1BiologicalDiffractionKatrina ForestNov. 10, 2006Proteins are chains of ~100-500 aminoacids connected by “peptide bonds”.Driven by Hydrogen Bonding, these chains fold intoregular secondary structures.Spacings in molecules can be interrogated with x-rays. E.g. C-C bond in a protein 0.15 nm2No X-Ray Lenses!X-Ray Diffraction from crystalline proteins. Figures from Glusker, “Crystal Structure Analysis”Diffraction grating reminder; more slits, sharper images.Closer spacings on grating--> wider spacings ondiffraction pattern.Interference leads to discretediffraction “spots”.Diffraction from atoms --- Electrons within atoms act as new x-ray point sources just as edges of slits do in diffraction grating.Diffraction from a 6-atom molecule.3Transform of molecule convoluted with diffraction from lattice spacings is diffraction pattern from crystalline array of identical molecules.Diffraction from a protein crystal (lysozyme).The Concept of Electron DensityRecall; ALL the positions in the diffraction patternare contributed to by scattering from each slit in the grating (or each atom in a protein).How to get from “spots” to electron density - the phase problem.ρΣ FWe have only measured the Amplitudes of the Structure Factors (F). To calculate the Electron Density (ρ) we also need the Phases.Structure determination requires calculationof the phase shifts to “recombine” the diffractionamplitudes into an image in the absence of an x-ray lens. The Phase ProblemGuess.Patterson methods.Heavy atom substitution to perturb intensities.Given protein --- Growing crystals[protein][precipitant]solublepptnucxtal01050mg/mlmM0 .5 1.0 1.5 2.04Precipitate of all kinds and sometimes crystalsData collection --CryopreservationRadiation sourcehttp://www.xray.cz/xray/csca/kol2002/doc/pavlina_rezacova.htmDrCBD-crystalWavelength (nm)300 400 500 600 700 8006980.2.4.6.81.0391Useful crystals with expected spectraEarly Electron Density for D.r. Phytochrome5How to get from electron density to a structure?Overall FoldPAS GAFAsp 207Met 259Tyr 263Phe 203Tyr 176Phe 198Cys 24Protein chromophore interactionsHis 260His 290Arg 254GGBP CrystallizationHigh Quality DiffractionSpace group C2: a=119.9 Å, b=36.2 Å, c=80.1 Å, b=124.5˚Strong Data to Detector Edge at 0.92 Å Resolution6Glucose BindingDomain
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