Protein structure: BT Chapter 1,2.
Lehninger, Chapter 4

Carbohydrate structure: Lehininger Chapter 7
MvHA Chapter 9, 10

Viewing three dimensional structures on your computer

3D structures of biological molecules can be downloaded from the World Wide Web (WWW) and viewed using Netscape or Internet Explorer (the Chime structure viewer seems to work only with Netscape). One source for structure viewers is the RASMOL Home Page.

For MacOSX, Windows, or Linux users, PyMol is one of the most powerful viewers, though it is not integrated with a browser.

3D structure examples

You can use the table below to download the information about a protein to your computer (select code), or to view the molecule's structure. With RASMOL, you can quickly see the structure of a protein by selecting Display/cartoons and Colour/structure.

For some demonstrations, you should install the CHIME Netscape plug-in, which allows you to see some impressive tutorials including a demonstration of protein dynamics.

Visit the RASMOL Home Page/Molecules for directions on how to get more structures, or go to the Protein Data Bank directly.

Protein Sequence and Structure Databases

• NCBI/Entrez - Most comprehensive, linked to PubMed.
  1. Best known: GenBank / GenPept , but probably least useful.
  2. Most annotated: RefSeq
  3. Best links to human disease: Locus Link and OMIM.
• Swissprot/Expasy - Most information about proteins
  1. Functional information
  2. Links to other databases
  3. Other Protein/Molecular Biology Tools
• Protein Identification Resource Most family/alignment information

The major protein structure databases:

• Protein Database (PDB) Central depository for all protein Xray and NMR structures
• NCBI/Entrez Molecular Modeling Database / CN3D Excellent integration of structure families and sequence alignments.

Suggested Exercises:

1. On your own computer, examine the structures of bovine pancreatic trypsin inhibitor (1BPT), myoglobin (1mbo), bovine trypsin (1chg), and flavodoxin (5nll).
2. Compare the information available about human paxillin at Entrez (Hint: search with "paxillin AND human") and Swissprot/ Expasy . (a) How many human paxillin sequences does each database have? (b) Which accession provides the most biologically useful information? (c) Where can you find the domain structure of paxillin? (d) Which organisms have Paxillin, or a paxillin homolog (Hint: use Entrez/Blink)?
3. What is the difference between a protein name, an Accession number, and a "GI" number?
4. Which databases produced the following sequence entries:
   1. GTM1_HUMAN
   2. XUFF11
   3. NP_000552
   4. 31924
   Which name for the protein is the most informative? The most reliable?
5. Examine some "derived" protein databases linked from Expasy/SwissProt. (Look for a protein that you have worked on, or use GTM1_HUMAN.) Which databases provide domain information? functional information?
6. Compare the information provided on the Bovine Chymotrypsin structure (1chg) from the PDB and Entrez/MMDB.

Questions on this topic from previous exams

1. Pick two amino-acids with beta-carbons. (a) Name the two amino acids. (b) Draw the di-peptide (show carbon, oxygen, nitrogen, single/double bonds, do not worry about chirality). Indicate (c) the peptide bond; (d) the alpha-carbons; (e) the bonds associated with the phi and psi angles.
2. For DNA, RNA, proteins, and carbohydates:
   1. Name the repeating subunit of the macromolecule
   2. Name the bond that connects the subunit
   3. indicate whether the macromolecular synthesis is template driven
   4. name a common role of the molecule in the cell

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