Automated protein fold determination using a minimal NMR constraint strategy

Deyou Zheng, Yuanpeng J. Huang, Hunter N B Moseley, Rong Xiao, James Aramini, G. V T Swapna, Gaetano T. Montelione

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, 13C-, 15N-enriched protein samples with selective protonation of side-chain methyl groups (13CH3). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain 15N, HN resonances, and side-chain 13CH3 methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide 1H/2H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A.

Original languageEnglish (US)
Pages (from-to)1232-1246
Number of pages15
JournalProtein Science
Volume12
Issue number6
DOIs
StatePublished - Jun 1 2003
Externally publishedYes

Fingerprint

Nuclear magnetic resonance
Proteins
Spectrum Analysis
Staphylococcal Protein A
Amides
Spectroscopy
Software
Protonation
Chemical shift
Experiments

Keywords

  • Automated NMR data analysis
  • Deuteration
  • Minimal NMR constraints
  • Selective labeling
  • Structural genomics

ASJC Scopus subject areas

  • Biochemistry

Cite this

Zheng, D., Huang, Y. J., Moseley, H. N. B., Xiao, R., Aramini, J., Swapna, G. V. T., & Montelione, G. T. (2003). Automated protein fold determination using a minimal NMR constraint strategy. Protein Science, 12(6), 1232-1246. https://doi.org/10.1110/ps.0300203

Automated protein fold determination using a minimal NMR constraint strategy. / Zheng, Deyou; Huang, Yuanpeng J.; Moseley, Hunter N B; Xiao, Rong; Aramini, James; Swapna, G. V T; Montelione, Gaetano T.

In: Protein Science, Vol. 12, No. 6, 01.06.2003, p. 1232-1246.

Research output: Contribution to journalArticle

Zheng, D, Huang, YJ, Moseley, HNB, Xiao, R, Aramini, J, Swapna, GVT & Montelione, GT 2003, 'Automated protein fold determination using a minimal NMR constraint strategy', Protein Science, vol. 12, no. 6, pp. 1232-1246. https://doi.org/10.1110/ps.0300203
Zheng D, Huang YJ, Moseley HNB, Xiao R, Aramini J, Swapna GVT et al. Automated protein fold determination using a minimal NMR constraint strategy. Protein Science. 2003 Jun 1;12(6):1232-1246. https://doi.org/10.1110/ps.0300203
Zheng, Deyou ; Huang, Yuanpeng J. ; Moseley, Hunter N B ; Xiao, Rong ; Aramini, James ; Swapna, G. V T ; Montelione, Gaetano T. / Automated protein fold determination using a minimal NMR constraint strategy. In: Protein Science. 2003 ; Vol. 12, No. 6. pp. 1232-1246.
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