Relax, a Flexible Program for the Back Calculation of NOESY Spectra Based on Complete-Relaxation-Matrix Formalism

Görler, Adrian; Kalbitzer, Hans Robert

doi:10.1006/jmre.1996.1033

Cited by 48 publications

(23 citation statements)

References 13 publications

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“…Nuclear Overhauser effects (NOEs) were assigned in an iterative manner alternating with structure calculations: Starting with a homology model of HPr from S. carnosus and the NOEs already assigned during the primary sequential assignment procedure (essentially the NOEs defining the a-helices and the (3-pleated sheets) a bundle of structures was calculated by room-temperature-restrained molecular dynamics. For the structures with the lowest conformational energies, individual NOESY spectra were recalculated using the complete relaxation matrix formalism [42,43]. Additional assignments were made by comparison of the calculated NOESY spectra with the experimental NOESY and NOESY-HSQC as well as qualitatively with TOCSY spectra.…”

Section: Methodsmentioning

confidence: 99%

Solution structure of the histidine-containing phosphocarrier protein fromStaphylococcus carnosus

et al. 1999

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The solution structure of histidine-containing phosphocarrier protein from Staphylococcus carnosus was determined by two-and three-dimensional nuclear magnetic resonance (NMR) spectroscopy on uniformly 15 N-enriched protein. The main structural element is an antiparallel (3-pleated sheet with four strands A, B, C, and D arranged with the topology A-D-B-C. Strand A comprises residues 2 to 8, strand B residues 32 to 37, strand C reidues 40 to 43, and strand D residues 59 to 66. Three right-handed helices are arranged on top of the (3-pleated sheet. Helix a reaches from residue 16 to 29, helix b from residue 48 to 53, and helix c from residue 72 to 83. Strands B and C of the (3-pleated sheet are connected by a type II' turn. The hydroxyl proton of Ser-31 is exchanging with the solvent so slowly that cross peaks can be detected in two-dimensional NMR spectra based on homonuclear J-couplings. The imidazole ring of the active-center His-15, which is partly charged in the structure determined at pH 7.2, is located above the N-terminal end of helix a, perpendicular to its axis. The N5 ' atom of His-15, accepting the phosphoryl from enzyme 1, is exposed to the solvent.

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Section: Methodsmentioning

confidence: 99%

Solution structure of the histidine-containing phosphocarrier protein fromStaphylococcus carnosus

et al. 1999

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“…The corresponding simulated spectrum was back-calculated from one of the final accepted structures using the full relaxation matrix approach implemented in the program RELAX. 50,51 The experimental spectrum was automatically assigned using the assignment program AUNOAS (to be published) that is part of AUREMOL. AUNOAS performs a structure-based assignment where for each back calculated signal a search for the corresponding experimental signal is performed.…”

Section: Structure Calculationsmentioning

confidence: 99%

Structure Determination and Ligand Interactions of the PDZ2b Domain of PTP-Bas (hPTP1E): Splicing-induced Modulation of Ligand Specificity

Kachel

Erdmann

Kremer

et al. 2003

Journal of Molecular Biology

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“…Analogous to crystallography R-factors, NMR R-factors are used to quantify how well a three-dimensional structure accounts for the spectral signals occurring in an experimental NMR spectrum. Using an implementation of the complete relaxation matrix analysis (RELAX, [56,57]) artificial NMR spectra are calculated for the given three-dimensional structure and compared to the experimental spectra. R-factors quantify the deviations between the two types of spectra and are therefore a measure for the quality of the trial structure.…”

Section: Methodsmentioning

confidence: 99%

A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

et al. 2005

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BackgroundWe have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350). The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS.ResultsTo test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ). The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms.ConclusionIn summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

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Relax, a Flexible Program for the Back Calculation of NOESY Spectra Based on Complete-Relaxation-Matrix Formalism

Cited by 48 publications

References 13 publications

Solution structure of the histidine-containing phosphocarrier protein fromStaphylococcus carnosus

Solution structure of the histidine-containing phosphocarrier protein fromStaphylococcus carnosus

Structure Determination and Ligand Interactions of the PDZ2b Domain of PTP-Bas (hPTP1E): Splicing-induced Modulation of Ligand Specificity

A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

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