Combining Evolutionary Covariance and NMR Data for Protein Structure Determination

Yuanpeng Janet Huang, Kelly P. Brock, Yojiro Ishida, Gurla V.T. Swapna, Masayori Inouye, Debora S. Marks, Chris Sander, Gaetano T. Montelione

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Abstract

Accurate protein structure determination by solution-state NMR is challenging for proteins greater than about 20 kDa, for which extensive perdeuteration is generally required, providing experimental data that are incomplete (sparse) and ambiguous. However, the massive increase in evolutionary sequence information coupled with advances in methods for sequence covariance analysis can provide reliable residue–residue contact information for a protein from sequence data alone. These “evolutionary couplings (ECs)” can be combined with sparse NMR data to determine accurate 3D protein structures. This hybrid “EC–NMR” method has been developed using NMR data for several soluble proteins and validated by comparison with corresponding reference structures determined by X-ray crystallography and/or conventional NMR methods. For small proteins, only backbone resonance assignments are utilized, while for larger proteins both backbone and some sidechain methyl resonance assignments are generally required. ECs can be combined with sparse NMR data obtained on deuterated, selectively protonated protein samples to provide structures that are more accurate and complete than those obtained using such sparse NMR data alone. EC–NMR also has significant potential for analysis of protein structures from solid-state NMR data and for studies of integral membrane proteins. The requirement that ECs are consistent with NMR data recorded on a specific member of a protein family, under specific conditions, also allows identification of ECs that reflect alternative allosteric or excited states of the protein structure.

Original languageEnglish (US)
Title of host publicationMethods in Enzymology
EditorsA. Joshua Wand
PublisherAcademic Press Inc.
Pages363-392
Number of pages30
ISBN (Print)9780128138601
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Enzymology
Volume614
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Keywords

  • AutoStructure/ASDP
  • Automated NMR data analysis
  • Evolutionary couplings
  • Hybrid methods
  • Maximum entropy
  • Multiple sequence alignment
  • Protein NMR spectroscopy
  • Protein families

Fingerprint Dive into the research topics of 'Combining Evolutionary Covariance and NMR Data for Protein Structure Determination'. Together they form a unique fingerprint.

  • Cite this

    Huang, Y. J., Brock, K. P., Ishida, Y., Swapna, G. V. T., Inouye, M., Marks, D. S., Sander, C., & Montelione, G. T. (2019). Combining Evolutionary Covariance and NMR Data for Protein Structure Determination. In A. J. Wand (Ed.), Methods in Enzymology (pp. 363-392). (Methods in Enzymology; Vol. 614). Academic Press Inc.. https://doi.org/10.1016/bs.mie.2018.11.004