Analysis of macromolecules, ligands and macromolecule-ligand...

X-ray or gamma ray systems or devices – Specific application – Diffraction – reflection – or scattering analysis

Reexamination Certificate

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C506S009000, C702S027000

Reexamination Certificate

active

07469036

ABSTRACT:
A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

REFERENCES:
patent: 5571902 (1996-11-01), Ravikumar et al.
patent: 5891643 (1999-04-01), Fesik et al.
patent: 6297021 (2001-10-01), Nienaber et al.
Von Dreele, R. B. “Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study” Acta Cryst. 2001, D57, 1836-1842.
Von Dreele, et al. “The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding” Acta Cryst. 2000, 1549-1553.
Vaguine, A. A.; Richelle, J.; Wodak, S. J. “SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model” Act Cryst. 1999, D55, 191-205.
Kumazawa, S.; Kubota, Y.; Takata, M.; Sakata, M. “MEED: a program package for electron-density-distribution calculation by the maximum-entropy method” J. Appl. Cryst. 1993, 26, 453-457.
Von Dreele, “Combined Rietveld and stereochemical restraint refinement of a protein crystal structure” J. Appl. Cryst. 1999, 32, 1084-1089.
Lengauer, T.; Rarey, M. “Computation methods for biomolecular docking” Curr. Opin. Structur. Biol. 1996, 6, 402-406.
Engel et al. “PowderSolve—a complete package for crystal structure solution from the powder diffraction patterns” J. Appl. Cryst. 1999, 32, 1169-1179.
Attwood, T. K.; Miller, C. J. “Which craft is best in bioinformatics” Computers and Chemistry 2001, 25, 329-339.
Von Dreele, R.B. et al.; “The First Protein Crystal Structure Determined From High Resolution X-Ray Powder Diffraction Data: A Variant of of T3R3 Human Insulin-Zinc Complex Produced by Grinding,” Acta Crystallographica Section D. vol. D56, pp. 1549-1553, (2000).
Oldfield, T.J.; “X-Ligand: An Application for the Automated Addition of Flexible Ligands into Electron Density,” Acta Crystallographica Section D. vol. D57, pp. 696 thru 705, (2001).
Chayen, Naomi F..; “Recent Advances in Methodology for the Crystallization of Biological Macromolecules,” Journal of Crystal Growth, vol. 198/199, pp. 649 thru 655, (1999).
Amos, Linda A. et al.; “Arrangement of Protofilaments in Two Forms of Tubulin Crystal Induced by Yinblastine,” Journal of Molecular Biology, vol. 178, pp. 711 thru 729, (1984).
Richards, Jane P. et al.; “Preparation of a Microcrystalline Suspension Formulation of Lys (B28) Pro (B29)- Human Insulin with Ultralente Properties,” Journal of Pharmaceutical Sciences, vol. 88, No. 9, pp. 861 thru 867, Sep. 1999.
Driessen. H. et al.; “Restrain: Restrained Structure-Factor Least-Squares Refinement Program for Macromolecular Structures,” Journal of Applied Crystallography, vol. 22, pp. 510-516, (1989).
Laskowski, Roman A. et al.; “Procheck: A Program to Check the Stereochemical Quality of Protein Structures,” Journal of Applied Crystallography, vol. 26, pp. 283-291, (1993).
McCusker, L.B. et al.; “Rietveld Refinement Guidelines,” Journal of Applied Crystallography, vol. 32, pp. 36-50, (1999).
Engel, G.E. et al.; “Powdersolve—A Complete Package for Crystal Structure Solution From Powder Diffraction Patterns,” Journal of Applied Crystallography, vol. 32, pp. 1169-1179, (1999).
Weber, Patricia C.; “Methods in Enzymology—vol. 276” ‘Overview of Protein Crystallization Methods.’ pp. 13 thru 22, Academic Press, (1997).
Brunger, Axel T.; “Methods in Enzymology—vol. 276.” ‘Patterson Correlation Searches and Refinement.’ pp. 558 thru 580, Academic Press, (1997).
Korszun, Z. Richard; “Methods in Enzymology—vol. 276.” ‘Neutron Macromolecular Crystallography.’ pp. 218 thru 232. Academic Press (1997).
Mattos, Carla and Ringe, Dagmar; “Locating and Characterizing Binding Sites on Proteins,” Nature Biotechnology, vol. 14, pp. 595 thru 599, May 1996.
Mattos, Carla and Ringe, Dagmar; “Proteins in Organic Solvents,” Current Opinion in Structural Biology, vol. 11, pp. 761-764, (2001).
Teplyakov, Alexei et al.; “On the Choice of an Optimal Wavelength in Macromolecular Crystallography,” Acta Crystallography, vol. D54, pp. 610-614, (1998).
Lugovskoy, Alexey A. et al.; “A Novel Approach for Characterizing Protein Liquid Complexes: Molecular Basis for Specificity of Small-Molecule Bcl-2 Inhibitors,” Journal of American Chemical Society, vol. 124, No. 7, pp. 1234 thru 1240, (2002).
Ota, Nobuyuki and Agard, David A.; “Binding Mode Prediction for a Flexible Ligand in a Flexible Pocket Using Multi-Conformation Simulate Annealing Pseudo Crystallographic Refinement,” Journal of Miolecular Biology, vol. 314, pp. 607-617, (2001).
Berman, Helen M. et al.; “The Protein Data Bank,” Nucleic Acids Research, vol. 28, No. 1, pp. 235-242, (2000).
Chayen, Naomi E.; “Recent Advances in Methodology for the Crystallization of Biological Macromolecules,” Journal of Crystal Growth, vol. 198/199, pp. 649-655, (1999).
Chu, Yeh-Ho et al.; “Affinity Capillary Electrophoresis—Mass Spectrometry for Screening Combinatorial Libraries,” Journal of Chemical Society, vol. 118, pp. 7827-7835 (1996).
Ecker, David J. et al.; “Combinatorial Drug Discovery: Which Methods Will Produce the Greatest Value?” BioTechnology, vol. 13, pp. 351-360, Apr. 1995.
Guex, Nicolas et al.; “Swiss-Model and the Swiss-Pdbviewer: An Environment for Comparative Protein Modeling,” Electrophoresis, vol. 18, pp. 2714-2723, (1997).
Karlsson, Robert et al.; “Kinetic Analysis of Monoclonal Antibody-Antigen Interactions with a New Biosensor Based Analytical System,” Journal of Immunological Methods, vol. 145, pp. 229-240 (1991).
Kumazawa, Shintaro et al.; “Meed: A Program Package for Electron-Density-Distribution Calculation by the Maximum-Entropy Method,” Journal of Applied Crystallography, vol. 26, pp. 453-457 (1993).
Moult, John et al.; “Critical Assessment of Methods of Protein Structure Predictions (CASP): Round III,” Proteins: Structure, Function, and Genetics Supplement, vol. 3, pp. 2-6 (1999).
Sim, G.A.; “A Note on the Heavy-Atom Method,” Acta. Cryst., vol. 13, pp. 511-512 (1960.
Sternberg, Nat et al.; “Display of Peptides and Proteins on the Surface of Bacteriophase (Lambda),” Proc. Natl. Acad. Sci., vol. 92, pp. 1609-1613, Feb. 1995.
Udenfriend, Sidney et al.; “Scintillation Proximity Assay: A Sensitive and Continuous Isotopic Method for Monitoring Ligand/Receptor and Antigen/Antibody Interactions.” Analytical Biochemistry, vol. 161, pp. 494-500 (1987).
Von Dreele, R.B.; “Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure,” Journal of Applied Crystallography, vol. 32, pp. 1084-1089 (1999).
Bergfors, Terese M. ed.; “Protein Crystallization: Techniques, Strategies, and Tips.” Cover page-Preface pp. v-vii, Chapter One (Alexander McP

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