Download Flexibility of a polypeptide chain

Flexibility of a polypeptide chain
the peptide bond is essentially planar (6 atoms are in plane: Ca, C=O, N-H,
and Ca, respectively)
40% double bond character around C-N
constrains the conformation
of the protein backbone
the double bond character is also
expressed in the respective
C-N bond length:
C-N: 1.49 Å, C=N: 1.27 Å
Protein conformation
phi
psi
torsion (or dihedral) angles
HN-Ca and Ca-CO are pure single bonds, high degree
of freedom for rotation around these bonds
lots of ways for a protein to fold if each amino acid
has two main chain bonds to rotate about
BUT! Any combination of phi and psi is possible?
Ramachandran plot
many combinations are disfavored due to steric collisions
(green regions are allowed, white regions are not)
What does thermodynamics have to
say about protein folding?
each copy of an unfolded polymer exists in a different conformation (random coil) yielding a mixture of many possible conformations, which would
theoretically oppose folding due to favorable enthropy
but in proteins, rigidity of peptide units and the restricted set of allowed
phi and psi values actually limit the number of possible structures
and it is overcome by interactions that favor the folded form e.g. hydrophobic interactions among apolar side-chains (rather than being exposed
to polar water), H-bonding network, S-S bridges, ion pairs, etc.
a highly flexible polymer, of any kind, with large number of possible
conformations to adopt would NEVER fold into a unique 3D structure!!
Secondary structural elements
alpha helix
beta pleated sheet
beta turn
omega loop
all forms stabilize via H-bridges
between amino acids nearby in
linear sequence
alpha helix
3.6 residues/turn
100o rotation/residue
rise/residue: 1.5 Å
pitch of helix: 5.4 Å
Screw sense of an alpha helix
right-handed (clockwise)
or
left-handed (counterclockwise)
more stable,
less steric clashes
between side
chains and
backbone
helical content of a protein may vary from 0-100%
Ferritin (iron storage protein)
contains 75% alpha helix
~25% of all soluble proteins are largely helical
an alpha helix is usually smaller than 45 Å
proteins embedded in or crossing biological membranes build
also up mainly from alpha helices
Beta (pleated) sheets
(beta because this structure was the 2nd one, after the alpha helix, that Linus Pauling
and Robert Corey envisioned/proposed in 1951, 6 years before the first ever
protein structure determined by X-ray crystallography by Kendrew in 1957, myoglobin )
composed of 2 or more beta strands (fully extended chains)
stabilized by H-bonding between polypeptide chains
purely parallel, purely antiparallel or mixed beta sheets exist
4-5 but even 10 or more strands make up a beta sheet
beta sheets generally adopt a twisted shape:
fatty acid binding proteins (important in lipid metabolism)
almost entirely are built from beta sheets:
MUSCLE FATTY ACID
BINDING PROTEIN
(1FTP.pdb)
Loops and turns
globular proteins can be made up if turns and loops are incorporated in structure
beta turn = reverse turn = hairpin turn
loop = omega loop (generally rigid, well-defined structures)
loops and turns generally lie on the protein surfaces and participate in protein-protein and other types of interactions
turn
loops
Superhelices
a-keratin (main component of wool and hair) consists of two right-handed
a-helices intertwined to form a left-handed superhelix called a coiled coil
(superfamily of coiled-coil proteins, ~60 proteins in humans)
2 or more a helices can entwine and form a stable, even 1000 Å (0.1 mm) or
longer, structure found in cytoskeleton, filaments, muscle proteins
3.5 residues/turn, heptad repeats, every 7th residue is Leu on each strand
and these two Leu interact (hydrophobic interaction), 2 Cys can also
interact (S-S) stabilizing fiber
wool can be stretched (some interactions among helices brake, S-S does
not and pulls back after release)
hair and wool have fewer cross-links, horn, claw, hoof are hard
Collagen
most abundant protein in mammals, main fibrous component of skin, bone,
teeth, cartilage and tendon
extracellular protein, rod shape, ~3000 Å long/15 Å in diameter, 3 helical
protein chains (~1000 residues each, every 3rd residue is Gly,
Gly-Pro-(Pro-OH) triad is frequent, Pro-OH (4-hydroxyproline) is a natural
amino acid derivative)
no H-bonds inside the helical strands, stabilization occurs via steric
repulsion between Pro and Pro-OH
~3 residues/turn, 3 helices wind in a superhelical cable that is stabilized
by H-bond in between strands (Pro-OH participates in H-bonding network
and lack of –OH on Pro in collagen lead to the disease scurvy (Vitamin C
deficiency, ascorbate reduces Fe3+ to Fe2+ in prolyl hydroxylase for its
continuous activity)
Pro rings are on the outside, Gly in every 3rd position is needed because
the superhelix is very crowded inside and there is no place for any other
bigger amino acid
Tertiary structure
the very first protein to be seen in atomic detail was myoglobin, the O2carrier protein in muscle, determined by Kendrew in 1957 (6 Å resolution)
Kendrew's original model of the myoglobin molecule, 1957, made of plasticine.
single polypeptide chain, 153 residues, heme prosthetic (helper) group
[heme: protoporphyrin IX and central iron ion], very compact molecule
(45 X 35 X 25 Å), 70% of amino acids are in 8 a helices, the rest are in
loops and turns
Heme
hydrophobic amino acids are yellow, charged ones
are blue, others are white
cross-section
interior of globular proteins are rich in hydrophobic amino acids like Leu,
Val, Met, Phe
charged and rather polar residues, like Glu, Asp, Lys, Arg (Gln, Asn) localize
on the exterior of proteins
in myoglobin there are two critical His in the interior that conduct binding
of O2
a helices and b sheets may often have an amphipathic character: one part
points towards the hydrophobic interior core of the protein, the other side
points into solution
burying polar main chain atoms in the hydrophobic interior is possible if all
N-H and C=O moieties are in a H-bonding network (a helix, b sheet)
proteins spanning biological membranes are the “exceptions that prove the
rule” as they have a reverse distribution of hydrophobic and hydrophilic
amino acids, like in porins, found in the outer membranes of bacteria
(they are “inside out” relative to proteins function in aqueous environment)
Motifs and supersecondary structures
certain combinations of secondary structure are present in many proteins
and frequently exhibit similar functions, these combinations are called
motifs or supersecondary structures
For instance, a helix-turn-helix motif, often found in DNA-binding proteins
some polypeptide chains fold into 2 or
more compact globular units or regions
that are connected by flexible regions,
these are called domains (30-400 amino
acids long)
cell-surface protein CD4 consists
of 4 similar domains
Quaternary structure
proteins containing more than one polypeptide chains adopt a quaternary
structure which describes the spatial arrangement of the subunits and the
interaction between them
each polypeptide chain is called a subunit
the number of subunits may vary and we designate this by calling the
protein a dimer, trimer, tetramer, etc.
there can be homo- and hetero-multimers which may be tightened together
covalently or non-covalently
the Cro protein of bacteriophage l
is a dimer of identical subunits
human hemoglobin , the O2-carrying protein of
blood, consists of two a-type and two b-type
subunits, a a2b2 hetero-tetramer
viruses make the most out of limited genetic information: they have a protein coat that
uses many, often identical, subunits repetitively in a symmetric array for their build-up:
e.g. the rhinovirus, the cause of the common cold, includes 60 copies of each of four
subunits forming a nearly spherical shell that encloses the viral genome
schematic view
electron micrograph
of virus particles