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Literature DB >> 21448734

Exclusively NOESY-based automated NMR assignment and structure determination of proteins.

Teppei Ikeya¹, Jun-Goo Jee, Yoshiki Shigemitsu, Junpei Hamatsu, Masaki Mishima, Yutaka Ito, Masatsune Kainosho, Peter Güntert.

Abstract

A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures.

Mesh：

Substances：
Bacterial Proteins

Year: 2011 PMID： 21448734 DOI： 10.1007/s10858-011-9502-8

Source DB: PubMed Journal: J Biomol NMR ISSN： 0925-2738 Impact factor: 2.835

38 in total

Review 1. The direct determination of protein structure by NMR without assignment.

Authors: R Andrew Atkinson; Vladimír Saudek
Journal: FEBS Lett Date: 2002-01-02 Impact factor: 4.124

2. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors: Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal: J Mol Biol Date: 2002-05-24 Impact factor: 5.469

Review 3. Force fields for protein simulations.

Authors: Jay W Ponder; David A Case
Journal: Adv Protein Chem Date: 2003

4. Using NMRView to visualize and analyze the NMR spectra of macromolecules.

Authors: Bruce A Johnson
Journal: Methods Mol Biol Date: 2004

5. Automated structure determination of proteins with the SAIL-FLYA NMR method.

Authors: Mitsuhiro Takeda; Teppei Ikeya; Peter Güntert; Masatsune Kainosho
Journal: Nat Protoc Date: 2007 Impact factor: 13.491

6. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination.

Authors: C Mumenthaler; P Güntert; W Braun; K Wüthrich
Journal: J Biomol NMR Date: 1997-12 Impact factor: 2.835

7. Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors: G Cornilescu; F Delaglio; A Bax
Journal: J Biomol NMR Date: 1999-03 Impact factor: 2.835

8. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities.

Authors: M Nilges
Journal: J Mol Biol Date: 1995-02-03 Impact factor: 5.469

9. Torsion angle dynamics for NMR structure calculation with the new program DYANA.

Authors: P Güntert; C Mumenthaler; K Wüthrich
Journal: J Mol Biol Date: 1997-10-17 Impact factor: 5.469

10. Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

Authors: P J Kraulis
Journal: J Mol Biol Date: 1994-11-04 Impact factor: 5.469

9 in total

Exclusively NOESY-based automated NMR assignment and structure determination of proteins.

Review 1. The direct determination of protein structure by NMR without assignment.

2. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Review 3. Force fields for protein simulations.

4. Using NMRView to visualize and analyze the NMR spectra of macromolecules.

5. Automated structure determination of proteins with the SAIL-FLYA NMR method.

6. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination.

7. Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

8. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities.

9. Torsion angle dynamics for NMR structure calculation with the new program DYANA.

10. Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

1. Accurate protein structure modeling using sparse NMR data and homologous structure information.

2. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins.

3. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA.

4. Combined automated NOE assignment and structure calculation with CYANA.

5. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.

6. The J-UNIO protocol for automated protein structure determination by NMR in solution.

7. An extended combinatorial 15N, 13Cα, and 13C' labeling approach to protein backbone resonance assignment.

8. Improved in-cell structure determination of proteins at near-physiological concentration.

9. Effects of NMR spectral resolution on protein structure calculation.