Beta structures

An awful lot of barrels...

• Functionally the most diversily populated group (antibodies, enzymes, transport proteins etc…)

• Second biggest group of protein domain structures (after )

Common properties

• Built up from four to over ten beta strands

• strands are arranged in predominantly antiparallel fashion

• Usually two beta sheets are formed, which pack each against other, resembling barrel or distorted barrel (=double sandwich)

Up-and-down barrels

• Simplest topology

• Similar arrangement to TIM barrels, but without helices and all strands are antiparallel

Retinol-binding protein (rbp)

• Retinol binds in the inside of barrel (typical for up-and-down barrels)

Retinol binding site in rbp

• Hydrophobic part fits in a hydrophobic pocket

• Hydroxyl group exposed to solvent

OH

Alterating patterns in amino acid sequence of rbp

• Hydrophobic amino acids are facing the core• Polar, charged and a few small hydrophobic are

exposed to the solvent

Up-and-down barrels can contain more than 8 strands

• Porin monomer from Rhodobacter has 14 strands

propeller in neuraminidase

• Influenza virus protein, involved in virion release from cells

• Tetrameric protein, one monomer consists of 6 up-and down sheets

• Builds a propeller-like structure

Neuraminidase tetramer

Active site in -propeller proteins

• On the top of propeller there are extensive loops

• The loops form active site

Greek key motifs in antiparallel barrels

-crystallin

• Found in lenses of your eyes

• Each domain built from 2 greek key motifs

• One connection across the barrel between two motifs

Evidence for two gene duplication events in -crystallin evolution

• Two domains have about 40% sequence identity

• Two motifs within the domain share 20-30% sequence identity

1.2.

x 2 x 2

Jelly roll -barrel

Arrangement of strands in jelly roll barrel

Two Greek key motifs in jelly-roll barrel

Jelly-roll barrel in viruses• Very common in subunits of spherical viruses• Barrel is distorted and with helices instead of some loops• Example: Rhinovirus (common cold, that is)

AH –

CHOO !

Comparison of all those -barrels

Up-and-down -crystallin-like

jelly-roll

Yet another barrel – chymotrypsin fold

• Present in chymotrypsin and all other serine proteases

• Several non-protease proteins also contain similar fold

• Six strands form the barrel

Structure of chymotrypsin

Domain 1

Domain 2

Beta helix

• Two different kinds – two-sheet helix and three-sheet helix

• Both represent deviations from idealized structure with a single spiral-like strand

Two sheet beta helix

Sequence pattern in two sheet beta helix

X7

U8

X9X7

U8

X9

• Gly-Gly-X-Gly-X-Asp-X-U-X

• X=any amino acid

• U=big hydrophobic, often Leu

• Ca ions sit in between loops

• Motif present in several bacterial proteases

Three sheet beta helix

Unlike two-sheet beta helices, there are no repetitive sequence patterns

Structure of pectate lyase

Spider silk

Structure of spider silk

• All-beta fibrous protein

• N- and C-terminal parts are variable

• A large, up to 800 residues long central region is made from repeats: -(Ala)8-10-Gly-Gly-X-

Structure of spider silk

Made up from beta sheets

About 30% of beta sheets form microcrystals

The rest of beta shets form a flexible matrix

Soluble form of spider silk is -helical!

Beta sheets form upon spinning

Properties of spider silk

• 5 times stronger than steel

• Very elastic – can be stretched 3-4 times its original size without breaking

• Lighter than cotton