Biochem 503, Fall 2008

Structure Comparison/Super-secondary structure/Structure Databases

(9/8/2008)

Branden and Tooze, Chapters 2 - 5

Lecture handout PDF

Topics

Sequence and structural similarity

  1. Sander C and Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment Proteins 9:56-68 (PubMed)

Structure Comparison:

  1. *** Holm L and Sander C (1996) Mapping the protein universe Science 273:595-603 (PubMed)

  2. Gibrat JF et al. (1996) Surprising similarities in structure comparison Curr. Opin. Struct. Biol. 6:377-85 (PubMed)

DALI http://www.ebi.ac.uk/dali/

VAST http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html

Protein "morphology"

Richardson JS (1981) The anatomy and taxonomy of protein structure Adv. Protein Chem. 34:167-339 (PubMed)

Richardson JS (1985) Describing patterns of protein tertiary structure Meth. Enzymol. 115:341-58 (PubMed)

Richardson JS et al. (1992) Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992 Biophys. J. 63:1185-209 (PubMed)

Swiss-Model protein structure course - chapter 2 - Super-secondary structure

Swiss-Model protein structure course - chapter 4 - folds

Protein topology representation:

http://www.dcs.gla.ac.uk/~drg/epsrc-vf/epsrc-vf.html

Protein structural motif databases

Structural assignments of PDB files: PDBSum

http://www.biochem.ucl.ac.uk/bsm/pdbsum/

CATH - Class, Architecture, Topology, Homologous superfamily

http://www.biochem.ucl.ac.uk/bsm/cath/ (U. London)

SCOP - Structural Classification of Proteins

http://scop.mrc-lmb.cam.ac.uk/scop/ (Cambridge)
http://scop.berkeley.edu/ (Berkeley)

Examples


(All examples are taken from the CATH classification examples.

All alpha
alpha-non-bundle - 1eca (hemoglobin) UVa/RasMol PDB/Chime VAST/Cn3D
alpha bundle - 2ccy (cytochrome c) UVa/RasMol PDB/Chime VAST/Cn3D
All beta
ribbon - 1tpm (tissue plasminogen activator, TPA) UVa/RasMol PDB/Chime VAST/Cn3D
single sheet - 3mon A UVa/RasMol   VAST/Cn3D
single sheet (full) - 3mon (monellin) UVa/RasMol PDB/Chime VAST/Cn3D
roll - 1pht (phosphitidyl inositol kinase, alpha subunit) UVa/RasMol PDB/Chime VAST/Cn3D
barrel - 2por (ompF porin) UVa/RasMol PDB/Chime VAST/Cn3D
clam - 3bcl (bacteriochlorophyll A) UVa/RasMol PDB/Chime VAST/Cn3D
sandwich - 2hla B UVa/RasMol PDB/Chime VAST/Cn3D
distorted sandwich - 1cdq (complement regulatory protein, NMR) UVa/RasMol VAST/Cn3D
treefoil - 1afc A (fibroblast growth factor) UVa/RasMol PDB/Chime VAST/Cn3D
orthogonal prism - 1msa A (lectin) UVa/RasMol PDB/Chime VAST/Cn3D
aligned prism - 1vmo (vitelline membrane protein) UVa/RasMol PDB/Chime VAST/Cn3D
4 propeller - 1hxn (hemopexin) UVa/RasMol PDB/Chime VAST/Cn3D
6,7,8 propeller - 4aah A (methanol dehydrogenase) UVa/RasMol PDB/Chime VAST/Cn3D
2 solenoid - 1kap (alkaline protease) UVa/RasMol PDB/Chime VAST/Cn3D
3 solenoid - 2pec (pectate lyase) UVa/RasMol PDB/Chime VAST/Cn3D
Alpha-Beta
roll - 1std (scytalone dehydratase) UVa/RasMol PDB/Chime VAST/Cn3D
barrel - 1tml (glucanase) UVa/RasMol PDB/Chime VAST/Cn3D
TIM barrel - 1tme (triosephosphate isomerase) UVa/RasMol PDB/Chime VAST/Cn3D
2 layer sandwich (ab) - 1brs D (endonuclease) UVa/RasMol   VAST/Cn3D
2 layer sandwich (ab) - 1brs (full) UVa/RasMol PDB/Chime VAST/Cn3D
3 layer sandwich (aba) - 1ntr (gene regulatory protein), NMR UVa/RasMol PDB/Chime VAST/Cn3D
3 layer sandwich (bba) - 1pya B (carboxy lyase) UVa/RasMol VAST/Cn3D
4 layer sandwich (abba) - 2dnj A (DNase I) UVa/RasMol PDB/Chime VAST/Cn3D
4 layer sandwich - full (abba) - 2dnj UVa/RasMol PDB/Chime VAST/Cn3D

Questions on this topic from previous exams

  1. What does RMSD stand for? In general, how is this measure of similarity calculated? How can it be used to infer homology?

  2. Given the following information:
      startstopadjacent
    structure
    helix 1 11 25  
    helix 2 40 45  
    helix 3 66 76  
    helix 4 94 105  
    helix 5 122 136  
    strand 1 31 34 strand 2
    strand 2 2 6 strand 1
    strand 3 48 53 strand 2
    strand 4 81 88 strand 3
    strand 5 115 118 strand 4
    Draw a 2D-distance plot for the structure.
  3. Shown are two views of 1sty, the structure of staph. nuclease. Based on these structures, assign 1sty to a structural class and architecture (fold). Justify your assignment.

  4. Draw two different topologies of a 4-helix bundle, numbering each of the alpha helices and indicating their N- and C- orientation. Could these two topologies be distinguished with a 2-D distance plot? Why or why not?

  5. For the following structure:

    What is the structural class of the protein (e.g. all-alpha)? What is its supersecondary structure (e.g. 4 helix bundle)? Why?

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