### Abstract

A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways. Derivatives of the NOE intensities with respect to the dihedral angles are analytically calculated, and efficiently evaluated with the use of a filter technique for identifying the dominant terms of these derivatives. This new method was implemented in the distance geometry program DIANA. As an initial test, we refined 30 rigid distorted helical structures, using a simulated data set of NOE distance constraints for a rigid standard α-helix. The final root-mean-square deviations of the refined structures relative to the standard helix were less than 0.1 Å, and the R-factors dropped from values between 7% and 32% to values of less than 0.5% in all cases, which compares favorably with the results from distance geometry calculations. In particular, because spin diffusion was not explicitly considered in the evaluation of 'exact'^{1}H-^{1}H distances corresponding to the simulated NOE intensities, a group of nearly identical distance geometry structures was obtained which had about 0.5 Å root-mean-square deviation from the standard α-helix. Further test calculations using an experimental NOE data set recorded for the protein trypsin inhibitor K showed that the complete relaxation matrix refinement procedure in the DIANA program is functional also with systems of practical interest.

Original language | English (US) |
---|---|

Pages (from-to) | 257-269 |

Number of pages | 13 |

Journal | Journal of Biomolecular NMR |

Volume | 1 |

Issue number | 3 |

DOIs | |

State | Published - Sep 1991 |

Externally published | Yes |

### Fingerprint

### Keywords

- Analytically calculated derivatives of NOE intensities
- Distance geometry
- Protein structure calculation
- R-factor
- Relaxation matrix refinement

### ASJC Scopus subject areas

- Spectroscopy
- Biochemistry
- Biochemistry, Genetics and Molecular Biology(all)

### Cite this

*Journal of Biomolecular NMR*,

*1*(3), 257-269. https://doi.org/10.1007/BF01875519

**Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.** / Mertz, John E.; Güntert, Peter; Wüthrich, Kurt; Braun, Werner.

Research output: Contribution to journal › Article

*Journal of Biomolecular NMR*, vol. 1, no. 3, pp. 257-269. https://doi.org/10.1007/BF01875519

}

TY - JOUR

T1 - Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities

AU - Mertz, John E.

AU - Güntert, Peter

AU - Wüthrich, Kurt

AU - Braun, Werner

PY - 1991/9

Y1 - 1991/9

N2 - A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways. Derivatives of the NOE intensities with respect to the dihedral angles are analytically calculated, and efficiently evaluated with the use of a filter technique for identifying the dominant terms of these derivatives. This new method was implemented in the distance geometry program DIANA. As an initial test, we refined 30 rigid distorted helical structures, using a simulated data set of NOE distance constraints for a rigid standard α-helix. The final root-mean-square deviations of the refined structures relative to the standard helix were less than 0.1 Å, and the R-factors dropped from values between 7% and 32% to values of less than 0.5% in all cases, which compares favorably with the results from distance geometry calculations. In particular, because spin diffusion was not explicitly considered in the evaluation of 'exact'1H-1H distances corresponding to the simulated NOE intensities, a group of nearly identical distance geometry structures was obtained which had about 0.5 Å root-mean-square deviation from the standard α-helix. Further test calculations using an experimental NOE data set recorded for the protein trypsin inhibitor K showed that the complete relaxation matrix refinement procedure in the DIANA program is functional also with systems of practical interest.

AB - A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways. Derivatives of the NOE intensities with respect to the dihedral angles are analytically calculated, and efficiently evaluated with the use of a filter technique for identifying the dominant terms of these derivatives. This new method was implemented in the distance geometry program DIANA. As an initial test, we refined 30 rigid distorted helical structures, using a simulated data set of NOE distance constraints for a rigid standard α-helix. The final root-mean-square deviations of the refined structures relative to the standard helix were less than 0.1 Å, and the R-factors dropped from values between 7% and 32% to values of less than 0.5% in all cases, which compares favorably with the results from distance geometry calculations. In particular, because spin diffusion was not explicitly considered in the evaluation of 'exact'1H-1H distances corresponding to the simulated NOE intensities, a group of nearly identical distance geometry structures was obtained which had about 0.5 Å root-mean-square deviation from the standard α-helix. Further test calculations using an experimental NOE data set recorded for the protein trypsin inhibitor K showed that the complete relaxation matrix refinement procedure in the DIANA program is functional also with systems of practical interest.

KW - Analytically calculated derivatives of NOE intensities

KW - Distance geometry

KW - Protein structure calculation

KW - R-factor

KW - Relaxation matrix refinement

UR - http://www.scopus.com/inward/record.url?scp=0026223897&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0026223897&partnerID=8YFLogxK

U2 - 10.1007/BF01875519

DO - 10.1007/BF01875519

M3 - Article

VL - 1

SP - 257

EP - 269

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 3

ER -