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Levels of Protein Structure

Primary to Quaternary Structure

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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

Amino group and acid group

Side chain at C

Chiral, only one enantiomer found in proteins (L-amino acids)

20 natural amino acids

N

O

CC

C

C

C

S

Methionine

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L-amino acids in Living organisms

N: 14C: 12O: 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

Asn (N)

Asp (D)

Gln (Q)Glu (E)

His (H)

Lys (K)

Arg (R)

Tyr (Y)

Trp (W)

Phe (F)

Gly (G)Pro (P)

Ile (I)

Met (M)

Leu (L)

Ala (A)

Val (V)

Ser (S)

Cys (C)

Thr (T)

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Amino Acids

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

A – AlaC – CysD – AspE – GluF – PheG – GlyH – HisI – IleK – LysL – Leu

M – MetN – AsnP – ProQ – GlnR – ArgS – SerT – ThrV – ValW – TrpY - Tyr

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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

Ile (I)Met (M)

Leu (L)

Val (V)

Ala (A)

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The Small Polar

Thr (T)

Cys (C)Ser (S)

Cystin

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The Unusual

P, G Also aliphatic Structural impact

Strictly speaking, proline is an imino acid

Gly (G)

Pro (P)

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The Acidic and Their Derivatives

Asn (N)Asp (D)

Gln (Q)Glu (E)

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The Basic

His (H)Lys (K)Arg (R)

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The Aromatic

Tyr (Y)Trp (W)

Phe (F)

His (H)

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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)

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…

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Myoglobin

Haemoglobin

Quaternary Structure Assembly of

monomers/subunits into protein complex– 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.

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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)

Myoglobin Aquaporin

Cross-section Cross-section

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Characteristics of Helices Aligned peptide

units Dipolar moment

Ion/ligand binding Secondary and

quaternary structure packing

Capping residues The helix

(i→i+4) Other helix types!

(310, )

N

C

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Helix Types

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-Sheets

Multiple strands sheet– Parallel vs. antiparallel– Twist

– Coil regions between the secondary structure elements

Thioredoxin

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-Sheets

Multiple strands sheet– Parallel vs.

antiparallel– Twist

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-Sheets

Multiple strands sheet– Parallel vs.

antiparallel– Twist

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-Sheets

Multiple strands sheet– Parallel vs.

antiparallel– Twist

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-Sheets

Multiple strands sheet– Parallel vs. antiparallel– Twist

Strand interactions are non-local

Flexibility– Vs. helices– Folding

Antiparallel Parallel

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Summary

Amino acids in Living organisms have L-configuration

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

NH2/NH3+

S/SH

GuanidineImidazolePhenyl

Indole

C

H-bond

Amide

C/CH/CH2/CH3

COOH OHPeptide unit (amide)

NC

O

NC

O

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Building Blocks

N

O

C

C

C

C

C

S

Methionine

Single amino acidResidue

NOC

C ONO

CC

On-1 Nn+1

Cn-1

O

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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 -helix.

4. Add side chains along the way (pointing “down”).

N

C