The Xplor-NIH NMR molecular structure determination package

Schwieters, Charles D.; Kuszewski, John; Tjandra, Nico; Clore, G. Marius

doi:10.1016/s1090-7807(02)00014-9

Cited by 2,230 publications

(2,300 citation statements)

References 55 publications

(83 reference statements)

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“…The structure calculations were carried out using a version of the Xplor-NIH program, 19,20 which includes a module that incorporates pseudocontact shifts as restraints in the structure calculations. 21 The structure calculations were carried out on an Apple XServe G5 cluster with 34 2.0 GHz processors.…”

Section: Structure Calculationsmentioning

confidence: 99%

“…plastocyanin was carried out using the structure calculation program Xplor-NIH. 19,20 The 1 H pseudocontact shifts obtained using the Cd 2C -substituted protein as the diamagnetic reference were included as restraints in the structure refinement by plastocyanin. 44 The calculated pseudocontact shifts were obtained from the crystal structure of P.l.…”

Section: Structure Refinementmentioning

confidence: 99%

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On the use of pseudocontact shifts in the structure determination of metalloproteins

Jensen

Hansen

Ayna

et al. 2006

Magnetic Reson in Chemistry

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The utility of pseudocontact shifts in the structure refinement of metalloproteins has been evaluated using a native, paramagnetic Cu 2+ metalloprotein, plastocyanin from Anabaena variabilis (A.v.), as a model protein. First, the possibility of detecting signals of nuclei spatially close to the paramagnetic metal ion is investigated using the WEFT pulse sequence in combination with the conventional TOCSY and 1 H-15 N HSQC sequences. Second, the importance of the electrical charge of the metal ion for the determination of correct pseudocontact shifts from the obtained chemical shifts is evaluated. Thus, using both the Cu + plastocyanin and Cd 2+ -substituted plastocyanin as the diamagnetic references, it is found that the Cd 2+ -substituted protein with the same electrical charge of the metal ion as the paramagnetic Cu 2+ plastocyanin provides the most appropriate diamagnetic reference signals. Third, it is found that reliable pseudocontact shifts cannot be obtained from the chemical shifts of the 15 N nuclei in plastocyanin, most likely because these shifts are highly dependent on even minor differences in the structure of the paramagnetic and diamagnetic proteins. Finally, the quality of the obtained 1 H pseudocontact shifts, as well as the possibility of improving the accuracy of the obtained structure, is demonstrated by incorporating the shifts as restraints in a refinement of the solution structure of A.v. plastocyanin. It is found that incorporation of the pseudocontact shifts enhances the precision of the structure in regions with only few NOE restraints and improves the accuracy of the overall structure.

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Section: Structure Calculationsmentioning

confidence: 99%

Section: Structure Refinementmentioning

confidence: 99%

On the use of pseudocontact shifts in the structure determination of metalloproteins

Jensen

Hansen

Ayna

et al. 2006

Magnetic Reson in Chemistry

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“…All NMR data were collected at 208C on Varian INOVA 500 and 600 MHz and Bruker AVANCE 600 and 800 NMR spectrometers. Complete 1 H, 13 C, and 15 N resonance assignments for full length YnzC and truncated YnzC-1-46 were determined using GFT 8,9 and conventional 10 triple resonance NMR methods, respectively, and deposited in the BioMagResDB (BMRB accession numbers 7225 and 15476). Resonance assignments were validated using the Assignment Validation Suite (AVS) software package.…”

Section: Methodsmentioning

confidence: 99%

Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis

Aramini¹,

Sharma²,

Huang³

et al. 2008

Proteins

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“…To determine the positions of the paramagnetic centers, a pseudoatom was docked on the SH3 protein on the basis of the distances derived from protein PREs by using Xplor-NIH. 40 An example of a script used for docking is included in the Supporting Information. On the basis of the ratios of I para and I dia , the nuclei were divided into three classes.…”

Section: ■ Experimental Proceduresmentioning

confidence: 99%

A Focal Adhesion Kinase-Derived Peptide Binds the Src SH3 Domain in Two Orientations, As Demonstrated Using Paramagnetic Nuclear Magnetic Resonance

et al. 2015

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SH3 binding peptides contain polyproline helices and are classified according to their binding orientations as N-to-C-terminal or C-to-N-terminal. We have tested the hypothesis that such a peptide binds in both orientations but with different populations. A focal adhesion kinase (FAK)-derived peptide was tested for its binding orientation on the Src SH3 domain. Paramagnetic tags were introduced at several positions on the SH3 domain, and on the basis of the paramagnetic relaxation enhancements (PREs) of the amide protons, the positions of the paramagnetic centers were determined. Two peptides were synthesized with 13 C-enriched Ala or Pro, at the N-terminal or C-terminal side of the peptide, and the intermolecular PREs were measured. The results provide compelling evidence that the FAK-derived peptide binds the SH3 domain in two orientations. In the major state, the SH3 domain binds the peptide in the N−C orientation, whereas 20% of the time, the peptide binds in the C−N orientation. We conclude that the distinction between N− C and C−N orientations, which is based on crystal structures, might be artificial. The pseudosymmetric nature of the polyproline helix might allow for binding in both orientations in the solution state.

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The Xplor-NIH NMR molecular structure determination package

Cited by 2,230 publications

References 55 publications

On the use of pseudocontact shifts in the structure determination of metalloproteins

On the use of pseudocontact shifts in the structure determination of metalloproteins

Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis

A Focal Adhesion Kinase-Derived Peptide Binds the Src SH3 Domain in Two Orientations, As Demonstrated Using Paramagnetic Nuclear Magnetic Resonance

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