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 CSTA  Vol.1 No.3 , December 2012
Enhancing Lab Source Anomalous Scattering Using Cr Kα Radiation for Its Potential Application in Determining Macromolecular Structures
Abstract: Obtaining phase information for the solution of macromolecular structures is a bottleneck in X-ray crystallography. Anomalous dispersion was recognized as a powerful tool for phasing macromolecular structures. It was used mainly to supplement the isomorphous replacement or to locate the anomalous scatterer itself. The first step in solving macromolecular structures by SAD (single-wavelength anomalous diffraction) is the location of the anomalous scatterers. The SAD method for experimental phasing has evolved substantially in the recent years. A phasing tool, 5-amino-2,4,6- triiodoisophthalic acid (I3C—magic triangle), was incorporated into three proteins, lysozyme, glucose isomerase and thermolysin using quick-soaking and co-crystallization method in order to understand the binding of metal ion with proteins. The high quality of the diffraction data, the use of chromium anode X-ray radiation and the required amount of anomalous signal enabled way for successful structure determination and automated model building. An analysis and/or comparison of the sulfur and iodine anomalous signals at the Cr Kα wavelength are discussed.
Cite this paper: S. Narayanan and D. Velmurugan, "Enhancing Lab Source Anomalous Scattering Using Cr Kα Radiation for Its Potential Application in Determining Macromolecular Structures," Crystal Structure Theory and Applications, Vol. 1 No. 3, 2012, pp. 84-91. doi: 10.4236/csta.2012.13016.
References

[1]   W. A. Hendrickson and C. M. Ogata, “Phase Determination from Multiwavelength Anomalous Diffraction Measurements,” Methods in Enzymology, Vol. 276, 1997, pp. 494-523. doi:10.1016/S0076-6879(97)76074-9

[2]   M. F. Perutz, “Isomorphous Replacement and Phase Determination in Non-Centrosymmetric Space Groups,” Acta Crystallographica, Vol. 9, No. 11, 1956, pp. 867-873. doi:10.1107/S0365110X56002485

[3]   J. C. Kendrew, G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff and D. C. Phillips, “A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis,” Nature, Vol. 181, No. 4610, 1958, pp. 662-666. doi:10.1038/181662a0

[4]   D. Blow, “Outline of Crystallography for Biologists,” Oxford University Press, Oxford, 2002.

[5]   F. H. C. Crick and B. S. Magdoff, “Expected Signal,” Acta Crystallographica, Vol. 9, No. 11, 1956, pp. 901-908. doi:10.1107/S0365110X56002552

[6]   S. Trakhanov and F. A. Quiocho, “Influence of Divalent Cations in Protein Crystallization,” Protein Science, Vol. 9, No. 4, 1995, pp. 1914-1919. doi:10.1002/pro.5560040925

[7]   U. A. Ramagopal, M. Dauter and Z. Dauter, “Phasing on Anomalous Signal of Sulfurs: What Is the Limit?” Acta Crystallographica, Vol. D59, Part 6, 2003, pp. 1020-1027. doi:10.1107/S0907444903007467

[8]   J. Karle, “Some Developments in Anomalous Dispersion for the Structural Investigation of Macromolecular Systems in Biology,” International Journal of Quantum Chemistry: Quantum Biology Symposium, Vol. 7, 1980, pp. 357-367.

[9]   W. A. Hendrickson, J. L. Smith and S. Sheriff, “Direct Phase Determination Based on Anomalous Scattering,” Methods in Enzymology, Vol. 115, 1985, pp. 41-55. doi:10.1016/0076-6879(85)15006-8 =

[10]   B.-C. Wang, “Resolution of Phase Ambiguity in Macromolecular Crystallography,” Methods in Enzymology, Vol. 115, 1985, pp. 90-111. doi:10.1016/0076-6879(85)15009-3

[11]   K. D. Cowtan and K. Y. Zhang, “Density Modification for Macromolecular Phase Improvement,” Progress in Biophysics and Molecular Biology, Vol. 72, No. 3, 1999, pp. 245-270. doi:10.1016/S0079-6107(99)00008-5

[12]   A. Dieckmann and J Rieskamp, “The Influence of Information Redundancy on Probabilistic Inferences,” Memory & Cognition, Vol. 35, No. 7, 2007, pp. 1801-1813. doi:10.3758/BF03193511

[13]   K. N. Vennila and D. Velmurugan, “In-House SAD Phasing with Surface-Bound Cerium Ions,” Acta Crystallographica, Vol. F67, No. 7, 2011, pp. 1662-1665. doi:10.1107/S1744309111035718

[14]   M. Yogavel, et al., “Structural Analysis of Actinidin and a Comparison of Cadmium and Sulfur Anomalous Signals from Actinidin Crystals Measured Using In-House Copper- and Chromium-Anode X-Ray Sources,” Acta Crystallographica, Vol. D66, No. 12, 2010, pp. 1323-1333. doi:10.1107/S0907444910040394

[15]   D. Velmurugan, et al., “Ab Initio Structure Determination of the Triple Mutant (K53,56,121 M) of Bovine Pancreatic Phospholipase A2 at Atomic and High Resolution Using ACORN,” Current Science, Vol. 90, No. 8, 2006, pp. 1091-1099.

[16]   W. A. Hendrickson and M. M. Teeter, “Structure of the Hydrophobic Protein Crambin Determined Directly from the Anomalous Scattering of Sulphur,” Nature, Vol. 290, No. 5802, 1981, pp. 107-113. doi:10.1038/290107a0

[17]   M. Yogavel, J. Gill and A. Sharma, “Iodide-SAD, SIR and SIRAS Phasing for Structure Solution of a Nucleosome Assembly Protein,” Acta Crystallographica, Vol. D65, 2009, pp. 618-622. doi:10.1107/S0907444909013171

[18]   J. E. Debreczeni, G. Bunkóczi, B. Girmann and G. M. Sheldrick, “In-House Phase Determination of the Lima Bean Trypsin Inhibitor: A Low-Resolution Sulfur-SAD Case,” Acta Crystallographica, Vol. D59, No. 2, 2003, pp. 393-395. doi:10.1107/S0907444902020917

[19]   M. Yogavel, J. Gill, P. C. Mishra and A. Sharma, “SAD Phasing of a Structure Based on Cocrystallized Iodides Using an In-House Cu Kalpha X-Ray Source: Effects of Data Redundancy and Completeness on Structure Solution,” Acta Crystallographica, Vol. D63, No. 8, 2007, pp. 931-934. doi:10.1107/S0907444907029174

[20]   T. Beck, G. Tim and G. M. Sheldrick, “The Magic Triangle Goes MAD: Experimental Phasing with a Bromine Derivative,” Acta Crystallographica, Vol. D66, No. 4, 2010, pp. 374-380. doi:10.1107/S0907444909051609

[21]   T. Beck, C. E. Cunha and G. M. Sheldrick, “How to Get the Magic Triangle and the MAD Triangle into Your Protein Crystal,” Acta Crystallographica, Vol. F65, No. 10, 2009, pp. 1-3. doi:10.1107/S1744309109036884

[22]   T. J. Boggon and L. Shapiro, “Screening for Phasing Atoms in Protein Crystallography,” Structure, Vol. 8, No. 7, 2000, pp. R143-R149. doi:10.1016/S0969-2126(00)00168-4

[23]   K. Wernimont, D. L. Huffman, A. L. Lamb, T. V. O’Halloran and A. C. Rosenzweig, “Structural Basis for Copper Transfer by the Metallochaperone for the Menkes/Wilson Disease Proteins,” Nature, Vol. 7, No. 9, 2000, pp. 766-771. doi:10.1038/78999

[24]   Z. Dauter, M. Dauter and K. R. Rajashankar, “Novel Approach to Phasing Proteins: Derivatization by Short Cryo-Soaking with Halides,” Acta Crystallographica, Vol. D56, No. 2, 2000, pp. 232-237. doi:10.1107/S0907444999016352

[25]   R. H. Szczepanowski, R. Filipek and M. Bochtler, “Crystal Structure of a Fragment of Mouse Ubiquitin Activating Enzyme,” The Journal of Biological Chemistry, Vol. 280, No. 50, 2005, pp. 22006-22011. doi:10.1074/jbc.M502583200

[26]   M. Harrel, et al., “The Binding Site of Acetylcholine Receptor as Visualized in the X-Ray Structure of a Complex between Alpha-Bungarotoxin and a Mimotope Peptide,” Neutron, Vol. 32, No. 2, 2001, pp. 265-270.

[27]   Z. Dauter and M. Dauter, “Entering a New Phase: Using Solvent Halide Ions in Protein Structure Determination,” Structure, Vol. 9, No. 2, 2001, pp. R21-R26. doi:10.1016/S0969-2126(01)00565-2

[28]   W. A. Hendrickson and M. M. Teeter, “Characterization of the Aromatic Proton Magnetic Resonance Spectrum of Crambin,” Nature, Vol. 290, No. 5802, 1981, pp. 107-113. doi:10.1038/290107a0

[29]   D. K. Carugo, J. R. Helliwell, H. Stuhrmann and M. S. Weiss, “Softer and Soft X-Rays in Macromolecular Crystallography,” Journal of Synchrotron Radiation, Vol. 12, No. 4, 2005, pp. 410-419. doi:10.1107/S0909049504025762

[30]   M. Cianci, et al., “Structure of Lobster Apocrustacyanin A1 Using Softer X-Rays,” J. R. Acta Crystallographica, Vol. D59, No. 9, 2001, pp. 1219-1229. doi:10.1107/S0907444901009350

[31]   C. Yang, J. W. Pflugarth, D. A. Courville, C. N. Stence and J. D. Ferrara, “Away from the Edge: SAD Phasing from the Sulfur Anomalous Signal Measured In-House with Chromium Radiation,” Acta Crystallographica, Vol. D59, No. 11, 2003, pp. 1943-1957. doi:10.1107/S0907444903018547

[32]   J. H. Naismith, et al., “Refined Structure of Cadmium-Substituted Concanavalin A at 2.0 A Resolution,” Acta Crystallographica, Vol. D49, No. 6, 1993, pp. 561-571. doi:10.1107/S0907444993006390

[33]   T. Beck, A. Krasauskas, T. Gruene and G. M. Sheldrick, “A Magic Triangle for Experimental Phasing of Macromolecules,” Acta Crystallographica, Vol. D64, No. 11, 2008, pp. 1-4. doi:10.1107/S0907444908030266

[34]   G. M. Sheldrick, “Experimental Phasing with SHELXC/D/E: Combining Chain Tracing with Density Modification,” Acta Crystallographica, Vol. D66, No. 4, 2010, pp. 479-485.

[35]   Z. Otwinowski and W. Minor, “Processing of X-Ray Diffraction Data Collected in Oscillation Mode,” In: C. W. Carter, Jr. and R. M. Sweet, Eds., Methods in Enzymology, Macromolecular Crystallography, Part A, New York, 1997, pp. 307-326.

[36]   G. M. Sheldrick, H. A. Hauptman, C. M. Weeks, M. Miller and I. Uson, “Ab Initio Phasing,” In: E. Arnold and M. Rossman, Eds., International Tables for Crystallography, IUCr and Kluwer Academic Publishers, Dordrecht, 2001, pp. 333-351.

[37]   I. Uson and G. M. Sheldrick, “Advances in Direct Methods for Protein Crystallography,” Current Opinion in Structural Biology, Vol. 9, No. 5, 1999, pp. 643-648. doi:10.1016/S0959-440X(99)00020-2

[38]   T. R. Schneider and G. M. Sheldrick, “Substructure Solution with SHELXD,” Acta Crystallographica, Vol. D58, No. 10, 2002, pp. 1772-1779. doi:10.1107/S0907444902011678

[39]   A. Perrakis, R. J. Morris and V. S. Lamzin, “Automated Protein Model Building Combined with Iterative Structure Refinement,” Nature Structural Biology, Vol. 6, No. 5, 1999, pp. 458-463. doi:10.1038/8263

[40]   G. N. Murshudov, A. A. Vagin and E. J. Dodson, “Refinement of Macromolecular Structures by the Maximum-Likelihood Method,” Acta Crystallographica, Vol. D53, No. 3, 1997, pp. 240-255. doi:10.1107/S0907444996012255

[41]   CCP4 (Collaborative Computational Project, Number 4), “The CCP4 Suite: Programs for Protein Crystallography,” Acta Crystallographica, Vol. D50, No. 5, 1994, pp. 760-763. doi:10.1107/S0907444994003112

[42]   W. L. DeLano, “The PyMOL Molecular Graphics System,” DeLano Scientific, San Carlos, 1998.

[43]   L. Q. Chen, et al., “Crystal Structure of a Bovine Neurophysin II Dipeptide Complex at 2.8 A Determined from the Single-Wavelength Anomalous Scattering Signal of an Incorporated Iodine Atom,” Proceedings of the National Academy of Sciences of the USA, Vol. 88, No. 10, 1991, pp. 4240-4244. doi:10.1073/pnas.88.10.4240

[44]   L. Brady, “A Serine Protease Triad Forms the Catalytic Centre of a Triacylglycerol Lipase,” Nature, Vol. 343, No. 6260, 1990, pp. 767-770. doi:10.1038/343767a0

[45]   Lehmann, “Location of the Sulfur Atoms from the Phased Anomalous Map Using Native Protein Data Can Be Very Helpful in Tracing the Peptide Chain,” Ph.D. Dissertation, University of Gottingen, 2000.

[46]   P. J. Loll, “De Novo Structure Determination of Vancomycin Aglycon Using the Anomalous Scattering of Chlorine,” Acta Crystallographica, Vol. D57, No. 7, 2001, pp. 977-980. doi:10.1107/S0907444901007314

[47]   G. G. Langer, S. X. Cohen, A. Perrakis and V. S. Lamzin, “Automated Macromolecular Model Building for X-Ray Crystallography Using ARP/wARP Version 7,” Nature Protocols, Vol. 3, No. 7, 2008, pp. 1171-1179. doi:10.1038/nprot.2008.91

 
 
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