The ThreeDimensional Structure of Proteins

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The Three-Dimensional Structure of Proteins
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Learning Objectives
Describe with simple diagrams and/or structures
the three common types of protein secondary
structure a helix, b sheet, and b turn.
Clearly diagram trans and cis peptide bonds with
amino acid residues, especially proline.
Describe the two general rules for soluble
proteins with reference to protein stability.
Describe the torsion angles f (phi) and y (psi).
Describe a Ramachandran plot.
Explain the five factors that affect the
stability of the a helix.
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Protein conformation is stabilized largely by
weak interactions
protein stability the tendency of a protein (or
other macromolecule) to maintain a native (and
therefore a functional) conformation.
General rules for soluble proteins
(1) hydrophobic residues are largely buried in
the protein interior, away from water. (2) the
number of hydrogen bonds within the protein is
maximized.
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The formation of one hydrogen bond facilitates
the formation of additional hydrogen bonds a
network of hydrogen bonds.
The presence of hydrogen-bonding or charged
groups within the interior of a protein without
suitable partners is destabilizing.
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The peptide bond is planar.
O
Ca
C
N
Ca
These six atoms lie in the same plane.
H
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Peptide bonds have some double-bond character due
to resonance. As such, they are not free to
rotate.
However, not all peptide bonds are trans.
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Cis and trans peptide bonds
O
Ca
C
N
Ca
Ca
Ca
H
C
N
trans
O
H
cis
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R
O
H
Ca
C
N
C
N
Ca
f
y
O
H
R
f
y
N
Ca
C
Ca
phi
psi
Both f and y are measured along the backbone of
the peptide chain.
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By convention, both f and y are defined as 0o
when the two peptide bonds flanking the a carbon
are in the same plane. This conformation,
however, is prohibited by steric overlap as shown.
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Ramachandran plot for L-alanine residues
Dark blue no steric overlap
Medium blue at the limits for unfavorable
contacts
Light blue permissible if flexibility in bond
angles are allowed
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The plots for the other amino acids with
unbranched side chains are nearly identical. The
allowed ranges for unbranched side chains such as
val, ile, and thr are somewhat smaller than for
alaine. Glycine is less sterically hindered and
exhibits a much broader range of allowed
conformations. The range for proline residues is
greatly restricted because f is limited by the
cyclic side chain to the range of -35o to -85o.
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Protein Secondary Structure
a helix
3.6 residues/turn
right-handed
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The a helix is stabilized by internal hydrogen
bonds. Every peptide bond (except those near the
ends of the helix) are involved in hydrogen
bonding with other peptide bonds further along
the helix.
1 4th residue (hydrogen bonding in
helix)
A sequence of negatively (or positively) charged
amino acids can disrupt helix stability via side
chain repulsion. Too many bulky R groups can
prevent proper internal hydrogen bond
arrangements.
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Amino acid sequence effects a helix stability
R4
adjacent residues in sequence, or adjacent in
three-dimensions.
R1
R5
R3
R2
top view of a helix
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Top view of a helix
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Side view of a helix
Residues 7, 10, and 13 are shown
backbone
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Side view of an a helix
Space filled representation of residues 7, 10,
and 13
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The twist of an a helix ensures that critical
interactions occur between an amino acid side
chain and the side chain three (and sometimes
four) residues away on either side of
it. Positively charged residues are often found
three residues away from negatively charged
residues. Hydrophobic residues may be similarly
clustered.
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Proline
Ca is part of a ring
f (N-Ca)
cannot rotate
The nitrogen of proline has no hydrogen to
hydrogen-bond to carbonyl group of another
peptide bond.
Proline introduces a destabilizing kink in an a
helix.
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N-terminal
Helix dipole
A small electric dipole exists in each peptide
bond. These dipoles are connected through the
hydrogen bonds of the helix. (The four residues
at each end of the helix do not participate fully
in the hydrogen bonding network). This results
in a net dipole extending down the helix that
increases with helix length.
C-terminal
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The partial positive and negative charges of the
helix dipole actually reside on the N-terminal
amino and C-terminal carbonyl groups near the
ends of the helix. Negatively charged residues
are often found near the N-terminal end of a
helix to stabilize the positive charge of the
dipole. Positively charged residues near the
N-terminal are destabilizing. The opposite
situation occurs at the C-terminal end of a helix.
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Constraints that affect the stability of the a
helix
(1) the electrostatic attraction (or repulsion)
between successive residues with charged side
chains (2) the bulkiness of adjacent R groups (3)
the interactions between side chains spaced three
(or four) residues apart (4) the occurrence of
pro or gly groups (5) the interaction between
residues near the helix termini and the helix
dipole
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Antiparallel b-sheet
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Parallel b-sheet
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b Turns
Turns or loops are the connecting links between
successive runs of a helices and b sheets. The
b turn is very common.
The b turn is a 180o turn involving four amino
acid residues with the carbonyl oxygen of the
first amino acid forming a hydrogen bond with the
amino group of the fourth residue.
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Type I turns occur more than twice as frequently
as type II turns. Glycine is always the third
residue in a type II b turn. b turns are often
near the surface of a protein where the two
central R groups can hydrogen bond with water.
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Glycine and proline residues often occur in b
turns glycine because it is small and flexible
proline (often found at position 2 in either type
of turn) because it can participate in cis
peptide bonds which is particularly good for
tight turns.
trans
cis
proline
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Relative probability that a given amino acid will
occur in the three common types of secondary
structure.
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Myoglobin (from sperm whale)
X-RAY
NMR