Biochem January 25, 2010 Figure 8: Forces that Stabilize tertiary structure In Proteins You can visualize all the non-covalent electrical forces as well as other interactions that are driven by thermodynamics that ultimately stabilize tertiary structure in proteins. You recognize the convention of having the free ?-amino terminal end (N) and the free carboxyl terminal end (C) on the right. These contribute to the electrical properties of the peptide as do the R groups in between. The first row is an ?-helix where the primary forces stabilizing that structure are H-bonds between Carbonyl Oxygens and Amino nitrogens. The most common configuration conforms to what we call the N+4 rule: where Carbonyl oxygen and Amino nitrogen are H-bonding among a span of 4 amino acid residues in the ?-helix. Sheet Structure: The second is showing the Anti parallel formation. One side is going upward and the other side is going downward. This is an example of ?-sheet. The stabilizing forces are the same thing as we saw in the ?-helix. Except this hydrogen boding is perpendicular to the chain across the plane of the ?-sheet. Hydrophobic Interactions: Not a matter of electrically driven attractive forces, more to do with their nonpolar nature and can?t h-bond with other dipolar molecules. Therefore, in order for them to become thermodynamically stable, they have to orient their R groups inwardly into Hydrophobic pockets where water is excluded. THIS IS NOT AN ELECTRICAL ATTRACTION. SIMPLY NONPOLAR GROUPS THAT ARE UNABLE TO ACHIEVE THERMODYNAMICALLY STABLE ELECTRICAL ARRANGEMENTS WITH WATER. The expulsion of water from these pockets and restoration of degrees of freedom of h-bonding of those water molecules satisfies the requirement. Disulfide Bond: These both used to be ?SH that were distantly situated and separated by many resides. Upon folding, these two groups got close enough together to undergo Oxidation and form a disulfide bridge. This is a very significant covalent stabilizing force. Quaternary Structure is what we call ?Clustering? or ?aggregation? of subunits into higher-ordered structures that resemble the molecule Hemoglobin. This hemoglobin picture has 2 ? chains and 2 ? chains. Quaternary structure takes multiple subunits (such as hemoglobin) and arranges them into an entire order of classifications resembling a quaternary structure. Any subunits are being stabilized by forces that stabilize peptides in tertiary structure. Stabilizing forces between any two or more subunits: Hydrophobic interactions would be nonpolar hydrophobic groups oriented inwardly toward hydrophobic pockets (an occasional Van der Waals). One thing you DO NOT SEE between any 2+ of these is covalent bonds, i.e. a disulfide bridge. You will see them within these subunits, but not between them.
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