FAST-NMR: Functional annotation screening technology using NMR spectroscopy

Kelly A. Mercier, Michael Baran, Viswanathan Ramanathan, Peter Revesz, Rong Xiao, Gaetano T. Montelione, Robert Powers

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analysis of protein-ligand interactions. This is based on basic tenets of biochemistry where proteins with similar functions will have similar active sites and exhibit similar ligand binding interactions, despite global differences in sequence and structure. Protein-ligand interactions are determined through a tiered NMR screen using a library composed of compounds with known biological activity. A rapid co-structure is determined by combining the experimental identification of the ligand binding site from NMR chemical shift perturbations with the protein-ligand docking program AutoDock. Our CPASS (Comparison of Protein Active Site Structures) software and database are then used to compare this active site with proteins of known function. The methodology is demonstrated using unannotated protein SAV1430 from Staphylococcus aureus.

Original languageEnglish (US)
Pages (from-to)15292-15299
Number of pages8
JournalJournal of the American Chemical Society
Volume128
Issue number47
DOIs
StatePublished - Nov 29 2006

Fingerprint

Nuclear magnetic resonance spectroscopy
Screening
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Technology
Proteins
Ligands
Catalytic Domain
Protein Sequence Analysis
Biochemistry
Sequence Homology
Genomics
Chemical shift
Binding sites
Bioactivity
Libraries
Staphylococcus aureus
Software
Binding Sites
Databases

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Mercier, K. A., Baran, M., Ramanathan, V., Revesz, P., Xiao, R., Montelione, G. T., & Powers, R. (2006). FAST-NMR: Functional annotation screening technology using NMR spectroscopy. Journal of the American Chemical Society, 128(47), 15292-15299. https://doi.org/10.1021/ja0651759

FAST-NMR : Functional annotation screening technology using NMR spectroscopy. / Mercier, Kelly A.; Baran, Michael; Ramanathan, Viswanathan; Revesz, Peter; Xiao, Rong; Montelione, Gaetano T.; Powers, Robert.

In: Journal of the American Chemical Society, Vol. 128, No. 47, 29.11.2006, p. 15292-15299.

Research output: Contribution to journalArticle

Mercier, KA, Baran, M, Ramanathan, V, Revesz, P, Xiao, R, Montelione, GT & Powers, R 2006, 'FAST-NMR: Functional annotation screening technology using NMR spectroscopy', Journal of the American Chemical Society, vol. 128, no. 47, pp. 15292-15299. https://doi.org/10.1021/ja0651759
Mercier KA, Baran M, Ramanathan V, Revesz P, Xiao R, Montelione GT et al. FAST-NMR: Functional annotation screening technology using NMR spectroscopy. Journal of the American Chemical Society. 2006 Nov 29;128(47):15292-15299. https://doi.org/10.1021/ja0651759
Mercier, Kelly A. ; Baran, Michael ; Ramanathan, Viswanathan ; Revesz, Peter ; Xiao, Rong ; Montelione, Gaetano T. ; Powers, Robert. / FAST-NMR : Functional annotation screening technology using NMR spectroscopy. In: Journal of the American Chemical Society. 2006 ; Vol. 128, No. 47. pp. 15292-15299.
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