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Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through sections 1-4 of the Swiss-PdbViewer Tutorial.

Topic: Amino Acids and Peptides

 

Alanine (convergent stereo view)

It may be CO-R-Ny, but it works. With the hydrogen of the alpha carbon pointing toward you, the amino acid is the L enantiomer if the path from the carboxyl carbon (CO) to the R group (R) to the amine group (N) is clockwise. If this path is counterclockwise, the amino acid is the D enantiomer.

Examples

1. The 20 Most Common Amino Acids

In the table below, click the name of an amino acid to view it with Swiss-PdbViewer or your favorite graphics program. Use these simple structures to get to know your viewer by trying out various functions, particularly rotation, translation, and zooming.

With Swiss-PdbViewer, you can load one model after another. Then press <control>-<tab> to turn off all but one model. Press <control>-<tab> repeatedly to move from one model to the next. The title bar of the grapics window tells you which model you are viewing. The Layer Infos window shows which model is on display, and provides display information about all models currently loaded.

Alanine

Glycine

Proline

Arginine

Histidine

Serine

Asparagine

Isoleucine

Threonine

Aspartic Acid

Leucine

Tryptophan

Cysteine

Lysine

Tyrosine

Glutamine

Methionine

Valine

Glutamic Acid

Phenylalanine

Exercises

  1. Confirm that each amino acid is the L-enantiomer.
  2. By looking at the side-chain functional groups, decide which side chains are acidic, basic, polar but uncharged, and nonpolar.
  3. The side chains of asp and glu are sometimes called acidic side chains. Those of arg, his, and lys are called basic. At pH 7, which of these side chains are acids, and which are bases?

2. Oxytocin: A Nonapeptide

Oxytocin is a pituitary hormone. The structure provided here is of oxytocin in the conformation with which it binds to its carrier protein neurophysin (PDB file 1NPO). (If you're interested, read more about the neurophysin/oxytocin complex.)

Exercises

  1. Find the N- and C-termini of the peptide. If you find this difficult, turn off side chains by clicking to remove checkmarks under side in the Control Panel. To cheat, turn on labels, but try to develop skill at recognizing structural features in the unlabeled, stick representation that most researchers use for exploring structure.
  2. Find a peptide bond. Is it cis- or trans-?
  3. Identify the amino acid residues in oxytocin (turn side chains on, of course).
  4. Oxytocin contains a disulfide bond. Measure the dihedral angle of atoms CB-S-S-CB. To do so, hold down <option> (right mouse on PC) while clicking the dihedral button (#7 from left in Tool Bar). Then click on atoms CB-S-S-CB in succession.
  5. Oxytocin contains a ring. What residues make the ring? What residues contribute backbone atoms to the ring? What residues contribute side-chain atoms to the ring? How many atoms are in the ring?

2. Nisin: An Antibiotic

The antibiotic nisin has been used as a food preservative. It is probably synthesized from common amino acids, but after synthesis, chemical modifications result in unusual ring systems and some uncommon amino acid residues. To make this exercise interesting, Deep View does not list individual residues of nisin.

  1. Identify and name as many common amino acid residues as you can.
  2. Draw the structures of the uncommon amino acids.
  3. Look carefully at the alpha carbons of each residue. Do all residues exhibit D-configuration?
  4. Speculate about how common residues might have been modified to produce the rings and other unusual aspects of nisin.

Images made with Swiss-PdbViewer and Canvas.

Topics List

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