Protein Domain structures can be divided into three main classes During the evolution, the structural core

e tends to be conserved Alpha domain structures (Core consists of alpha helices) Domain structures (antiparallel beta sheets)

Alpha / Domain structures (predominantly parallel beta

sheet surrounded by alpha helices)

Alpha-Domain Structures

Myoglobin proteins Membrane covered by

first

structure

to

be

determined

Representative example of one class of alpha domains in bound proteins the chains region inside for the the

membranes are frequently alpha helices whose surface are hydrophilic side suitable hydrophobic environment inside the membrane Also form the structural and motile proteins like keratin, fibrinogen

Alpha domains
Short alpha helices are connected by loop regions and packed together to produce a hydrophobic core Single alpha helix does not have a hydrophobic core, it is marginally stable in solution Two (or 3, 4, etc) helices can pack together and form a hydrophobic core

Packing interactions within the core hold the helices together in a

stable globular structure while the hydrophilic residues on the surface make the protein soluble in water

Two common types

Coiled coil

Four helix bundle

 Side chain interactions are maximized if the 2 helices are

not straight rods but are wound around each other in a supercoil Coiled coil Coiled coils in fibers can extend over many hundreds of amino acids to produce long flexible dimers that contribute to the strength and flexibility of the fibers

Occurrence of coiled coil structures

Fibrinogen blood coagulation RNA and DNA binding proteins Collectins cell surface recognition proteins Spectrin, Dystropin Actin, Myosin

Coiled coil (leucine zipper repetitive heptad amino acid pattern)

The simplest way to join two alpha helices

2 helices are intertwined and gradually coil around each

other instead of being a straight rod In fibrous proteins (keratin, myosin) coiled-coil can be very

long (hundreds of amino acids)

In globular proteins coiled-coils are much shorter (~10-30 aa)

The heptad repeat

 d: Very often Leu (hence leucine zipper)

a: often hydrophobic
e, g: often charged b,c,f: charged or polar

The above prefernces are strong enough to be predicted

from sequence

Why a heptad ?

a helix: 3.6 residues per turn 310 helix: 3 residues per turn a helix in coiled coil is a bit distorted and has 3.5 residues per turn. 3.5x2=7, so two turns of helix form one heptad repeat The left handed supercoil of 2 right handed alpha helices reduces the no of residues per turn in each helix from 3.6 to 3.5 so that the pattern of side chain interaction between the helices repeat every seven residues after 2 turn

 When 2 helices form a coiled coil structure, the side chains

of these d residues frequently Leu, Ile pack against every 2nd turn of the alpha helices

a is also hydrophobic hence pack against each other

e and g are charged residues hence border the hydrophobic residues

Leu packs against Leu

Original concept

Real life

(zipper)

Interactions in coiled-coil

Packing in Alpha domains

Side chain of an alpha helix are arranged in a helical row along the surface of the helix, hence form ridges separated by shallow furrows or grooves on the surface

Two models

Knobs in Holes put forward by Francis Crick

Ridges Ridges in one alpha helix fit into groove of an adjacent helix

Packing in Coiled coils Knobs in holes Alpha helices are stabilized in proteins by being packed together through hydrophobic side chains Side chains are projected onto a plane parallel with the helical axis for both alpha helices of the coiled coil

 The side chain positions of the first helix (knobs) superimpose between the side chain positions in the second helix (holes) Each side chain in the hydrophobic region of one of the

alpha helices can contact 4 side chains from the second

alpha helices

 The side chain of a residue in position d in one helix

is directed into a hole at the surface of the second

helix surrounded by one d residue, 2 a residues and one e residue with the no: n, n 3, n+ 4 and n + 1 respectively

d
a

Leucines (knobs) of one helix sit in hydrophobic holes

of other helix

Four helix bundle

The most usual way of packing alpha helices in globular proteins

Helical axes are almost parallel in each other

Adjacent alpha helices are always antiparallel The side chains of each helix in the 4-helix bundle are

arranged so that hydrophobic side chains are buried between

the helices and hydrophilic side chains are on the outer surface of the bundle

This creates a hydrophobic core in the middle of the bundle

along its length, where the side chains are so closely packed that water is excluded

Occurrence

Myohemerythrin O2 transport protein in marine worms Cytochrome C1 Cytochrome b 562 Ferritin Coat protein of TMV

Helices can be either parallel or anti parallel in four helix bundle

Packing in 4 helix bundles Ridges of one alpha helix fit into

grooves of an adjacent helix Two alpha helices packed together into a coiled coil are building blocks within a domain or a fiber but are not sufficient to form a complete domain Larger number of alpha helices are packed together in a complex pattern to form a globular domain Since the side chains of an alpha helix are arranged in a helical row along the surface of the helix, they form ridges separated by grooves or shallow furrows on the surface

Groove

Ridge

Ridge

Two variants of ridges in grooves model

1. Packing in 2 helices with ridges 4 residues apart (Globin fold)

In order to pack the 2 helices against each other, one of

these must be turned around 180 out of the plane of the paper and placed on top of the other

In the interface between the 2 helices, the directions of

the ridges and grooves are then on the opposite sides of the vertical axis The alpha helices must thus be inclined by an angle of about 50 in order for the ridges of one helix to fit into the grooves of the other and vice versa

 1 helix with ridges 4 residues apart + 1 helix with ridges 3 residues apart 20o angle (4 helix bundle)

In the red helix the ridges are formed by side chains separated by four residues and in the blue helix by three residues. The helices are shifted by 20 in order to pack ridges into grooves.

Rop Protein RNA Binding protein

Monomeric subunit (63 aminoacids)

2 anti parallel alpha helices joined by a short loop of three amino acids RNA RNA Two such subunits each with the same structure form the dimeric

Rop molecule in which the subunits

are arranged as a bundle of four helices along their long axis aligned

Alpha-helical domains can be large and complex

Bacterial muramidase (involved in cell wall formation) 618 amino acids N terminal 450 aa 27 alpha helices arranged in 2 layered ring with a right handed twist The ring has a large central hole like in a doughnut The remaining residues form the catalytic domain that lies in top of the ring

Globin fold

One of the most important structures Present in many proteins with unrelated functions All organisms contain proteins with globin fold Evolved from a common ancestor Humans: myoglobin & hemoglobin Algae: light capturing assembly

 The globin fold usually consists of eight alpha helices (AH) The two helices at the end of the chain are antiparallel, forming a helix-turn-helix motif, but the remainder of the fold does not include any characterized supersecondary structures The eight alpha helices are connected by a rather short loop regions

 These helices pack against each other with larger angles, around 50 between them than occurs between antiparallel helices (approximately 20) so that the helices form a hydrophobic packet for the heme active site A, B, C, D,E and F are aligned in different direction hence not adjacent to each other G and H are anti parallel pair with extensive packing interactions between them

Myoglobin

C D

E
N

Hemoglobin The hemoglobin molecule is built up of four polypeptide chains: two a chains and two b chains. Each chain has a three-dimensional structure similar to that of myoglobin: the globin fold In sickle-cell anemia, Glu 6 in the b chain of hemoglobin is mutated to Val, thereby creating a hydrophobic patch on the surface of the molecule

 Sickle-cell hemoglobin

molecules
patch

polymerize
by

due to the hydrophobic introduced the mutation Glu 6 to Val in the b chain