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) 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
Quaternary Structure
Assembly of Myoglobin
monomers/subunits
a
into protein complex
Backbone-backbone,
backbone-side-chain &
side-chain-side-chain
interactions:
Intramolecular vs. Haemoglobin
intermolecular contacts.
For ligand binding side a b
chains may or may not
contribute. For the latter,
mutations have little
effect.
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 Membrane protein
solution)

Myoglobin Aquaporin
Hydrophobic vs. Hydrophilic
Globular protein (in Membrane protein
solution)

Cross-section Cross-section

Myoglobin Aquaporin
From Unfolded to Native State
Transition state
one or more
DG = DH - TDS E
narrow
ensembles
------------------------- T
DG: Free (Gibbs)
energy
DH: Enthalpy U

(interactions) DG F
DS: Entropy
(conformations/ Native
Unfolded state, fold, one
states) ensemble 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
Ce
Amino group and acid Sd
group
Cg
Side chain at Ca Cb

Chiral, only one

enantiomer found in C
Ca
proteins (L-amino acids) N
O
20 natural amino acids
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 M Met
C Cys N Asn
D Asp P Pro
E Glu Q Gln
F Phe R Arg
G Gly S Ser
H His T Thr
I Ile V Val
K Lys W Trp
L Leu Y - Tyr

Livingstone & Barton, CABIOS, 9, 745-756, 1993

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

Residue
Torsion Angles
Characteristics of Helices
C

Backbone
interactions
are local

Aligned
peptide units
Dipolar
moment
N
Helix Types
b-Sheets
Multiple strands Antiparallel Parallel
sheet
Parallel vs. antiparallel
Twist

Strand interactions are

non-local

Flexibility
Vs. helices
Folding
b-Sheets

Thioredoxin
b-Sheets

Thioredoxin
b-Sheets

Thioredoxin
b-Sheets

Thioredoxin
Not All b-Sheets Are Flat
Nitrophorin Thioredoxin
Residue Patterns
Helices C Sheets
Helix capping Amphiphilic residue
Amphiphilic residue patterns
patterns Residue preferences at
N 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 non-

local interactions.

Secondary structure elements are

associated with specific residue patterns.
a-sheet and b-helices
a-sheet b-helix

Theoretical Real 1M8N