Structure XPLOR

The full potenhal of RDCs, however, can be seen by the incorporation of RDC data in structure calculations. Several programs hke XPLOR-NIH, DISCOVER or GROM ACS allow the incorporation of RDCs as angular or combined angular and distance dependent restraints. Several studies on sugars have been reported (see, e.g. Ref [43] and references therein) and Fig. 9.8 shows the comparison of three structural models for the backbone of the cyclic undecapeptide cyclosporin A, derived from X-ray crystahography, ROE data in CDCI3 as the solvent, and RDCs and ROEs obtained in a PDMS/CDCfi stretched gel [22]. Due to the sensitivity to... 

Molecular Replacement. The tertiary structure of crystalline ALBP was solved by using the molecular replacement method incorporated into the XPLOR computer program (Brunger et al., 1987). The refined crystal structure of myelin P2 protein without solvent and fatty acid was used as the probe structure throughout the molecular replacement studies. We are indebted to Dr. A. Jones and his colleagues for permission to use their refined P2 coordinates before publication. 

Structure Refinement. The refinement of the structure was based on an energy function approach (Brunger etal., 1987) arbitrary combinations of empirical and effective energy terms describing crystallographic data as implemented in XPLOR. Molecular model building was done on an IRIS Workstation (Silicon Graphics) with the software TOM, a version of FRODO (Jones, 1978). 

Figure 16 Yearly number of publications in the CJACS file mentioning the Cambridge Structural Database or the Protein Data Bank. The search queries for each curve were (1) protein w)data(w)bank, (2) xplor or x(w)plor, and (3) cam-bridge(w)structural(w)database. To minimize extraneous hits and to ensure have comparable curves, alternate names of the databases, such as CSD, Brookhaven, or PDB, were not used.

Schwieters CD, et al. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 2003 160 65-73. Brunger AT, et al. Crystallography NMR system A new software suite for macromolecular structure determination. Acta Crystallogr. D. Biol. Crystallogr. 1998 54 905-921. 

Finally, NMR-derived distance information as well as information about dihedral angles (obtained from chemical shifts) is incorporated into structure calculations performed using molecular dynamics and simulated annealing programs such as CNS (48) and XPLOR-NIH (49) to calculate the protein stmcture. 

The molecular dynamics for NMR structure determination and the torsion angle dynamics were extensively reviewed by Giintert.35 The method was also reviewed by Clore and Schwieters.20 The molecular dynamics programs, e.g., CHARMM,42 AMBER,43 and GROMACS44 can be used for the structure determination. XPLOR,38 its successor CNS,45 and XPLOR-NIH12... 

The procedure also used random array initial structures for molecular dynamics algorithm using XPLOR-NIH.12 Sixteen thousand initial structures were subjected to an initial simulated annealing (5,000 K, 80 ps). This means that the initial structures did not cover the entire conformational space, but were randomly distributed all over the space. The conformational... 

Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc 48(l) 47-62... 

Schwieters CD et al (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160(l) 65-73... 

TROSY spectra. Relative domain orientation could then be modelled in MODULE, prior to refinement of the entire structure in XPLOR-NIH under RDC, ambiguous NOE and radius of gyration restraints. In the model, domains 2, 4 and 6 pack together into a core flanked by propeller blades of 1,3 and 5, explaining the increased rotational tumbling measured from amide backbone dynamics in these domains. Mitogen-activated... 

XPLOR computer program for X-ray structure refinement using molecular dynamics... 

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