Trident Nano-Indexing the Proteomics Table: Next-Version Clustering of Iron Carbide NPs and Protein Corona

Molecules. 2022 Sep 6;27(18):5754. doi: 10.3390/molecules27185754.

Abstract

Protein corona composition and precise physiological understanding of differentially expressed proteins are key for identifying disease biomarkers. In this report, we presented a distinctive quantitative proteomics table of molecular cell signaling differentially expressed proteins of corona that formed on iron carbide nanoparticles (NPs). High-performance liquid chromatography/electrospray ionization coupled with ion trap mass analyzer (HPLC/ESI-Orbitrap) and MASCOT helped quantify 142 differentially expressed proteins. Among these proteins, 104 proteins showed upregulated behavior and 38 proteins were downregulated with respect to the control, whereas 48, 32 and 24 proteins were upregulated and 8, 9 and 21 were downregulated CW (control with unmodified NPs), CY (control with modified NPs) and WY (modified and unmodified NPs), respectively. These proteins were further categorized on behalf of their regularity, locality, molecular functionality and molecular masses using gene ontology (GO). A STRING analysis was used to target the specific range of proteins involved in metabolic pathways and molecular processing in different kinds of binding functionalities, such as RNA, DNA, ATP, ADP, GTP, GDP and calcium ion bindings. Thus, this study will help develop efficient protocols for the identification of latent biomarkers in early disease detection using protein fingerprints.

Keywords: biomarker; biomaterials; cancer; early disease detection; nanoparticle corona; proteomics table; signaling.

MeSH terms

  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Calcium
  • Carbon Compounds, Inorganic
  • Cluster Analysis
  • Guanosine Triphosphate
  • Iron Compounds
  • Nanoparticles* / chemistry
  • Protein Corona* / chemistry
  • Proteins / metabolism
  • Proteomics / methods
  • RNA

Substances

  • Carbon Compounds, Inorganic
  • Iron Compounds
  • Protein Corona
  • Proteins
  • iron carbide
  • Adenosine Diphosphate
  • RNA
  • Guanosine Triphosphate
  • Adenosine Triphosphate
  • Calcium

Grants and funding

This work was supported in part by the Higher Education Commission (HEC), who funded the National Research Programme for Universities (NRPU) (9458) and RMIT University Vice-chancellor Fellowship Scheme. We also acknowledge Islamia University Bahawalpur, Pakistan. The authors also acknowledge the financial support provided by the Guangdong science and technology planning project (2016A020210066) and Guangzhou science and technology planning project (201707010461), Guangdong Provincial Department of Agriculture and Rural Affairs Project, Grant/Award Number: 2020KJ115, 2021KJ115. The authors would like to acknowledge access to the RMIT Micro Nano Research Facility (MNRF) in the Victorian node of the Australian National Fabrication Facility (ANFF) and the RMIT Microscopy and Microanalysis Facility (RMMF).