Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP L

J Mol Biol. 2008 Jan 4;375(1):151-64. doi: 10.1016/j.jmb.2007.09.030. Epub 2007 Sep 16.


The study of multidomain or large proteins in solution by NMR spectroscopy has been made possible in recent years by the development of new spectroscopic methods. However, resonance overlap found in large proteins remains a limiting factor, making resonance assignments and structure determination of large proteins very difficult. In this study, we present an expressed protein ligation protocol that can be used for the segmental isotopic labeling of virtually any multidomain or high molecular mass protein, independent of both the folding state and the solubility of the protein fragments, as well as independent of whether the fragments are interacting. The protocol was applied successfully to two different multidomain proteins containing RNA recognition motifs (RRMs), heterogeneous nuclear ribonucleoprotein L and Npl3p. High yields of segmentally labeled proteins could be obtained, allowing characterization of the interdomain interactions with NMR spectroscopy. We found that the RRMs of heterogeneous nuclear ribonucleoprotein L interact, whereas those of Npl3p are independent. Subsequently, the structures of the two RRMs of Npl3p were determined on the basis of samples in which each RRM was expressed individually. The two Npl3p RRMs adopt the expected beta alpha beta beta alpha beta fold.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs*
  • Amino Acid Sequence
  • Amino Acid Substitution
  • Carbon Isotopes / metabolism
  • Cysteine / metabolism
  • Electrophoresis, Polyacrylamide Gel
  • Fungal Proteins / chemistry*
  • Heterogeneous-Nuclear Ribonucleoprotein L / chemistry*
  • Heterogeneous-Nuclear Ribonucleoprotein L / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein L / isolation & purification
  • Heterogeneous-Nuclear Ribonucleoprotein L / metabolism
  • Humans
  • Hydrogen-Ion Concentration
  • Isotope Labeling / methods
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Weight
  • Nitrogen Isotopes / metabolism
  • Nuclear Magnetic Resonance, Biomolecular*
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / isolation & purification
  • Nuclear Proteins / metabolism
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / isolation & purification
  • RNA-Binding Proteins / metabolism
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / isolation & purification
  • Saccharomyces cerevisiae Proteins / metabolism
  • Static Electricity
  • Temperature


  • Carbon Isotopes
  • Fungal Proteins
  • Heterogeneous-Nuclear Ribonucleoprotein L
  • NPL3 protein, S cerevisiae
  • Nitrogen Isotopes
  • Nuclear Proteins
  • RNA-Binding Proteins
  • Recombinant Fusion Proteins
  • Saccharomyces cerevisiae Proteins
  • Cysteine

Associated data

  • PDB/2JVO
  • PDB/2JVR
  • PDB/BMRB15485
  • PDB/BMRB15487