8. alpha domain structure

7/27/2019 8. Alpha Domain Structure

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Protein Domain structures can be divided into three mainclasses During the evolution, the structural core 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)


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Alpha-Domain Structures

Myoglobin first structure to be determined

Representative example of one class of alpha domains inproteins

Membrane bound proteins the region inside the

membranes are frequently alpha helices whose surface are

covered by hydrophilic side chains suitable for the

hydrophobic environment inside the membrane

Also form the structural and motile proteins like keratin,

fibrinogen


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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


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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


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Occurrence of coiled coil structures

Fibrinogen blood coagulation

RNA and DNA binding proteins

Collectins cell surface recognition proteins

Spectrin, Dystropin

Actin, Myosin


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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 verylong (hundreds of amino acids)

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

aa)


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The heptad repeat


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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


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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 residuesper 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


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

of these dresidues frequently Leu, Ile pack against every

2nd turn of the alpha helices

ais also hydrophobic hence pack against each other

e and g are charged residues hence border the

hydrophobic residues


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Original concept

(zipper)

Real life

Leu packs against Leu


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Interactions in coiled-coil


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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


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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


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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


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The side chain of a residue in position din one helix

is directed into a hole at the surface of the second

helix surrounded by onedresidue, 2aresidues and

one eresidue with the no: n, n 3, n+ 4 and n + 1

respectively


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Leucines (knobs) of one helix sit in hydrophobic holes

of other helix

a

d


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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


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Occurrence

Myohemerythrin O2 transport protein in marine worms

Cytochrome C1

Cytochrome b 562

Ferritin

Coat protein of TMV


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


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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


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Ridge

RidgeGroove


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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


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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.


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Rop Protein

RNA Binding protein

Monomeric subunit (63 aminoacids)

2 anti parallel alpha helices joined

by a short loop of three amino acids

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

RNA RNA


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Alpha-helical domains can be large and complex

Bacterial muramidase(involved in cell wallformation)

618 amino acids

N terminal 450 aa 27

alpha helices arranged in2 layered ring with aright handed twist

The ring has a largecentral hole like in a

doughnut The remaining residues

form the catalyticdomain that lies in top ofthe ring


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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


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The globin fold usually consists of eight alpha helices (A-

H)

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


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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


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Myoglobin

A

B

C

D

E

FH

G

N

C


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Hemoglobin

The hemoglobin molecule isbuilt up of four polypeptidechains: two a chains andtwo b chains. Each chainhas a three-dimensional

structure similar to that ofmyoglobin: the globin fold

In sickle-cell anemia, Glu 6in the b chain of

hemoglobin is mutated toVal, thereby creating ahydrophobic patch on thesurface of the molecule


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8. alpha domain structure

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