Transcript Beta structures - Uppsala University

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 a/b)
Common properties
• Built up from four to over ten beta strands
• b strands are arranged in predominantly
antiparallel fashion
• Usually two beta sheets are formed, which
pack each against other, resembling barrel
or distorted barrel (=double b 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 b
strands
b propeller in neuraminidase
• Influenza virus protein,
involved in virion release
from cells
• Tetrameric protein, one
monomer consists of 6 upand down b sheets
• Builds a propeller-like
structure
Neuraminidase tetramer
Active site in b-propeller proteins
• On the top of propeller there are extensive
loops
• The loops form active site
Greek key motifs in antiparallel b
barrels
g-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 g-crystallin evolution
• Two domains have about 40% sequence
identity
• Two motifs within the domain share 2030% sequence identity
1.
x2
2.
x2
Jelly roll b-barrel
Arrangement of b strands in jelly
roll barrel
Two Greek key motifs in jellyroll 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)
Comparison of all those b-barrels
Up-and-down
g-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
• 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
U8
X9
X9
U8
X7
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 a-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