides were fractionated by offline high-pH reversed-phase chromatography prior to LC-MS analysis, to increase crosslinked peptide coverage. The software package Scout was used for crosslinked peptide identification, as it showed significantly improved sensitivity compared to MaxQuant and XlinkX. Across the 7 patients, >6,000 crosslinked peptides were identified from 777 different platelet proteins. For analysis of platelet proteins without 3D structural information, we generated structural predictions with Colabfold (Alphafold2-Multimer), incorporating knowledge of each protein’s post-translational processing and multimerisation state. Crosslinking distance constraints were used to validate novel predicted structures for many crucial platelet proteins, including multimerin-1, thrombospondin-1, clusterin, and filamin A, paving the way for future functional investigations. Additionally, over 300 unique protein-protein interactions were identified from the interprotein crosslinks we observed, including previously known positive controls such as fibrinogen trimers, as well as many novel interactions requiring further investigation. The comprehensive human platelet protein 3D structures validated here by crosslinked peptide analysis will allow identification of novel regulatory mechanisms and the development of targeted therapeutics addressing platelet-associated disorders.