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structure-calculations

structure-calculations - Protein Structure Determination...

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Protein Structure Determination Using NMR Restraints BCMB/CHEM 8190
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Programs for NMR Based Structure Determination • CNS - Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.;Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Cryst. D 1998 , 54, 905. • X-PLOR-NIH - Schwieters, C. D.; Kuszewski, J. J.; Tjandra, N.; Clore, G. M. J.Magn.Reson. 2003 , 160, 65. • DYANA/CYANA - Güntert, P.; Mumenthaler, C.; Wüthrich, K. J. Mol. Biol . 1997 , 273, 283. -Güntert, P. Prog. NMR Spectrosc. 2003 , 43, 105-125 . • ARIA - Linge, J. P.; Habeck, M.; Rieping, W., et al. Bioinformatics 2003 , 19, 315-316.
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Websites • CNS - http://cns.csb.yale.edu/v1.1/ • X-PLOR - http://xplor.csb.yale.edu/xplor/ • X-PLOR-NIH - http://nmr.cit.nih.gov/xplor-nih/ • CYANA/DYANA - http://www.las.jp/prod/cyana/eg/index.html • ARIA - http://www.pasteur.fr/recherche/unites/Binfs/aria/
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Overview of Structure Calculations Molecular topology information Experimental structural restraints (NOE, coupling constants, H-bond) Template structure Distance geometry Simulated annealing Regularization Simulated annealing refinement Structure selection Analysis/validation (RMSD, “Procheck”, back calculation) Adapted from Brünger, A. T., “X-PLOR Version 3.1, A System For X-ray Crystallography and NMR”
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Molecular topology -example: topology fi le entry for alanine -the empirical energy function (“force fi eld”) is de fi ned for the amino acids -in CNS/X-PLOR, “parameter” fi les and “topology” fi les • parameter fi les: energy constants, standard values • topology fi les: atom names/types/charges masses/connectivities for each amino acid type residue ALA group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end atom CA type=CH1E charge= 0.00 end atom HA type=HA charge= 0.10 end atom CB type=CH3E charge=-0.30 end atom HB1 type=HA charge= 0.10 end …etc… bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB HB3 bond CA C bond C O …etc…
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- NOE data from 2D and 3D experiments are a primary source of information I cp = C{exp(- ± T) • (1 - exp(-2 ² T)} ± = 2W 1 + W 2 + W 0 , ² = (W 2 - W 0 ) - crosspeak intensity proportional to 1/r 6 for short mixing times Experimental Restraints
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NOESY spectrum of ACP
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Experimental Restraints - Sequential NOEs (NOEs between neighboring residues) de fi ne secondary structure NOE interactions in an idealized ± -helix - Short, well-de fi ned 1 H- 1 H distances can be used to calibrate NOE intensities - In proteins, NOE intensities are usually converted to approximate distance ranges “strong” 1.8-2.7 Å “medium” 1.8-3.3 Å “weak” 1.8-5.0 Å “very weak” 1.8-6.0 Å (lower bound is sum of van der Waals radii for two protons)
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Experimental Restraints - Long range NOEs (side chain to side chain) are among the most important in structure determination - Can provide proper relative orientation of structural elements (if enough are measured and properly assigned) - Provide important conformational restraints for structural elements in distant sections of the sequence
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Experimental Restraints - Example of a CNS/X-PLOR/X-PLOR-NIH input fi le for NOE-based distance restraints !V2
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