Selective amino acid segmental labeling of multi-domain proteins

Methods Enzymol. 2015;565:389-422. doi: 10.1016/bs.mie.2015.05.028. Epub 2015 Jun 18.


The steady technical advances of nuclear magnetic resonance (NMR) over the past decades enabled a significant increase in the molecular size of protein particles that can be subjected to a structural and functional characterization in solution. The larger molecular weight of such proteins is accompanied with an increase in NMR signals that complicate spectral interpretation due to signal overlap. The application of segmental isotope labeling to selected domains in multi-domain proteins can significantly facilitate spectral interpretation by reducing the number of observable signals. However, severe signal overlap may persist within individual domains that show low signal dispersion. To further reduce the number of signals and spectral complexity in such systems, we developed a procedure for selective amino acid-type labeling in individual domains of multi-domain proteins. This strategy combines efficient amino acid-type labeling amenable by cell-free protein expression with near-seamless domain ligation achievable by expressed protein ligation. By application of simple dual labeling schemes, this approach further allows residue-specific isotope labeling to position NMR-observable probes at desired sites within segments of multi-domain proteins. This chapter describes a detailed protocol for selective amino acid-type segmental labeling of multi-domain proteins and illustrates its application to a multi-domain RNA-binding protein. The applied ligation approach is further suitable for efficient ligation of unlabeled and/or uniformly labeled domains produced solely by recombinant in vivo expression.

Keywords: Amino acid-specific isotope labeling; Cell-free protein expression; Expressed protein ligation; NMR spectroscopy; Protein ligation; Segmental isotope labeling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / metabolism*
  • Isotope Labeling
  • Magnetic Resonance Spectroscopy
  • Proteins / metabolism*


  • Amino Acids
  • Proteins