| Chem 431 |
Biochemistry |
Fall 2001 |
| Lecture Notes:: 14 September |
© R. Paselk 2001 |
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- Peptides and Protein Primary Structure
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- Now that we have looked at peptide bond formation, we next
want to look at the structure of this bond and the sequence of
amino acid residues (primary structures) of proteins. (Note that
"residue" refers to the remainder of a molecule after
it is incorporated into a polymer.)
- The peptide bond is formed with the elimination of water,
giving a planar bond between the carboxyl carbon and the amino
nitrogen. [overhead 5.8 MvH] This is due to the partial double
bond character on the amide/peptide bond as seen in the shorter
bond length (0.133 nm vs. 0.146 nm). [overhead 7-2, V&V]
This bond is nearly always trans in proteins due to steric interactions
of the amide hydrogen and oxygen. [overhead 7-6 V&V].
- Linear peptides will have free amino- and carboxy- terminal
groups. Thus they will exhibit titration curves similar to a
free amino acid, but with the pKa values shifted closer
to simple acid and amine values (there will be no charge stabilization).
- By convention the amino terminal residue is written on the
left progressing to the carboxyl terminal residue on the right
[overhead 2-21, S]: +H3N-aa-aa-aa-aa-CO2-.
- Can determine the composition of a peptide by acid hydrolysis
and amino acid analysis.
- Can sequence proteins by specific enzyme and chemical hydrolysis
to give peptides which can then be run through sequenators (up
to about 100 aa's).
- Amino acid sequences have been used to help determine relatedness
of organisms [overheads 6-5, 6-14, 6-15, 6-17].
3D Structure of Proteins
Overview: Proteins are commonly large (MW > 6,000),
globular molecules serving many functions.
Proteins are complex systems - difficult to understand at a
fundamental structural level. Thus we search for patterns using
normal perceptual tools: regularity, clustering, cleavage/separation/emptiness.
We are then able to discern alpha helices, beta sheets, beta
turns, and "random" regions. 310 helical
regions show up with computer searches. None of these is more
random than others, they are simply easier or more difficult for
us to perceive as ordered. They exist through our rationalization.
Often structural elements also appear to serve a functional role,
thou this is through our dissection of the molecular machine.
Let's go back and look at overall shape and interpret it. Look
for substructures that recur in various molecules. Perhaps we
see a globule is made of subglobules. Look closer and we see alpha
helices and beta structures. Finally we can discern aa residues.
In order to understand and categorize their organization, protein
structure has been divided into four hierarchical levels and a
couple of sublevels:
- Primary structure (1°) : the linear order or sequence
of peptide bonded amino acid residues, beginning at the N-terminus.
(Characteristic bond type: covalent.)
- Secondary structure (2°): the steric relations
of residues nearby in the primary structure which give rise to
local regularities of conformation. These structures are maintained
by hydrogen bonds between peptide bond carbonyl oxygens and amide
hydrogens. The major secondary structural elements are the alpha
helix and the beta strand. (Characteristic bond type: hydrogen.)
- 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.
(Characteristic bond type: hydrophobic; others: hydrogen, ion-pair,
van der Waals.)
- Quarternary structure (4°): the association of
two or more independent proteins via non-covalent forces to give
a multimeric protein. The individual peptide units of this protein
are referred to as subunits, and they may be identical or different
from one another. (Characteristic bond type: hydrophobic; others:
hydrogen, ion-pair, van der Waals.)
Secondary Structure
- First let's look at what is possible given the bond angles
etc. between amino acid residues. Begin by going back and looking
at the peptide bond.
Can think of as a series of rigid peptide units linked through
alpha carbons (Figure 6.2, pg 161) [overhead 5.6, P; model].
- Most peptide bonds are trans because of reduced steric hindrance.
Most exceptions are with proline which has nearly equal hindrance
in both cis and trans [overhead 5.8 P]
- Any rotation in the peptide chain will therefore take place
around the two bonds of the alpha carbon, referred to as the
phi (f) and psi (y)
bonds. There are a restricted number of angles which these bonds
can achieve (Figure 6.3, pg 162) [overhead 5.9 P, V&V 7.6].
Of course the range of angles will be further reduced due to
side chains.
- If we assume hard spherical atoms with van der Waals radii,
we can determine the accessible phi (f)
and psi (y) angles. This procedure
was followed by Ramachandran to produce the Ramachandran plot,
an example is seen in Figure 6.6 of pg. 128 of your text [overhead
6.2, MvH; 7.7 V&V].
- There are only a few regions of possible angles available
to the alpha carbon bonds as shown on this plot.
- Note that the common secondary structures, the alpha helix,
the beta strand, and the collagen triple helix all occur in these
regions.
- Of course real atoms are somewhat compressible and real bonds
can bend a little, so we might wonder how this plot stacks up
to reality. A study of the distribution of conformation angles
of a thousand amino acid residues in eight proteins as determined
by x-ray diffraction showed that most of the values do indeed
fall in the predicted regions. Most of the residues outside of
these regions are glycines, with the least restriction.
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- Last modified 14 September 2001
Pathway Diagrams
