Protein Data Bank websites

The Structure of DNA Elucidation of the three-dimensional structure of DNA helped researchers understand how this molecule conveys information that can be faithfully replicated from one generation to the next. Tb see the secondary structure of double-stranded DNA, go to the Protein Data Bank website (www.rcsb.org pdb). Use the PDB identifiers listed below to retrieve the data pages for the two forms of DNA... 

For updating the information presented in this chapter, a literature search on the keyword nitrogenase modified with structure, X ray, Mossbauer, iron sulfur cluster, or model compound will generate citations referring to the newest research results. A search of the Protein Data Bank (PDB) at the website address http //www.rcsb.org/pdb/ will yield the latest updates on X ray, NMR, and other submitted structural data. 

The ExPASy server (www.expasy.chl is one of the most useful servers, where almost any bioinforma tic tool can be found, together with useful links to other websites such as NCBI or EBI. The several access databases are descriptive, easy to follow, and up to date. Protein data bank searches with SwissProt or Trembl, as well as sequence alignments using either SimAlign (for two sequences) or ClustalW (for more than two protein sequences) can be started from ExPASy, to name just a few of the possibilities available. Access is also given to the Roche Applied Science Biochemical pathways where either keyword searches for particular enzymes or for metabolites can be performed, or entire metabolic pathways or sections thereof can be visualized. Proteomics evaluation is also available on ExPASy, which features free 2D-PAGE software called Melanie. 

Fig. 1. The number of water soluble (o) and membrane proteins (x) solved per year, relative to the date of the first structure determination in each class, myoglobin (Kendrew et al., 1960), and the photosynthetic reaction center (Deisenhofer et al., 1985), respectively. The data for water-soluble proteins are from Matthews (1976), while those for membrane proteins are from the website http //www.mpibp-frankfurt.mpg.de/michel/public/memprostruct.html. Adjusting for the 25 year difference, it is evident that progress in the structure determination of membrane proteins mirrors that experienced for water-soluble proteins. For perspective, there were 18,838 total available structures in the Protein Data Bank as of October 3, 2002, with 3298 structures deposited in 2001 (see http //www.rcsb.org/pdb/holdings table.html).

Figure 16 Membrane organization in oxygen-evolving photo synthetic systems. The four main complexes present in the membrane are (from left to right) Photosystem 11, the Cytochrome b f complex. Photosystem I, and ATP synthase. All complexes now have published crystal structures, ribbon diagrams of which are shown in the Figure. Coordinates taken from the Protein Data Bank and visualized using Accelrys DSViewer Pro, or 2-D pictures were taken from the PDB website and modified...

TATA Binding Protein and the TATA Box To examine the interactions between transcription factors and DNA, go to the Protein Data Bank (www.rcsb.org/pdb) and download the PDB file ITGH. This file models the interactions between a human TATA-binding protein and a segment of double-stranded DNA. Use the Noncovalent Bond Finder at the Chime Resources website (www.umass.edu/microbio/ chime) to examine the roles of hydrogen bonds and hydro-phobic interactions involved in the binding of this transcription factor to the TATA box. 

PROCHECKcan be downloaded from the following web site http //www.biochenL ucl.ac.uk/ roman/procheckyprocheck.html. To run PROCHECK, one simply types procheck mycoordinates.pdb resolution limit , where mycoordinates.pdb should contain coordinates of your refined protein structure in standard Protein Data Bank (PDB) format, and resolutionjimit should correspond to the high resolution limit of the data (in A) used in the refinement. Alternatively, one can submit coordinates to either of two websites the SAVS server or the PDB validation server (www.deposit.pdb.org/validate/). For additional information, consult the PROCHECK manual www.biochem.ucl.ac.uk/ roman/procheck/manual/. 

---