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Questions and Answers
In all protein microarray methods except one, proteins are usually laid on the surface in what manner?
In all protein microarray methods except one, proteins are usually laid on the surface in what manner?
What is the primary purpose of analytical microarrays?
What is the primary purpose of analytical microarrays?
What is the main difference between analytical and functional protein microarrays?
What is the main difference between analytical and functional protein microarrays?
What is the primary application of functional protein microarrays?
What is the primary application of functional protein microarrays?
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What is the purpose of immobilizing purified proteins on a solid surface in functional protein microarrays?
What is the purpose of immobilizing purified proteins on a solid surface in functional protein microarrays?
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What is an example of a commercial microarray chip?
What is an example of a commercial microarray chip?
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What is the purpose of using Cy-3 and Cy-5 dyes in microarray detection?
What is the purpose of using Cy-3 and Cy-5 dyes in microarray detection?
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What is an application of microarrays in diagnostics?
What is an application of microarrays in diagnostics?
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What is an application of microarrays in proteomics?
What is an application of microarrays in proteomics?
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What is an example of a microarray chip used for cell signaling?
What is an example of a microarray chip used for cell signaling?
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Study Notes
History of X-Ray Diffraction
- 1895: X-rays discovered by Roentgen
- 1914: First diffraction pattern of a crystal made by Knipping and von Laue
- 1915: Theory to determine crystal structure from diffraction pattern developed by Bragg
- 1953: DNA structure solved by Watson and Crick
- Present day: Diffraction improved by computer technology; methods used to determine atomic structures and in medical applications
What is X-Ray Diffraction
- Developed by English physicists Sir W.H.Bragg and his son Sir W.L.Bragg in 1913
- Explains why cleavage faces of crystals appear to reflect X-ray beams at certain angles of incidence (theta, q)
- Related to X-ray wave interference
- Direct evidence for the periodic atomic structure of crystals
Crystal Structure
- Crystalline materials characterized by orderly periodic arrangements of atoms
- Unit cell is the basic repeating unit that defines a crystal
- Crystallographic planes are identified by Miller indices
Template Identification
- Search with sequence: Blast, Psi-Blast, and fold recognition methods
- Use biological information: functional annotation in databases, active site/motifs
Alignment
- Initial alignment
- Improve alignment
- Backbone generation
- Loop modeling
- Side chains
- Refinement
- Validation
Template Quality
- Selecting the best template is crucial
- Most successful method in CASP6 was SCWRL by Dunbrack et al.
- Graph-theory knowledge-based method to solve the combinatorial problem of side chain modeling
Side Chains - Accuracy
- Prediction accuracy is high for buried residues, but much lower for surface residues
- Experimental reasons: side chains at the surface are more flexible
- Theoretical reasons: much easier to handle hydrophobic packing in the core than the electrostatic interactions, including H-bonds to waters
Refinement
- Energy minimization
- Molecular dynamics
- Big errors like atom clashes can be removed, but force fields are not perfect and small errors will also be introduced
Error Recovery
- If errors are introduced in the model, they normally cannot be recovered at a later step
- The alignment cannot make up for a bad choice of template
- Loop modeling cannot make up for a poor alignment
Validation
- Most programs will get the bond lengths and angles right
- Ramachandran plot of the model usually looks pretty much like the Ramachandran plot of the template
- Inside/outside distributions of polar and apolar residues can be useful
- Biological/biochemical data: active site residues, modification sites, interaction sites
ProQ Server
- Neural network-based predictor that predicts the quality of a protein model
- Optimized to find correct models in contrast to other methods that are optimized to find native structures
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Description
Explore the history of X-ray diffraction, from its discovery in 1895 to its application in determining crystal structures and DNA. Learn about the key milestones and figures in this field.
