Transcript Amino acids & proteins part 2

Levels of Protein
Structure
Primary to Quaternary Structure
1
Learning Objectives
 After today you should be able to:
– Define the structural levels of proteins.
– Identify the structural units of the protein backbone.
– Explain why some backbone conformations are
“forbidden”, i.e. not found in natural proteins.
– Name properties on which the amino acids can be
grouped.
– Name more amino acids than you could before
One and three letter codes
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Amino Acids
 Proteins are built from
amino acids
Ce
 Amino group and acid
group
Sd
Cg
 Side chain at Ca
Cb
 Chiral, only one
enantiomer found in
proteins (L-amino acids)
N
Ca
C
O
 20 natural amino acids
Methionine
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L-amino acids in Living organisms
N: 14
C: 12
O: 16
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How to Group Them?
 Many features
– Charge +/• Acidic vs. basic (pKa)
– Polarity (polar/non-polar)
• Type, distribution
– Size
• Length, weight, volume, surface area
– Type (Aromatic/aliphatic)
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The Amino Acids
Thr (T)
Phe (F)
Val (V)
Ala (A)
His (H)
Arg (R)
Ser (S)
Leu (L)
Cys (C)
Asp (D)
Met (M)
Lys (K)
Asn
(N)
Ile (I)
Trp (W)
Glu (E)
Gln
(Q)
Tyr (Y)
Pro (P)
Gly (G)
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Amino Acids
A – Ala
C – Cys
D – Asp
E – Glu
F – Phe
G – Gly
H – His
I – Ile
K – Lys
L – Leu
Livingstone & Barton, CABIOS, 9, 745-756, 1993
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M – Met
N – Asn
P – Pro
Q – Gln
R – Arg
S – Ser
T – Thr
V – Val
W – Trp
Y - Tyr
Blosum62 substitution matrix
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The Evolution Way
 Based on
Blosum62
matrix
 Measure of
evolutionary
substitution
probability
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The Simple Aliphatic
Val (V)
Ala (A)
Leu (L)
Met (M)
Ile (I)
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The Small Polar
Ser (S)
Cys (C)
Thr (T)
Cystin
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The Unusual
 P, G
 Also aliphatic
 Structural impact
Gly (G)
 Strictly speaking,
proline is an imino
acid
Pro (P)
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The Acidic and Their Derivatives
Asp (D)
Asn (N)
Glu (E)
Gln (Q)
13
The Basic
Arg (R)
Lys (K)
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His (H)
The Aromatic
Phe (F)
His (H)
Trp (W)
Tyr (Y)
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Proteins Are Polypeptides
 The peptide bond
 A polypeptide chain
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Ramachandran Plot
 Allowed backbone torsion angles in proteins
N
H
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Small Exercise (5 minutes)
 For the polypeptide on the
left discuss the following
with your neighbour:
– Why is the lower right
quadrant a ”forbidden”
region in the
Ramachandran plot?
– What makes Gly a special
amino acid when it comes
to Ramachandran plots?
– What about Pro?
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Structure Levels
 Primary structure = Sequence
(of amino acids)
MSSVLLGHIKKLEMGHS…
 Secondary Structure = Helix,
sheets/strands, bends, loops &
turns (all defined by H-bond
pattern in backbone)
 Structural Motif = Small,
recurrent arrangement of
secondary structure, e.g.
–
–
–
–
Helix-loop-helix
Beta hairpins
EF hand (calcium binding motif)
Many others…
 Tertiary structure = Arrangement
of Secondary structure elements
within one protein chain
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Quaternary Structure
 Assembly of
monomers/subunits
into protein complex
 Myoglobin
a
– Backbone-backbone,
backbone-side-chain &
side-chain-side-chain
interactions:
 Haemoglobin
• Intramolecular vs.
intermolecular contacts.
• For ligand binding side
chains may or may not
contribute. For the latter,
mutations have little
effect.
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a
b
b
a
Hydrophobic Core
 Hydrophobic side chains go into the core of
the molecule – but the main chain is highly
polar.
 The polar groups (C=O and NH) are
neutralized through formation of H-bonds.
Myoglobin
Surface
Interior
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Hydrophobic vs. Hydrophilic
 Globular protein (in
solution)
 Membrane protein (in
membrane)
Myoglobin
Aquaporin
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Hydrophobic vs. Hydrophilic
 Globular protein (in
solution)
 Membrane protein (in
membrane)
Cross-section
Cross-section
Myoglobin
Aquaporin
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Characteristics of Helices
 Aligned peptide
units  Dipolar
moment
 Ion/ligand binding
 Secondary and
quaternary
structure packing
 Capping residues
 The a helix
(i→i+4)
 Other helix types!
(310, p)
C
N
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Helix Types
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b-Sheets
 Multiple strands 
sheet
Thioredoxin
– Parallel vs. antiparallel
– Twist
– Coil regions between
the secondary structure
elements
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b-Sheets
 Multiple strands 
sheet
– Parallel vs.
antiparallel
– Twist
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b-Sheets
 Multiple strands 
sheet
– Parallel vs.
antiparallel
– Twist
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b-Sheets
 Multiple strands 
sheet
– Parallel vs.
antiparallel
– Twist
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b-Sheets
 Multiple strands 
sheet
Antiparallel
– Parallel vs. antiparallel
– Twist
 Strand interactions are
non-local
 Flexibility
– Vs. helices
– Folding
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Parallel
Summary
 Amino acids in Living organisms have Lconfiguration
 One & three letter codes
 Groups of amino acids: hydrophobic ...
 The backbone of polypeptides form regular
secondary structures.
– Helices, sheets & loops.
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Building Blocks
Ca
Peptide unit (amide)
COOH
O
OH
C
N
C/CH/CH2/CH3
O
Indole
N
C
Amide
S/SH
H-bond
Phenyl
Imidazole
Guanidine
NH2/NH3+
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Building Blocks
Ce
Sd
On-1
Cn-1
N
Ca
Nn+1
C
O
Residue
N
Ca
C
O
c3
Cg
O
c2 C
b c
1
Single amino
acid
N f
Ca y
C
O
O
Methionine
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Procedure
1. Build backbone in
extended
conformation (strand).
2. Twist to align all
peptide units (look at
the C=O groups).
3. Add H-bonds (i+4) to
construct an ideal ahelix.
4. Add side chains along
the way (pointing
“down”).
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C
N