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 % sequence identity 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 X7X7 U8U8 X9X9 X7X7 U8U8 X9X9 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) 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