06_17Marzo2016_beta sheets

two SECONDARY STRUCTURES

Protein Secondary Structure refers to highly regular local sub-structures
on the actual polypeptide backbone chain.

The beta sheet

a repetitive string of identical φ;ψ couples
approximately [-130,-130]

Turns in Globular Proteins

The “beta sheet torsion”

Beta strands have a tendency to twist in the right hand direction. This
leads to important consequences in how the beta strands are
connected.

Strands can form twisted sheets or
saddles

Strands can form barrels

Beta Sandwiches!

β-sandwich domains are characterized by two opposing antiparallel β-
sheets, trought beta-beta associations.

Connectivities

Pattern of Connections

antiparallel beta sheets

up-and-down structural motif (connectivity n+1)
!  Beta meander
!  Beta propeller

connectivity n+3 (or n+2)
!  Greek key
!  Jelly roll

The beta meander

small lipid binding motif

the architecture of lipocalines
example: the retinol-binding protein

Porins

Porins are all beta barrel proteins that
cross a cellular (outer) membrane and
act as a pore through which molecules
can diffuse (passive transport).

They are present in
•  the outer membrane of Gram- (and

some Gram+),
•  t h e m i t o c h o n d r i a ( T O M

translocases),
•  the chloroplast (TOC complex).

The beta propeller

it is a type of all-β protein architecture characterized by 4 to 8
blade-shaped beta sheets arranged toroidally around a central axis.

An enzyme's active site is often found
in the cleft formed in the center of the
propeller by loops connecting the
successive four-sheet motifs.
example: neuraminidase viral protein

WD40 repeats, also known as beta-transducin repeats, are short fragments found primarily in
eukaryotes. They are often assembled in 4 to 16 repeated units to form a structural domain critical
for protein-protein interactions. example: G-proteins

The Greek Key
(a connectivity n±3)

Immunoglobulines

the IgG barrel scaffolds and

their variable loops

another tag of association: The beta helix

an helix of short parallel strands

The helical pattern can allocate either two or three face.

In the 2-stranded beta helix motif, the two "layers" of
beta sheets are connected by glycine-rich six-residue
loops that invariably contain an aspartate to bind one
calcium ion per loop.

In the 3-stranded beta helix motif, one of the three
sheets that form the repeating structural motif is
restricted to two residues, and can appear "bent"
relative to the other two, which face each other as in
the two-stranded helix.
Examples:
Pectate lyase and antifreezing proteins

The “jelly-roll”

four pairs of antiparallel beta sheets, only one of which is
adjacent in sequence, are "wrapped" in three dimensions to
form a barrel shape.

a β-hairpin rolled up

the Jelly Roll of Life

http://schaechter.asmblog.org/schaechter/2014/05/the-jelly-roll-of-life.html

Inspection of proteins from Sulfolobus Turreted
Icosahedral virus (STIV), and of other viruses
lying in the PRD1-adenovirus lineage (which
unites icosahedral dsDNA viruses with large
facets and a double beta-barrel trimer coat
protein), reveals that their major capsid
proteins contain jelly roll structures

Electron microscopy image of assembled STIV
virions preparing to escape from Sulfolobus
solfataricus

20 triangular faces, 30 edges, and 12 vertices The pentameric A223 structure was built by
combining cryoEM with X-ray crystallography of its
C-terminal domain jelly-roll.

Jellow roll as scaffold for the
PROTEIN SPLICING

autocatalitic

Nterminal-extein INTEIN Cterminal-extein INTEIN PROTEINA MATURA

the proposed mechanism,
in accordance with

a water-less medium :

Jellow roll as scaffold for the
PROTEIN SPLICING

autocatalitic

Nterminal-extein INTEIN Cterminal-extein INTEIN PROTEINA MATURA

maxi-inteins split-inteins

mini-inteins

Semisynthesis of proteins using
split-inteins