x-ray crystallography for DNA protein interaction investigation

Background (by Bernhard Rupp)

What is X-ray Crystallography ?

X-ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals. It is not an imaging technique. X-rays have the proper wavelength (in the Ångström range, ~10-8 cm) to be scattered by the electron cloud of an atom of comparable size. Based on the diffraction pattern obtained from X-ray scattering off the periodic assembly of molecules or atoms in the crystal, the electron density can be reconstructed. Additional phase information must be extracted either from the diffraction data or from supplementing diffraction experiments to complete the reconstruction (the phase problem in crystallography). A model is then progressively built into the experimental electron density, refined against the data and the result is a quite accurate molecular structure.

Why Crystallography ?

The knowledge of accurate molecular structures is a prerequisite for rational drug design and for structure based functional studies to aid the development of effective therapeutic agents and drugs. Crystallography can reliably provide the answer to many structure related questions, from global folds to atomic details of bonding. In contrast to NMR, which is an indirect spectroscopic method, no size limitation exists for the molecule or complex to be studied. The price for the high accuracy of crystallographic structures is that a good crystal must be found, and that limited information about the molecule's dynamic behavior in solution is available from one single diffraction experiment. In the core regions of the molecules, X-ray and NMR structures agree very well, and enzymes maintain their activity even in crystals, which often requires the design of non-reactive substrates to study enzyme mechanisms.

5. Methods (From Wikipedia, the free encyclopedia)


5.1 Crystallization
5.2 Data collection
5.2.1 Mounting the crystal
5.2.2 X-ray sources
5.2.3 Recording the reflections
5.3 Data analysis
5.3.1 Crystal symmetry, unit cell, and image scaling
5.3.2 Initial phasing
5.3.3 Model building and phase refinement
5.4 Deposition of the structure

Protein crystallography
Tutorials
Primary databases
Derivative databases


Springer Protocols: Abstract: Preparation of DNA-Protein Complexes ...
Although a plethora of techniques is now available to study DNA-protein interaction, none provides detailed structural information at the molecular level ...
Protein:DNA Interaction Group
extensive surface for mediating protein-protein interactions. .... microscopy and X-ray crystallography. In the last year we have been able to purify the ...www.embl-grenoble.fr/groups/dna/rr03_94.pdf
Identification of DNA Recognition Sequences and Protein ...
meric and heteromeric protein-protein interaction and DNA-. protein interaction. ..... demonstrated by EMSA and X-ray crystallography of single- ...mcb.asm.org/cgi/reprint/18/11/6447.pdf
Structure determination techniques - X-ray and NMR
Protein secondary structure, DNA double helix and RNA stem and loop ... X-ray crystallography requires the growth of protein crystals up to 1 mm in size ...www.whatislife.com/reader/techniques/techniques.html
X-Ray Crystallography
The atoms in crystals interact with X-ray waves in such a way as to produce interference. The interaction can be thought of as if the atoms in a crystal ...www.tulane.edu/~sanelson/eens211/x-ray.htm
X-Ray Crystallography Subject Guide - Chemistry Library - UW-Madison
X-Ray Crystallography. Introduction; Repositories/Databases; Online Learning; Organizations; Books & Reference Works; Selected Journals; Journal Databases ...chemistry.library.wisc.edu/subject-guides/x-ray-crystallography.html
SCSB X-ray Crystallography
X-Ray Crystallography Homepage, X-ray Crystallography at the Sealy Center for Structural Biology ... PIPE (GO) Protein-protein & Protein-DNA interactions ...www.xray.utmb.edu/xray_software.html
The Structure of the DNA Molecule
After all, DNA is composed of a mere 4 subunits while protein is composed of 20, and DNA ... Together, Watson and Crick used X-ray crystallography data, ...www.accessexcellence.org/AE/AEC/CC/DNA_structure.html
DNA Structure and Function
Isolated T2, like other viruses, is just a crystal of DNA and protein, ... Someone else showed them Franklin’s photographs of DNA x-ray crystallography, ...biology.clc.uc.edu/courses/bio104/dna.htm
Overview of macromolecular crystallography
This series will cover the theory and practice of X-ray crystallography, .... or you know the structure of a closely-related protein) you can place a model ...www-structmed.cimr.cam.ac.uk/Course/Overview/Overview.html
Damaged DNA and Its Repair, Biomolecular X-Ray Crystallography Center
Without surprise, it has been uncovered that mutations in DNA repair genes ... for Calcium Regulation and Its Interaction with a Membrane Protein, Junctin, ...kang7.chem.wsu.edu/~kang/research.html
X-Ray Crystallography Gives Scientists New Understanding Of ...
X-Ray Crystallography Gives Scientists New Understanding Of Molecular Motor .... Scientists Map Structure Of DNA-doctoring Protein Complex (Dec. ...www.sciencedaily.com/releases/1999/10/991019075233.htm
Ethylation interference and X-ray crystallography identify similar ...
Our results strongly support the idea that the interactions between protein and the DNA phosphate backbone in the crystallized complex1 are the same as ...www.nature.com/nature/journal/v316/n6029/abs/316651a0.html
X-Ray Crystallography Reveals Helicase that Unwinds DNA
Peering at a Machine that Pries Apart DNA X-Ray Crystallography Gives ... In T7, the helicase is a double-decker protein with two enzyme activities. ...www.hms.harvard.edu/news/releases/1099helicase.html
Research projects X-ray crystallography Nederlands Kanker Instituut
Using X-ray crystallography we can obtain a pictorial view of the .... The protein-DNA recognition takes place through base and backbone contacts, ...xtal.nki.nl/Titia_group/proj_files/projects2.html
Identification of DNA Recognition Sequences and Protein ...
Biochemical characterization of the Roaz protein-protein interaction. .... by EMSA and X-ray crystallography of single-finger or two-finger peptides (28). ...www.pubmedcentral.nih.gov/articlerender.fcgi?artid=109231
Functional Characterization of DNA-binding Domains of the Subunits ...
timately, x-ray crystallography should definitively reveal the. structure of the DNA-protein interaction between the. AHR ARNT dimer and the XRE, ...www.jbc.org/cgi/reprint/271/15/8843.pdf
BioMed Central Full text Energetics of the protein-DNA-water ...
Even x-ray crystallography at high resolution likely underestimates the number of solvent ... Matthews, in his pioneering work on protein-DNA interaction, ...www.biomedcentral.com/1472-6807/7/4
NMR, synchrotrons & X-ray crystallography for pharmaceutical ...
NOE Nuclear Overhauser Effect: The interaction between the dipole moments ... Is there any kind of protein crystallography that isn't x-ray crystallography? ...www.genomicglossaries.com/content/nmr_email.asp

High Throughput Methods in Proteomics (very good slide shows)