Classes of Proteins Flashcards
The Classes of Proteins:
Based on structure and solubility, proteins
can be grouped into three large classes:
.1.Fibrous Proteins
2. Globular Proteins
3. Membrane Proteins
Fibrous:
proteins in this class are
elongated molecules with well-defined
secondary structures and function primarily
in a structural role, i.e. they hold things
together.
a- and b-keratins, fibroin, collagen, elastin
Globular:
most of
the catalytic work is
done by this class
of protein so named
because of their
compact 3-D fold.
* Synthesizing, transporting, metabolizing,
catalyzing, etc
Fibrous Proteins contain…
polypeptide
chains organized parallel along a single
axis, producing long fibers or large sheets.
- They are mechanically strong, play
structural roles in nature; - Difficult to dissolve in water;
- a-Keratins, Fibroin and Collagen are
examples of fibrous proteins
The properties of fibrous proteins typically…
impart strength and/or
flexibility to the structures in which they are found.
Simple repeating unit of a given secondary structure.
Fibrous proteins are..
insoluble in water, due to a high percentage of
hydrophobic amino acids associated with them.
Composed of supramolecular complexes, wherein the hydrophobic
surfaces pack against each other, and are thus excluded from water.
a-Keratin are found in…
hair, fingernails, claws, horns, beaks, and a large fraction of animal skin.
a-Keratin sequence consists…
of 311-314 residue alpha helical rod segments
capped with non-helical N- and C-termini
Primary structure of helical rods consists
of 7-residue repeats, which
promote association of helices
b-keratins are found in silk and consist of gly-ala repeat sequences;
- Ala is small and can be packed within the sheets
The keratins: a-keratins are…
major proteins of hair
and fingernails and a large fraction of animal skin.
Individual molecules contain
long sequences over 300 residues that are wholly a-helical.
Pairs of these molecules twine about one
another in a left-handed coiled-coil structure.
(amino acid side chains interdigitate).
In hair, two coiled…
coils further twist
together to form a 4 molecule protofibril.
8 protofibrils combine to make a microfibril
that is the basis of hair structure
The keratins (a) properties:
They are stretchy and flexible, but can be hardened by the introduction of
disulfide cross-links within the several levels of fiber structure. (12% CYS)
Structure of a-keratin
Found in hair, wool, nails, claws, quills, horns, hooves, and
the outer layer of skin.
a-keratins are found in
hair and nails. Nails have
more disulfide cross-links than hair, therefore are
less flexible than hair.
The process of introducing a “permanent wave” into
human hair involved
reduction of the disulfides,
rearrangement of the fibers and re-oxidation to “set
the waves”.
b-keratins, as their name implies
contains the
much more extended b-sheet structure. Thus, they
are much less flexible than helical a-keratins.
- b-keratins are found in structures like the feathers
and scales of birds and reptiles.
Another b-sheet protein is
Fibroin…
found in the fibers
spun by silkworms and spiders.
Silkworm fibroin contains long
regions of antiparallel b-sheet
interrupted by periodic
compactly folded regions
The b-sheet regions comprise multiple..
repetitions containing Gly, Ser and
Ala residues such that they pack on top of one another making them
strong, inextensible yet flexible.
This is because bonding between the sheets involves only weak van der
Waals interactions between the side chains, which provide little resistance
to bending.
Silk is composed of…
fibroin proteins, which
are composed mainly
of stacked antiparallel
b-sheets.
In antiparallel sheets…
hydrophobic side chains
will typically be on just
one face of the sheet,
while hydrophilic side
chains will reside on the
other.
Globular proteins are more…
numerous than
fibrous proteins in cells. Globular proteins can
be classified according to the type and
arrangement of secondary structure
Globular Proteins: Richardson’s classification
-Antiparallel alpha helix proteins
-Parallel or mixed beta sheet proteins
-Antiparallel beta sheet proteins
- Metal-and disulfide-rich proteins
This classification is too simple to reflect the
function and evolutionary origins of proteins.
Packing of Globular Proteins: 1/2
*Secondary structures pack closely to one another and
also intercalate with extended polypeptide chains
*Most polar residues face the outside of the protein and
interact with solvent
- Most hydrophobic residues face the interior of the protein
and interact with each other
*van der Waals’ volume is about 72-77% of the total protein volume; about 25% is not occupied by protein
atoms. These cavities provide flexibility in protein
conformation and dynamics.
- Random coil or loops maybe of importance in protein
function (interacting with other molecules, enzyme
reactions)
Atomic motions:
are random and within short
distances (~0.5Å). These motions are arise from
kinetic energies and are a function of temperature.
Collective motions:
refer to motions of a group of
atoms as a single unit. Usually longer distance and
slower.
Conformational changes:
involve motions of
domains or segments in proteins. May occur in
response to stimuli.
Protein structures are…
dynamic
Levinthal’s Paradox:
a new folding view is needed
Consider a protein with 100 amino acids
Levinthal’s paradox illustrates
that proteins
must only sample through limited
conformations, or fold by “specific pathways”.
Much research effort is devoted to searching
for the principles of the “specific pathways”.
Folding Pathways (hypothesis)
- protein folding is
initiated by reversible and rapid formation of
local secondary structures
-Secondary structures then form domains
through the cooperative aggregation of
folding nuclei.
-Domains finally form the final protein through
“Molten globule” intermediates.
