Difference between revisions of "Lecture 09"

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*[http://swift.cmbi.kun.nl/WIWWWI//fullcheck.html '''Whatcheck''']<br>
 
 
*[http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html '''Procheck''']
 
*[http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html '''Procheck''']
 
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Latest revision as of 20:53, 9 December 2007

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Protein Structure Databases


 


 

Objectives for this part of the course


  • Understand that "sequence" and "structure" are abstractions of biopolymers.
  • Understand that "structure" is an idealized concept, applied to an ensemble of dynamic molecules.
  • Be aware of principal methods of experimental structure determination and some of their limitations regarding interpretation of data and resulting accuracy.
  • Understand that structures may have considerable local and global uncertainties.
  • Know that structure abstractions can be stored, retrieved and visualized and become familiar with the principal databases and information sources for that purpose.
  • Be familiar with the contents of a PDB formatted file.


 

Links summary



 

Lecture slides


 



 
 

"Sequence" and "structure" are abstractions of biopolymers


 

Slide 004
Lecture 09, Slide 004
The letter Y represents highly compressed information.
Slide 005
Lecture 09, Slide 005
Which amino acid tyrosine is regarded to be similar to depends on which property we are considering.
Slide 006
Lecture 09, Slide 006



 
 

Structure can be determined experimentally


 

Slide 008
Lecture 09, Slide 008
Slide 009
Lecture 09, Slide 009
Slide 010
Slide 011
Lecture 09, Slide 011
The inability to measure the phases of diffracted photons prevents the reconstruction of the diffracting objects from on set of experimental measurements alone. Additional information must be sought, based on the fact that photons that are in phase enhance the measured intensities, whereas photons that are phase-shifted by 180° cancel each other's intnesities. Thus measuring intensity changes if additional diffraction centres are placed into the structure allows us to infer relative phases, and if several relative phases are known, we can triangulate thier absolute values. Experimental error makes this a difficult problem, but undr favourable circumstances, the electron density map will be interpretable; a structurl model can the be built and refined.
Slide 012
Lecture 09, Slide 012
Slide 013
Lecture 09, Slide 013
Slide 014
Lecture 09, Slide 014
Slide 015
Lecture 09, Slide 015
Slide 016
Lecture 09, Slide 016
*Procheck
Slide 017
Lecture 09, Slide 017



 
 

Structure abstractions can be held in databases


 

Slide 019
Lecture 09, Slide 019
Slide 020
Lecture 09, Slide 020
The PDB
Slide 021
Lecture 09, Slide 021
Slide 022
Lecture 09, Slide 022
Slide 023
Lecture 09, Slide 023
Slide 024
Lecture 09, Slide 024
Additional complications arise from "insertion codes". These are leters that allow the insertion of residues in a common numbering scheme of sequences that are compared between several homologes. In principle this is a good idea, since this makes comparison of residues much easier. But strings such as "23A" can no longer be tretaed as "sequence numbers" - thet are sequence labels and using them correctly can be a challenge.
Slide 025
Lecture 09, Slide 025
Potential pitfalls:
* Record type: changes not consistently applied for modifications
* Atom number: rarely used and a nuisance to update when changing.
* Item
* Atom name: careful about columns
* Amino acid type: selenocysteine. Some very old files use TRY for TRP
* Chain
* Alternate location
* Sequence number
* X,Y, and Z are given in Å (10<sup-10 m = 0.1 nm) values in a cartesian (i.e. orthogonal) coordinate system; but origin and orientation is arbitrary!
* Occupancy can describe: special locations, partially bound ligands, unobserved fragments of structure
* B-values, (also called temperature factors) are a measure of the volume of space around into which a
 
Read the Coordinate section of the PDB format specification (V 2.3)
Slide 026
Slide 027
Lecture 09, Slide 027
Slide 028
Lecture 09, Slide 028
Slide 029
Slide 030
Lecture 09, Slide 030
Slide 031
Slide 032
Lecture 09, Slide 032
PDBsum is a secondary database thst stores analyss and interpretation information for PDB coordinate sets.
Slide 033
Lecture 09, Slide 033

 


 
 


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