Download 6. Appendix: Protein structure

6. Appendix: Protein structure
The following section contains a very brief introduction to some aspects of protein and peptide
structure. It is basically a summary of the description given by Mathews and van Holde in
"Biochemistry" and is just intended to help you work through this practical. For more detailed
information you should consult one of the references given or any modern text on Biochemistry.
6.1 The Building Blocks.
Proteins are composed of amino acids. The general formula for an α−L−amino acid is
H
Cα
HOOC
NH2
R
The name α−amino acid is derived from the fact that there is an amino group and a carboxyl group
attached to the first or α−carbon. Different amino acids are distinguished by the nature of their
respective side chain or R−group. The structural formulas of the 20 amino acids coded by genes and
normally occurring in proteins are shown in Fig A.1. The name of amino acids is often shortened by
a 3 or 1 letter abbreviation. For example, the amino acid glycine is normally abbreviated as gly or by
the letter G. All amino acids except glycine are chiral molecules which can exist in two different
configurations, L and D. The 20 amino acids occurring in proteins have the L configuration. In
Figure A.1 the amino acids have been grouped according to the chemical nature of the side chain.
The charges assigned to each amino acid correspond to pH 7.4 (physiological pH).
Proteins are polymers of amino-acids. Two amino acids can be linked together by the
formation of a peptide bond between the α−amino group of one amino acid and the α−carboxyl
group of another, in a condensation reaction that produces a peptide and water. An example of such
a reaction is shown in Fig A.2. The resulting dipeptide still contains a free α−amino group and a free
α−carboxyl group and so further amino acids could be added to each end to form a chain. Chains
containing a few amino acids are referred to as oligopeptides. If the chain is very long it is called a
polypeptide.
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Figure A.1 Structures of the 20 common amino acids.
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6.2 The Nature of the Peptide Bond
The shaded portion in Fig A.2 corresponds to the peptide bond. The nature of the peptide
bond is very important in determining the structure of peptides and proteins. The peptide bond is
Figure A.2 The formation of the dipeptide Gly−Ala. The resulting planar peptide bond is
shaded.
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planar. Normally very little twisting around the N−C bond is observed. The reason for this is that
the bond can be considered as a resonance hybrid between
O
H
O−
H
C
N
C
N+
giving the C−N interaction significant double bond character. This is shown diagrammatically in Fig
A.3. Even though it is planar, the peptide bond can exist in two possible conformations, trans and
cis. The trans conformation, Fig A.3, is normally strongly favoured. The main exception is for
peptide bonds from any amino acid to proline, where the cis configuration is also common.
Figure A.3 The structure of the peptide bond. The delocalization of the π−electron orbital over
O−C−N accounts for the partial double bond character of the C−N bond.
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6.3 Primary, Secondary and Tertiary Structure.
The amino acid sequence of a peptide is referred to as the primary structure of the peptide
and is the most basic level of protein structure. Short segments of the peptide chain are capable of
forming into stable regular structures such as helices and sheets and are referred to as secondary
structures. The arrangement of the secondary structure elements gives the overall fold of the protein
and is referred to as the tertiary structure of the protein. The planar nature of the peptide bond is one
of the main determining factors of the possible types of secondary structure. This limits the
rotational freedom of the peptide backbone to just two angles labeled ψ and φ shown in Fig A.4. The
two other
Figure A.8 Rotation around bonds in a polypeptide chain. The two adjacent peptide planes are
shaded. Rotation is only allowed about the N−Cα and the Cα−C bonds.
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main factors are steric considerations, atoms cannot approach each other closer than their van der
Waals radii, and hydrogen bonding considerations. A hydrogen bond is a strong non-covalent
interaction between a hydrogen covalently bound to an electronegative atom (e.g. −OH or =NH) and
another electronegative atom with a lone pair of electrons (e.g. |O=). The formation of
intramolecular hydrogen bonds act to stabilize given types of secondary structure. This was
recognized in the 1950's by Linus Pauling and his coworkers who, working mainly with molecular
models, predicted that only a limited number of stable structures were possible. They correctly
predicted that the major structural elements in proteins would be the α−helix and the β−sheet. The
α-helix is stabilized by the formation of hydrogen bonds within the same chain, between amino acid
residues separated by three residues. That is hydrogen bonds form between residues 1 and 5, 2 and 6,
and so on. This is shown in Fig A.5. In a β−sheet hydrogen bonds are formed between two linear
parts of a chain. This gives rise to two forms of β−sheet, parallel and antiparallel, depending on the
orientation of hydrogen bonding parts of the chain as shown in Fig A.6.
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Figure A.5 Arrangement of atoms in a right-handed α−helix. Note the hydrogen bonds between
the first and fifth residue, the second and sixth, and so on.
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(a)
(b)
Figure A.6 Parallel β−sheet (a) and antiparallel β−sheet (b).
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