Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress by the Northeast Structural Genomics Consortium in standardizing the NMR data collection process for protein structure determination and in building an integrated platform for automated protein NMR structure analysis. Our integrated platform includes the following principal steps: (1) standardized NMR data collection, (2) standardized data processing (including spectral referencing and Fourier transformation), (3) automated peak picking and peak list editing, (4) automated analysis of resonance assignments, (5) automated analysis of NOESY data together with 3D structure determination, and (6) methods for protein structure validation. In particular, the software AutoStructure for automated NOESY data analysis is described in this chapter, together with a discussion of practical considerations for its use in high-throughput structure production efforts. The critical area of data quality assessment has evolved significantly over the past few years and involves evaluation of both intermediate and final peak lists, resonance assignments, and structural information derived from the NMR data. Methods for quality control of each of the major automated analysis steps in our platform are also discussed. Despite significant remaining challenges, when good quality data are available, automated analysis of protein NMR assignments and structures with this platform is both fast and reliable.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Abstract Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as proteinā??protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron...
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Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
J Biomol NMR. 2011 Jan 28;
Authors: Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S
Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of...
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[NMR paper] Automated analysis of protein NMR assignments and structures.
Automated analysis of protein NMR assignments and structures.
Related Articles Automated analysis of protein NMR assignments and structures.
Chem Rev. 2004 Aug;104(8):3541-56
Authors: Baran MC, Huang YJ, Moseley HN, Montelione GT
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[NMR paper] Automated analysis of NMR assignments and structures for proteins.
Automated analysis of NMR assignments and structures for proteins.
Related Articles Automated analysis of NMR assignments and structures for proteins.
Curr Opin Struct Biol. 1999 Oct;9(5):635-42
Authors: Moseley HN, Montelione GT
Recent developments in protein NMR technology have provided spectral data that are highly amenable to analysis by advanced computer software systems. Specific data collection strategies, coupled with these computer programs, allow automated analysis of extensive backbone and sidechain resonance assignments and...
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[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige
Automated analysis of protein NMR assignments using methods from artificial intelligence.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence.
J Mol Biol. 1997 Jun 20;269(4):592-610
Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT
An expert system for determining resonance assignments from NMR spectra of proteins is...
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[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige
Automated analysis of protein NMR assignments using methods from artificial intelligence.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence.
J Mol Biol. 1997 Jun 20;269(4):592-610
Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT
An expert system for determining resonance assignments from NMR spectra of proteins is...
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08-22-2010 03:03 PM
[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Protein Eng. 1996 Nov;9(11):1063-5
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
An integrated platform for automated analysis of protein NMR structures.
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