Proteomic analysis of defined HDL subpopulations reveals particle-specific protein clusters: relevance to antioxidative function

Arterioscler Thromb Vasc Biol. 2009 Jun;29(6):870-6. doi: 10.1161/ATVBAHA.109.186031. Epub 2009 Mar 26.


Objective: Recent proteomic studies have identified multiple proteins that coisolate with human HDL. We hypothesized that distinct clusters of protein components may distinguish between physicochemically-defined subpopulations of HDL particles, and that such clusters may exert specific biological function(s).

Methods and results: We investigated the distribution of proteins across 5 physicochemically-defined particle subpopulations of normolipidemic human HDL (HDL2b, 2a, 3a, 3b, 3c) fractionated by isopycnic density gradient ultracentrifugation. Liquid chromatography/electrospray mass spectrometry identified a total of 28 distinct HDL-associated proteins. Using an abundance pattern analysis of peptide counts across the HDL subfractions, these proteins could be grouped into 5 distinct classes. A more in-depth correlational network analysis suggested the existence of distinct protein clusters, particularly in the dense HDL3 particles. Levels of specific HDL proteins, primarily apoL-I, PON1, and PON3, correlated with the potent capacity of HDL3 to protect LDL from oxidation.

Conclusions: These findings suggest that HDL is composed of distinct particles containing unique (apolipo)protein complements. Such subspeciation forms a potential basis for understanding the numerous observed functions of HDL. Further work using additional separation techniques will be required to define these species in more detail.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antioxidants / analysis*
  • Apolipoprotein L1
  • Apolipoproteins / blood
  • Aryldialkylphosphatase / blood
  • Centrifugation, Isopycnic
  • Chromatography, Liquid
  • Esterases / blood
  • Humans
  • Lipoproteins, HDL / blood
  • Lipoproteins, HDL2 / blood*
  • Lipoproteins, HDL3 / blood*
  • Male
  • Protein Binding
  • Proteomics* / methods
  • Spectrometry, Mass, Electrospray Ionization


  • APOL1 protein, human
  • Antioxidants
  • Apolipoprotein L1
  • Apolipoproteins
  • Lipoproteins, HDL
  • Lipoproteins, HDL2
  • Lipoproteins, HDL3
  • Esterases
  • Aryldialkylphosphatase
  • PON1 protein, human
  • PON3 protein, human