|Lecture Notes: 12 February
© R. Paselk 2006
Peptide Titration-Review peptide structure and titration curves on your own. The simple titration curve below can serve as a model, but note that amino acids and peptides will have AT LEAST two titrations with two buffer regions et. Note also the differences in the amino- and carboxy- terminii pKas between free amino acids and terminal amino acid residues in peptides.
3-D Structure of Proteins 2
Review Structures from last time...
Last time looked at what is possible given the bond angles etc. between amino acid residues. Now can look at specific structures.
Tertiary structure (3°): the steric relations of residues distant in the primary sequence; the overall folding pattern of a single covalently linked molecule. (Characteristic bond type: hydrophobic; others: hydrogen, ion-pair, van der Waals, disulfide.)
- Super secondary structure (motifs): defined associations of secondary structural elements. (Characteristic bond type: hydrogen & hydrophobic.)
- Domains: independent folding regions within a protein. The group/pattern of secondary structures forming a Domain's tertiary structure is called a Fold. (Characteristic bond type: hydrophobic; others: hydrogen, ion-pair, van der Waals.) Large proteins (>200 aa's) usually fold up in smaller pieces of 100-200 aa's called domains. Recall that we define a Domain as an independent folding region in a protein. Often defined by clefts in 3D structure giving globular elements connected by "hinges" (single strand segments connecting the domains). Domains have the advantages of speeding up the folding process (fold domains independently, then assemble resultant folded domains - effectively processing folding of domains in parallel). Another advantage of domain structure is that nature can take bits of DNA specifying particular domains with particular functions and assemble them in new combinations to get new activities (e.g. combine an ATP binding site and a sugar binding site to give a sugar phosphorylating protein).
- IgG example domains, exons and evolution. [overheads: IgG/proteins; 7.23 MvH]
- Quaternary structure consisting of two heavy chains and two light chains ( or 22), each heavy chain has four related domains (three constant and one variable domain) while each light chain consists of two related domains (one constant and one variable domain). All twelve domains have a "collapsed -barrel domain" or immunoglobin fold. Note that the two heavy chains are identical to each other as are the two light chains. The binding sites are composed of variable domains contributed by a heavy and light chain in each case - this enables a large number of different binding specificities (e.g. 100 H + 100 L gives 100x100 = 10,000 possibilities from 200 unique sequences). Finally, note that the different variable domains are coded by different exons which can be shuffled during immunsystem cell development, serving as a model of evolutionary development - in each individual a unique population of cells in created which is then used as a pool for clonal development depending on the environment in response to antigen exposure.
- In a similar manner we see that many enzymes have active sites created between two domains, often one domain binds one substrate while the second binds a second substrate. Its as if these proteins were designed by taking "off-the-shelf" components, assembling them, and then over time (and generations) tuning the combination up.
Secondary and Super Secondary Examples
Alpha helix: (Figure 4.10, pg 90 of your text) [overhead 2.31 S, 5.15 P] The most frequent secondary structure is the right-handed -helix.
- In this cylinder-like structure the amino acid residues curl around in a spring/rod-like structure.
- There is a rise/residue (movement along the axis) of 0.15 nm and a pitch (rise/turn) of 0.54 nm.
- There are 3.6 residues per turn and 13 atoms/H-bonded "ring" - this makes it a 3.613 helix.
- Very importantly, the H-bonds are nearly linear and therefore of near maximum strength. The side chains of the helix stick out from the sides.
- The stability of the helix is determined in part by the side chains. Thus glycine allows too much rotational freedom to favor this structure, while very large or like charged side chains can also destabilize it.
- As you might expect a proline residue stops a helix abruptly since proline' s angles are not accommodated in the helix.
Beta Strand: (Figure 4.15, pg 93 of your text) [overhead 5.19 P] The next secondary structural element is the beta-strand, which is seen in the supersecondary structures called parallel and anti-parallel beta sheets [overheads 7.16 & 17 V&V].
- The beta strand is in a sense an abstract structure, since, unlike the -helix, a beta-strand does not exist alone, there is always another strand to make a sheet.
- In the older literature beta-sheets are considered secondary structures, but they are more consistently considered super secondary with the current nomenclature.
- Beta strands are nearly fully extended, thus they have very little extensibility (stretch).
- Beta strands are stabilized by hydrogen bonding to adjacent beta-strands. Thus they are stabilized by inter-strand H-bonds whereas -helices are stabilized by intra-strand H-bonds.
Aside: Fibrous proteins:
- alpha-keratin (hair etc., alpha-helix based) [overhead 7-11 V&V, 7-25 & 26]; stretched alpha-keratin (parallel -pleated sheet) [overhead, Figure 7-26].
Last modified 14 February 2010