BCH 261 Lecture Notes - Lecture 9: Peptide Bond, Protein Structure, The Sequence

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30 Nov 2020
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Lecture 9 - Chapter 6: 3D Structure
4 levels of protein structure
Primary Sequence:
Peptide bond = resonance hybrid
Bond resonates b/w single bond & 2x bond b/s of this partial
double-bond character rotations a/b this bond is prevented
& thus conformatio of peptide backbone is contrained
Two configurations are possible for a planar peptide bond. In
the trans configuration, the two a-carbon atoms are on
opposite sides of the peptide bond. In the cis configuration,
these groups are on the same side of the peptide bond.
Almost all peptide bonds in proteins are trans. This
preference for trans over cis can be explained by the fact
that steric clashes between groups attached to the a-carbon
atoms hinder the formation of the cis configuration but do not
arise in the trans configuration
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Rotation of bonds in peptides is described by two
angles termed ϕ (phi, between N and Cα) and ψ (psi,
between Cα and the carbonyl C). Also ω (omega,
between N and carbonyl C), usually 180 an rarely 0.
In contrast with the peptide bond, the
bonds between the amino group and the
a-carbon atom and between the a-
carbon atom and the carbonyl group are
pure single bonds. The two adjacent
rigid peptide units can rotate about
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these bonds, taking on various
orientations.
Structural Components of Proteins
The subsequent elucidation of the 3D structure of myoglobin and
other proteins showed that the righthanded α helix is the
common form. Extended left-handed α helices are theoretically
less stable and have not been observed in proteins.
α helix proved to be the predominant structure in α-keratins. About
25% of all amino acid residues in proteins are found in α helices
Alanine shows the greatest tendency to form α helices in most
experimental model systems.
Are all combinations of 𝜙& 𝜓 possible? Not all values are possible w/o
collisions b/w atoms
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