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Protein structure is conceptually divided into four levels of organization
• Primary structure is the amino acid sequence of a protein's polypeptide chain.
• Different regions of the sequence form local regular secondary structures, such as
alpha helices or beta strands.
• The tertiary structure or fold is formed by packing such structural elements into one
or several compact globular units called domains.
• The final protein may contain several polypeptide chains arranged in a quaternary
structure.
By formation of such tertiary and quaternary structure, amino acids far apart in the
sequence may be brought close together in three dimensions to form a functional
region, an active site.
Animations: http://www.sumanasinc.com/webcontent/animations/biology.html
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The "handedness" of amino acids
Looking down the H-Ca bond from the hydrogen atom, the L-form
has CO, R, and N substituents from Ca going in a clockwise
direction. There is a mnemonic rule to remember this; for the Lform the groups read CORN in clockwise direction.
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Hydrophobic amino acids
Weak interaction only (van der Waals) with other residues as well as the solvent.
Special attention to
• Phenylalanine: aromatic
• Methionine: containing inert sulfur; encoded by START codon
• Proline: cyclic residue, no free rotation around the Ca-N bond
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Charged amino acids
-
+
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Hydrophilic amino acids
Strong interaction (hydrogen bonds) with the solvent and other residues.
Special attention to
• Serine, threonine: alcohol group.
• Cysteine: containing sulfur as thiol; oxidized by O2 to yield S-S bonds.
• Tyrosine, tryptophan: aromatic residues.
• Histidine: pK near neutral.
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Summary
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Hydrophobicity Scales and Plots
Residue
Kyte-Doolittle
Hopp-Woods
Alanine
-
A
1.8
-0.5
Arginine
-
R
-4.5
3.0
Asparagine -
N
-3.5
0.2
Aspartic acid -
D
-3.5
3.0
Cysteine
-
C
2.5
-1.0
Glutamine -
Q
-3.5
0.2
Glutamic acid - E
-3.5
3.0
Glycine
-
G
-0.4
0.0
Histidine
-
H
-3.2
-0.5
Isoleucine
-
I
4.5
-1.8
Leucine
-
L
3.8
-1.8
Lysine
-
K
-3.9
3.0
Methionine -
M
1.9
-1.3
Phenylalanine - F
2.8
- 2.5
Proline
-
P
-1.6
0.0
Serine
-
S
-0.8
0.3
Threonine
-
T
-0.7
-0.4
Tryptophan -
W
-0.9
-3.4
Tyrosine
-
Y
-1.3
-2.3
Valine
-
V
4.2
-1.5
Opsin: 349 aa; window=21
7 transmembrane helices
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Proteins are built up by amino acids that are linked by peptide bonds to
form a polypeptide chain.
a. Schematic diagram of an amino
acid. A central carbon atom (Ca) is
attached to an amino group (NH2),
a carboxyl group (COOH), a
hydrogen atom (H), and a side
chain (R).
b. In a polypeptide chain the carboxyl
group of amino acid n has formed a
peptide bond, C-N, to the amino
group of amino acid n + 1. One
water molecule is eliminated in this
process. The repeating units, or
residues, are divided into mainchain atoms and side chains.
The main-chain part, which is
identical in all residues, contains a
central Ca atom attached to an NH
group, a C'=O group, and an H
atom. The side chain R, which is
different for different residues, is
bound to the Ca atom.
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A polypeptide chain may be viewed as divided into block peptide units
Each peptide unit contains the Ca atom and the C'=O group of residue n as well as the
NH group and the Ca atom of residue n + 1. Each such unit is a planar, rigid group with
known bond distances and bond angles. R1, R2, and R3 are the side chains attached to
the Ca atoms that link the peptide units in the polypeptide chain. The peptide group is
planar because the additional electron pair of the C’=O bond is delocalized over the
peptide group such that rotation around the C’-N bond is prevented by an energy barrier.
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Cterm
A structural biologist glance at a
polypeptide
Each planar peptide unit is rigid
and has two degrees of freedom; it
can rotate around two bonds, its
N--Ca bond and its Ca--C' bond.
The angle of rotation around the
N--Ca bond is called phi (f) and
that around the Ca--C' bond is
called psi (y).
Nterm
The conformation of the mainchain atoms is therefore
determined by the values of these
two angles for each amino acid.
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Allowed combinations of the
conformational angles phi and psi.
Ramachandran plots
Since phi (f) and psi (y) refer to
rotations of two rigid peptide units
around the same Ca atom, most
combinations produce steric
collisions either between atoms in
different peptide groups or between a
peptide unit and the side chain
attached to Ca. These combinations
are therefore not allowed.
(a) Colored areas show sterically
allowed regions. The areas labeled a,
b, and L correspond to conformational
angles found for the usual righthanded a helices, b strands, and
left-handed a helices, respectively.
(b) Observed values for all residue
types except glycine. Each point
represents f and y values for an
amino acid residue in a well-refined Xray structure to high resolution.
(c) Observed values for glycine.
Notice that the values include
combinations of f and y that are not
allowed for other amino acids.
( J. Richardson, Adv. Prot. Chem. 34: 174175, 1981.)
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Structure-stabilizing non-covalent bonds
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The disulfide bond is usually the end product of air oxidation
2 -CH2SH + 1/2 O2 ↔ -CH2-S-S-CH2 + H2O
Disulfide bonds form
between the side
chains of two cysteine
residues. Two SH
groups from cysteine
residues, which may
be in different parts of
the amino acid
sequence but adjacent
in the threedimensional structure,
are oxidized to form
one S-S (disulfide)
group.
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Intrinsic metal atoms in proteins
(a) The di-iron center of the enzyme
ribonucleotide reductase. Two iron
atoms form a redox center that
produces a free radical in a nearby
tyrosine side chain. The iron atoms are
bridged by a glutamic acid residue and
a negatively charged oxygen atom
called a m-oxo bridge. The coordination
of the iron atoms is completed by
histidine, aspartic acid, and glutamic
acid side chains as well as water
molecules.
(b) The catalytically active zinc atom in
the enzyme alcohol dehydrogenase.
The zinc atom is coordinated to the
protein by one histidine and two
cysteine side chains. During catalysis
zinc binds an alcohol molecule in a
suitable position for hydride transfer to
the coenzyme moiety, a nicotinamide.
[(a) Adapted from P. Nordlund et al., Nature 345: 593598, 1990.]
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Folding topology of globular proteins
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Intramolecular hydrogen bonds
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Breaking H-bonds causes denaturation
Urea (NH2-CO-NH2), a chaotropic agent at high concentrations (2-8 M)
breaks H-bonds between protein surface atoms and the aqueous
solvent, resulting in the loss of native folding. Its slow removal (e.g., by
dialysis) often restores the original fold.
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Basic elements of secondary structure
The alpha-helix
Stabilized by hydrogen
bonds between the amino
–NH and the carbonyl –
CO, both belonging to
peptide bonds, 4 residues
apart on the same
sequence fragment.
The beta-sheet
Stabilized similarly by
hydrogen bonds but the
interacting moieties (i.e.,
– NH and –CO) are
located on different but
contiguous beta-strands.
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