343

Question 13.2

https://www.rcsb.org/pdb/home/home.do. This is the protein database, the large repository

for all protein structures. Also relatively limited, reference to the PDB database. This has

120,642 Biological Molecular Structures (July 2016; 100,848 X-ray crystal structures,

10,078 NMR structures, 787 by electron microscopy). Funded by the Research

Collaboratory for Structural Bioinformatics, rcsb.org (Rutgers University, UC San

Diego, SDSC).

There is also the “Molecule of the Month” series, where one structure at a time is pre­

sented in detail in a very didactic way. The RCSB PDB Molecule of the Month: Inspiring

a Molecular View of Biology; Goodsell DS, Dutta S, Zardecki C, Voigt M, Berman HM,

et al. (2015) The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of

Biology. PLOS Biology 13(5): e1002140. https://doi.org/10.1371/journal.pbio.1002140

Important main categories:

• Health and diseases

• Essential molecules of life

• Biotechnology and nanotechnology

• Structure and structural elucidation.

SCOP: Structural Classification of Proteins (scop.mrc-lmb.cam.ac.uk/scop/). SCOP

classifies all protein structures and specifies how they are built in detail, e.g. beta-sheet

with a helix packed against it.

Link to “Atlas of protein structures": https://www.bioinformatics.org/molvis/atlas/

atlas.htm.

But with protein design, these tight limits no longer apply (see follow-up tasks). CATH:

Class, Architecture, Topology/fold, Homology read here https://www.cathdb.info/.

Question 13.3

For example, seek out the “Reactibody” by Carletti E et al. (Released: 2011 Sep 21):

https://www.rcsb.org/pdb/explore.do?structureId=2XZA (catalytic antibody).

Question 13.4

Tissue plasminogen activator and engineering of loop structure: An optimal response is to

visualize the PDB structure 5BRR, such as with RasMol (5BRR Michaelis complex of

tPA-S195A:PAI-1, Gong L, Liu M, Zeng T, Shi X, Yuan C, Andreasen PA, Huang M

(2015) Crystal Structure of the Michaelis Complex between Tissue-type Plasminogen

Activator and Plasminogen Activators Inhibitor-1. J. Biol. Chem. 290 p. 25795–25,804).

There you can look at the loop regions of tPA (their removal would prolong the effect) and

an inhibitor in complex with tPA. View the structure for this with RasMol or PyMOL.

20.13  Life Always Invents New Levels of Language