Abstract
Publisher Summary This chapter describes the structural features of chromodomains and mentions how this information can be used to identify chromodomains from amino acid sequences. The chapter employs various biophysical techniques to study the chromodomain and chromo shadow domains of HP1β. Chromodomains are one of a number of similar domains that are involved in chromatin structure. Chromodomains can be divided into two subfamilies—namely, the chromodomains and the chromo shadow domains. Fluorescence spectroscopy is an ideal method to study the interaction of the HP1β chromodomain with histone H3. The interaction is mediated via the methyl groups of lysine 9 of histone H3, which fit into a hydrophobic pocket on the surface of the chromodomain formed by the aromatic residues Tyr 21, Phe 45, and Trp 42. Protein fluorescence originates from the aromatic residues, Phe, Tyr, and Trp. However, the fluorescence of proteins containing all three aromatic amino acids is usually dominated by tryptophan. In addition, the chapter also describes how proteins can be characterized and purified using steady-state fluorescence spectroscopy, analytical ultracentrifugation (AUC), and nuclear magnetic resonance (NMR) spectroscopy.
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