Lecture 09

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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

• The PDB
  

• see: Bernhard Rupp's introduction to crystal structure
  
• Procheck
  
• Coordinate section of the PDB format specification (V 2.3)
  
• the HIC-Up database of hetero compounds in PDB files
  
• The PQS service for Probable Quarternary Structures at the EB
  
• The Nucleic Acid Structure Database
  
• PDBsum
  

 

Lecture slides

 

 
 

"Sequence" and "structure" are abstractions of biopolymers

 

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The letter Y represents highly compressed information.

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Which amino acid tyrosine is regarded to be similar to depends on which property we are considering.

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Structure can be determined experimentally

 

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see: Bernhard Rupp's introduction to crystal structure

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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.

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*Procheck

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Structure abstractions can be held in databases

 

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The PDB

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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.

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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)

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See the HIC-Up database of hetero compounds in PDB files.

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The PQS service for Probable Quarternary Structures at the EB

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The Nucleic Acid Structure Database

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PDBsum is a secondary database thst stores analyss and interpretation information for PDB coordinate sets.

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