Preparation, Biochemical Analysis, and Structure Determination of the Bromodomain, an Acetyl-Lysine Binding Domain

Methods Enzymol. 2016;573:321-43. doi: 10.1016/bs.mie.2016.01.018. Epub 2016 Mar 24.

Abstract

The bromodomain (BrD) represents an evolutionarily conserved protein domain whose function mostly is to recognize acetylated lysine residues in histones and nuclear proteins in regulation of gene transcription in chromatin. The highly conserved BrD structure features an unusual left-handed, antiparallel four-helix bundle and a hydrophobic pocket between the interhelical ZA and BC loops important for acetyl-lysine binding. Many proteins, particularly transcriptional activators, contain BrDs, and mutation or deletion of the BrDs impairs the protein function, implying their critical role in human biology and disease. In this chapter, we provide general protocols of the preparation, biochemical analysis, and structure determination of BrDs, aiming to offer a general guideline for structural and biochemical functional characterization of BrD-containing proteins.

Keywords: Acetyl-lysine binding; Bromodomain; Chromatin biology; Gene transcription; Histone lysine acetylation; NMR spectroscopy; Protein purification and characterization; Structural biology.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cell Cycle Proteins
  • Chromatography, Affinity / methods
  • Chromatography, Gel / methods
  • Crystallography, X-Ray / methods*
  • Escherichia coli / genetics
  • Genetic Vectors / genetics
  • Histone Chaperones
  • Humans
  • Mass Spectrometry / methods
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / isolation & purification
  • Phylogeny
  • Sequence Alignment
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / isolation & purification
  • Transformation, Genetic

Substances

  • BRD4 protein, human
  • Cell Cycle Proteins
  • Histone Chaperones
  • Nuclear Proteins
  • Transcription Factors
  • BRD1 protein, human