Elements of Protein Structure
As we saw in Metabolism lecture 1, proteins are made up of covalently linked
amino acids, joined in condensation reactions. To the right is a model of the
protein Eotaxin, (as
deduced by the NMR studies of Crump
et al, 1998). Can you see any other covalent bonds holding the
protein together?
Four of the yellow sulphur atoms in the Eotaxin molecule
belong to cysteine residues which can form intermolecular disulphide bonds. Click
on the button below for a close-up of those two bonds.
Van
der Waals forces are transient, electrostatic attractions
between two atoms, due to the fluctuating electron cloud surrounding each
atom which has a temporary electric dipole. Although relatively weak, the
sheer number of these
interactions within a protein can still have a large part to say in the overall
conformation or shape of a protein. Click on the button below to see a
representation of the electron clouds surrounding each atom.
Can you see any elements of secondary structure in
the Eotaxin model?
Eotaxin, like other
chemokine proteins, has a distinct
"Greek Key" motif (pictured left) made up of three anti-parallel
b-pleated
sheets overlayed by a C-terminal a-helix.
b-pleated
sheets and a-helices
are held together by hydrogen bonds. Click on the button below to see them
represented in green.
Clicking
on the button below will highlight the hydrophobic residues tyrosine26,
isoleucine29 and tryptophan57. Do the side chains of these residues point into
the exterior or the interior of the protein?
Like the majority of
proteins, eotaxin is held together by several bonds
and adopts the most energetically favourable structure in solution. This means
close packing of the majority of aromatic side chains with other non-polar side
chains so that they are not accessible to solvent (i.e. within the interior of
the protein).
This
page is maintained by James Pease
Based on a template by A. Herráez
as modified by J. Gutow.
Page skeleton and JavaScript generated by export to web function using Jmol 12.0.1 2010-07-21 21:46 on 18-Aug-2010.
Jmol: an open-source Java viewer for chemical structures in 3D.
