ACDEFGHIKLMNPQRSTVWY

primary structure

Principles of Protein Structure

Different Levels of Protein Structure

NH2

Lysine

Histidine

Valine

Arginine

Alanine

COOH

Common Secondary Structure Elements

• The Alpha Helix

Properties of alpha helix

• 3.6 residues per turn, 13 atoms between H-bond donor and acceptor

• approx. -60º; approx. -40º

• H- bond between C=O of ith residue & -NH of (i+4)th residue

• First -NH and last C=O groups at the ends of helices do not participate in H-

bond

• Ends of helices are polar, and almost always at surfaces of proteins

• Always right- handed

• Macro- dipole

Alpha Helix

Helical wheel

Residues i, i+4, i+7 occur on

one face of helices, and

hence show definite pattern

of hydrophobicity/

hydrophilicity

Introduction to Molecular Biophysics Association of helices: coiled coils

These coiled coils have a heptad repeat abcdefg with nonpolar residues at

position a and d and an electrostatic interaction between residues e and g.

Isolated alpha helices are

unstable in solution but are

very stable in coiled coil

structures because of the

interactions between them

The chains in a coiled-coil have

the polypeptide chains aligned

parallel and in exact axial

register. This maximizes

coil formation between chains.

The coiled coil is a protein motif that is often used to control oligomerization.

They involve a number of alpha-helices wound around each other in a highly

organised manner, similar to the strands of a rope.

Introduction to Molecular Biophysics The Leucine Zipper Coiled Coil

Initially identified as a structural motif in proteins involved in eukaryotic

transcription. (Landschultz et al., Science 240: 1759-1763 (1988).

Originally identified in the liver transcription factor C/EBP which has a Leu

at every seventh position in a 28 residue segment.

Association of helices: coiled coils

The helices do not have to run in the same direction for this type of

interaction to occur, although parallel conformation is more common.

Antiparallel conformation is very rare in trimers and unknown in

pentamers, but more common in intramolecular dimers, where the two

helices are often connected by a short loop.

Chan et al., Cell 89, Pages 263-273.

Since the dipole moment of a peptide bond is 3.5 Debye units, the alpha

helix has a net macrodipole of:

n X 3.5 Debye units (where n= number of residues)

This is equivalent to 0.5 – 0.7 unit charge at the end of the helix.

Basis for the helical dipole

In an alpha helix all of the peptide

dipoles are oriented along the

same direction.

Consequently, the alpha helix has

a net dipole moment.

The amino terminus of an alpha helix is positive and the

carboxy terminus is negative.

Common Secondary Structure Elements

• The Beta Sheet

Secondary structure: reverse turns

Secondary Structure:

Phi & Psi Angles Defined

• Rotational constraints emerge from interactions with bulky groups (ie. side chains).

• Phi & Psi angles define the secondary structure adopted by a protein.

The dihedral angles at C atom of every residue

provide polypeptides requisite conformational

diversity, whereby the polypeptide chain can fold into

a globular shape

Ramachandran Plot

Structure Phi (F) Psi(Y)

Antiparallel b-sheet -139 +135

Parallel b-Sheet -119 +113

Right-handed -helix +64 +40

310 helix -49 -26

p helix -57 -70

Polyproline I -83 +158

Polyproline II -78 +149

Polyglycine II -80 +150

Phi & Psi angles for Regular Secondary

Structure Conformations

Table 10

Secondary Structure

Beyond Secondary Structure

Supersecondary structure (motifs): small, discrete, commonly

observed aggregates of secondary structures

b sheet

helix-loop-helix

bb

Domains: independent units of structure

b barrel

four-helix bundle

*Domains and motifs sometimes interchanged*

Common motifs

Supersecondary structure:

Crossovers in b--b-motifs

Right handed

Left handed

•Consists of two helices and a short extended amino acid chain between them.

•Carboxyl-terminal helix fits into the major groove of DNA.

•This motif is found in DNA-binding proteins, including l repressor, tryptophan

repressor, catabolite activator protein (CAP)

Helix Turn Helix Motif

What is a Protein Fold?

Compact, globular folding arrangement of the polypeptide chain

Chain folds to optimise packing of the hydrophobic residues in the interior

core of the protein

Common folds

Tertiary structure examples: All-

Alamethicin The lone helix

Rop helix-turn-helix

Cytochrome C four-helix bundle

http://www.expasy.ch/cgi-bin/sw3d-search-ac?PD1AMT

Tertiary structure examples: All-b

b sandwich b barrel

Tertiary structure examples: /b

placental ribonuclease inhibitor /b horseshoe

triose phosphate isomerase /b barrel

Four helix bundle

•24 amino acid peptide with a hydrophobic surface

•Assembles into 4 helix bundle through hydrophobic regions

•Maintains solubility of membrane proteins

Oligonucleotide Binding (OB) fold

TIM Barrel

•The eight-stranded /b barrel (TIM barrel)

•The most common tertiary fold observed in

high resolution protein crystal structures

•10% of all known enzymes have this domain

Zinc Finger Motif

Domains are independently folding structural units.

Often, but not necessarily, they are contiguous on the peptide chain.

Often domain boundaries are also intron boundaries.

Domain swapping:

Parts of a peptide chain can reach into neighboring structural elements: helices/strands in other domains or whole domains in other subunits.

Domain swapped diphteria toxin:

• Helix bundles

Long stretches of apolar amino acids

Fold into transmembrane alpha-helices

“Positive-inside rule”

Cell surface receptors

Ion channels

Active and passive transporters

• Beta-barrel

Anti-parallel sheets rolled into cylinder

Outer membrane of Gram-negative bacteria

Porins (passive, selective diffusion)

Transmembrane Motifs

Quaternary Structure

• Refers to the organization of subunits in a protein with multiple subunits

• Subunits may be identical or different

• Subunits have a defined stoichiometry and arrangement

• Subunits held together by weak, noncovalent interactions (hydrophobic,

electrostatic)

• Associate to form dimers, trimers, tetramers etc. (oligomer)

• Typical Kd for two subunits: 10-8 to 10-16M (tight association)

–Entropy loss due to association - unfavorable

–Entropy gain due to burying of hydrophobic groups - very favourable

• Stability: reduction of surface to volume ratio

• Genetic economy and efficiency

• Bringing catalytic sites together

• Cooperativity (allostery)

Structural and functional advantages of

quaternary structure

Quaternary structure of

multidomain proteins