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
○
○ 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
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