Lecture 1. Introduction to X-ray Crystallography. Tuesday, February 1, 2011

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1 Lecture 1 Introduction to X-ray Crystallography Tuesday, February 1, 2011

2 Protein Crystallography Crystal Structure Determination in Principle: From Crystal to Structure Dr. Susan Yates

3 Contact Information Dr. Susan Yates (please put BCHM313 in subject line) Botterell Hall, Rm623 Office hours by appointment 9 lectures (Feb 1-18, 2011)

4 Outline X-ray Crystallography Schedule (subject to change) Lecture 1: Introduction into technique, X-rays, and Crystals Lecture 2: Crystals: Theory and Practice Lecture 3: Instrumentation, Waves and Diffraction Lecture 4: Bragg s law, Handling diffraction data Lecture 5: Solving the Phase Problem Lecture 6: Modeling Building, Structure Refinement Lecture 7: Accessing Crystal Structure Quality Lecture 8: The Protein Data Bank, Coordinates Lecture 9: Crystallography Review

5 Protein Structure Determination How? X-ray crystallography NMR spectroscopy Electron microscopy 87.0% X-ray Crystallography entries 8619 entries NMR Spectroscopy Electron Microscopy 0.5% (312 entries) 12.6% PDB Statistics Release Entries as of Oct. 19, 2010

6 Early Milestones of Crystallography 1840 First documented protein crystallization Earthworm Hemoglobin by F.L.Hunfield 1845 A. Bravais - correctly predicted 14 lattice systems (Later to be called Bravais Lattices) 1895 Wilhelm Rontgen observed highly penetrating radiation from fast electrons impinging on matter 1912 Max von Laue demonstrated the wave nature of X-rays, by diffraction from a crystal of copper sulphate 1913 Sir L. Bragg solved structure of NaCl

7 Nobel Prize Winners associated with Crystallography 1901 Physics (W.C. Röntgen) Discovery of X-rays 1914 Physics (M. Von Laue) Diffraction of X-rays by crystals 1915 Physics (W.H. Bragg & W.L. Bragg) Use of X-rays to determine crystal structure 1929 Physics (L.-V. de Broglie) The wave nature of the electron 1937 Physics (C.J. Davisson & G. Thompson) Diffraction of electrons by crystals 1946 Chemistry (J.B. Sumner) Discovers that enzymes can be crystallized 1954 Chemistry (L.C. Pauling) Nature of the chemical bond and its application to the elucidation of the structure of complex substances 1962 Chemistry (J.C. Kendrew & M. Perutz) For their studies of the structures of globular proteins 1962 Physiology/Medicine (F. Crick, J. Watson & M. Wilkins) Helical structure of DNA 1964 Chemistry (D. Hodgkin) Structure of many biochemical substances including Vitamin B Chemistry (C.B. Anfinsen) Folding of protein chains 1976 Chemistry (W.N. Lipscomb) Structure of boranes 1982 Physics (K.G. Wilson) Theory of critical phenomena in connection with phase transitions

8 Nobel Prize Winners associated with Crystallography 1982 Chemistry (A. Klug) Development of crystallographic electron microscopy and discovery of the structure of biologically important nucleic acid protein complexes 1985 Chemistry (H. Hauptman & J. Karle) Development of direct methods for the determination of crystal structures 1988 Chemistry (J. Deisenhofer, R. Huber & H. Michel) Determination of the 3- dimensional structure of a photosynthetic reaction centre 1991 Physics (P.-G. de Gennes) Methods of discovering order in simple systems can be applied to polymers and liquid crystals 1992 Physics (G. Charpak) Discovery of the multi wire proportional chamber 1994 Physics (C. Shull & N. Brockhouse) Neutron diffraction 1996 Chemistry (R. Curl, H. Kroto & R. Smalley) Discovery of the fullerene form of carbon 1997 Chemistry (P.D. Boyer, J.E. Walker & J.C. Skou) Elucidation of the enzymatic mechanism underlying the synthesis of ATP and discovery of an iontransporting enzyme 2003 Chemistry (R. MacKinnon) Potassium channels 2006 Chemistry (R.D. Kornberg) Studies of the molecular basis of eukaryotic transcription 2009 Chemistry (V. Ramakrishnan, T.A. Steitz & A.E. Yonath) Studies of the structure and function of the ribosome

9 Why is Three-Dimensional Structure Important? Picture is worth a thousand words

10 What Structure Can Tell You? Understand biological processes at the basic level Understand disease at an atomic level Help develop new drugs Engineer new and improved proteins for various applications Protein fold Infer sequence-structure relationships Enzyme mechanisms (to some extent) Protein-protein, -DNA, -RNA interfaces Ligand-binding sites Conformational changes Flexible regions

11 Looking at the Objects Around You Use your eyes/microscope/telescope! Solving a structure purely observationally Works for cells, tissues, galaxies etc. Look at the structure and describe or model what you see So why can t we just look at a protein with microscope?

12 Because Even a light microscope has its limits Diffraction limit Cannot image things that are much smaller than the wavelength of the light you are using Wavelength for visible light ( nm) but atoms are separated by distances of the order of 0.1 nm (1 Å)

13 Diffraction Limit Fundamental physical principle In order to see a detail (x) meters in extent, the illuminating radiation you use must have a wavelength at most double that size So protein molecules are invisible to visible light! Even a concentrated solution of protein is transparent Light passes without interacting, so no information on the protein is encoded in the emission

14 How about X-rays?

15 X-rays! Wavelength range from Å 10-8 cm = 1 Å

Picking your Ruler To measure something accurately, you need the appropriate ruler Distance between cities, use kilometres Length of your hand, use centimetres Crystallographers measure

16 Picking your Ruler To measure something accurately, you need the appropriate ruler Distance between cities, use kilometres Length of your hand, use centimetres Crystallographers measure distances between atoms in Å Perfect "rulers" to measure Å distances are X-rays X-rays used by crystallographers are ~ 0.5 to 1.5 Å Just the right size to measure the distance between atoms in a molecule

17 X-rays! They are close to inter-atomic distance! To measure atomic distances through interference and to determine the structure of molecules, our ruler must have atomic dimensions This is why X-rays are required for crystallographic structure determinations

18 How Does a Microscope Work? Light strikes the object and is diffracted in various directions The lens collects the diffracted rays and reassembles them to form an image Lens focuses visible light

19 An X-ray Microscope? Can't build an X-ray microscope No X-ray lens With X-rays, we can detect diffraction from molecules, but we need a different approach to reassemble the image Lens focuses visible light, but the refractive index for very short wavelengths is ~ 1, so far no material can be used to focus X-rays

20 Let s Begin our Journey X-RAY CRYSTALLOGRAPHY

21 Microscope vs. X-ray Crystallography Optical microscope "Impossible" X-ray microscope

onto an electronic detector Like a disco ball spraying light across a dance

22 X-ray Crystallography High-powered X-rays are aimed at a tiny crystal containing trillions of identical molecules Crystal scatters the X-rays onto an electronic detector Like a disco ball spraying light across a dance floor Electronic detector similar to those used to capture images in a digital camera

23 Steps in Solving an X-ray Structure

24 Know Your Protein Sequence, molecular weight Disulfides, glycoprotein?, phosphorylated? Maximum stability/activity, degradation? Cofactors Tags used in purification Secondary structure prediction Homologs with known structure

25 Pure A Good Protein Sample SDS-PAGE, Mono Q, IEF, mass spectroscopy Defined buffer Defined concentration No aggregation Dynamic light scattering, size exclusion To improve: salt, ph, temperature, detergent, batch, cofactors, binding partners, mutagenesis Need lots of protein too!

26 Steps in Solving an X-ray Structure

27 Why Crystals? X-ray scattering from a single molecule would be unimaginably weak and could never be detected above the noise level (scattering from air and water) A crystal arranges huge numbers of molecules in the same orientation, so that scattered waves can add up in phase and raise the signal to a measurable level A crystal acts as an amplifier!

28 What is a Crystal? Crystal acts as an X-ray diffraction amplifier

29 Packing of Molecule

30 Three-Dimensional Crystals Periodic array of atoms, molecules, viruses... Translational symmetry along three vectors a, b, c

31 Crystal Lattice Periodic arrangement in 3 dimensions A crystal unit cell is defined by its cell constants and is the building block for the whole crystal Edges: a, b, c Angles: α, β, γ

32 Building crystals Theory and Practice Next time

Introduction. Chem 6850/8850 X-ray Crystallography The University of Toledo.

Introduction. Chem 6850/8850 X-ray Crystallography The University of Toledo. Introduction Chem 6850/8850 X-ray Crystallography The University of Toledo cora.lind@utoledo.edu Course Goals To develop an understanding of basic crystallographic concepts - Helpful if you ever need to