Molecule of the Month: PDB Pioneers
A dozen historic structures set the foundation for the PDB archive
Enzyme Active Sites
Exploring the Structure
Pioneering Protein Structures
Many of the PDB files for these pioneering structures have been modified and improved over the past 40 years, but you can still find all of them in the database. Of course, today you don't have to wait for them to arrive in the mail: you can just download them from the internet, or use the Jmol image included here to flip through all of them. When you're browsing, notice that these proteins are small and compact, and they are also fairly plentiful proteins. These things made these early structures possible, because the first techniques of protein crystallography required lots of purified protein and lots of stable crystals. Today, sophisticated crystallization techniques and very bright synchrotron X-ray sources allow researchers to solve structures of much larger and more complex molecules, using much less material.
These early structures gave the first view of each protein, but they only provide a single snapshot of the protein. In each case, later structures fill out the biological story of how the protein works. You can find additional structures in the PDB that show the effect of mutations, ligand and inhibitor binding, motion of the protein, and other aspects of their function. For instance, you might look for structures that show features outlined in the "Topics for Further Discussion" below.
Topics for Further Discussion
- Find structures that show the allosteric motion of hemoglobin.
- Find structures that show the differences between hemoglobins from different organisms.
- Find structures that show the the binding of pancreatic trypsin inhibitor to trypsin.
- Find structures that show the the effect of mutations in lysozyme.
- Find structures that show the binding of the cofactor NADH to lactate dehydrogenase.
October 2011, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2011_10