Download E U F T DG Unfolded state, ensemble Native fold, one

Protein Structure
Elements
Primary to Quaternary Structure
Learning Objectives
• After this lesson you should be able to:
–
–
–
–
Define the structural levels of proteins.
Identify regular secondary structure elements.
Identify the structural units of the protein backbone.
Explain why some backbone conformations are favoured
and some are “forbidden” (not found in natural proteins).
– Name properties on which the amino acids can be
grouped.
– Explain the driving forces behind protein folding related
to the properties of the backbone and the side chains.
Proteins Are Polypeptides
• The peptide bond
• A polypeptide chain
Structure Levels
• Primary structure = Sequence
(of amino acids)
• 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
MSSVLLGHIKKLEMGHS…
Quaternary Structure
• Assembly of
monomers/subunits
into protein complex
• Myoglobin
a
– Backbone-backbone,
backbone-side-chain &
side-chain-side-chain
interactions:
• Intramolecular vs.
intermolecular contacts.
• For ligand binding side
chains may or may not
contribute. For the latter,
mutations have little
effect.
• Haemoglobin
a
b
b
a
A Bit About Protein Folding
How and why proteins fold
Why Fold?
• Hydrophobic collapse
– Hydrophobic residues cluster to “escape”
interactions with water.
– Polar backbone groups form secondary
structure to satisfy hydrogen bonding donors
and acceptors.
– Initially formed structure is in molten globule
state (ensemble).
– Molten globule condenses to native fold via
transition state
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
Hydrophobic vs. Hydrophilic
• Globular protein (in
solution)
Myoglobin
• Membrane protein
Aquaporin
Hydrophobic vs. Hydrophilic
• Globular protein (in
solution)
Cross-section
• Membrane protein
Cross-section
Myoglobin
Aquaporin
From Unfolded to Native State
DG = DH - T×DS
------------------------DG: Free (Gibbs)
energy
DH: Enthalpy
(interactions)
DS: Entropy
(conformations/
states)
Transition state
one or more
narrow
ensembles
E
T
U
DG
Unfolded state,
ensemble
F
Native
fold, one
structure
Protein Stability & Dynamics
• Folded proteins are:
– Only marginally stable (enthalpy and entropy
almost balance at physiological temperatures)
• Allows for easy degradation and reuse.
• Amyloid exception.
– Dynamic
• “Breathing” motions on pico- to nanosecond scale.
• Allows substrates/products to enter/leave enzymes.
• Allows allosteric regulation of activity.
Amino Acids
• Proteins are built from
amino acids
• Amino group and acid
group
Ce
Sd
Cg
• Side chain at Ca
• Chiral, only one
enantiomer found in
proteins (L-amino acids)
• 20 natural amino acids
Cb
N
Ca
C
O
Methionine
Amino Acid Properties
• Many features
– Charge +/• Acidic vs. basic (pKa)
– Polarity (polar/non-polar)
• Type, distribution
– Size
• Length, weight, volume, surface area
– Type (Aromatic/aliphatic)
Grouping 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
M – Met
N – Asn
P – Pro
Q – Gln
R – Arg
S – Ser
T – Thr
V – Val
W – Trp
Y - Tyr
The Evolution Way
• Based on
Blosum62
matrix
• Measure of
evolutionary
substitution
probability
Backbone Properties
• Amide bond planarity
• 2 degrees of rotational
freedom per residue
Ramachandran Plot
• Allowed backbone torsion angles in proteins
Peptide
bond
N
H
Residue
Torsion Angles
Characteristics of Helices
C
• Backbone
interactions
are local
• Aligned
peptide units
 Dipolar
moment
N
Helix Types
b-Sheets
• Multiple strands 
sheet
– Parallel vs. antiparallel
– Twist
• Strand interactions are
non-local
• Flexibility
– Vs. helices
– Folding
Antiparallel
Parallel
b-Sheets
Thioredoxin
b-Sheets
Thioredoxin
b-Sheets
Thioredoxin
b-Sheets
Thioredoxin
Not All b-Sheets Are Flat
• Nitrophorin
• Thioredoxin
Residue Patterns
• Helices
C
– Helix capping
– Amphiphilic residue
patterns
N
• Sheets
– Amphiphilic residue
patterns
– Residue preferences at
edges vs. middle
• Special residues
– Proline
• Helix breaker
– Glycine
• In turns/loops/bends
Turns, Loops & Bends Revisited
• Between helices
and sheets
• On protein surface
• Intrinsically
“unstructured”
proteins
Summary
• The backbone of polypeptides form regular
secondary structures.
– Helices, sheets, turns, bends & loops.
• These are the result of local as well as nonlocal interactions.
• Secondary structure elements are
associated with specific residue patterns.
a-sheet and b-helices
a-sheet
Theoretical
b-helix
Real
1M8N