Download Globular proteins

The first tertiary structure known was that of Myoglobin by John
Kendrew (1950)
It provided several clues about the globular protein structure.
It is a small (Mr 16,700) oxygen binding protein in muscle cells
70% amino acid residues are in a helical form,
The peptide backbone is made up of relatively straight a helices
joined by bends and b turns.
Three of the 4 proline residues are present at the bends.
The clues:
1. The nonpolar residues Val, Leu, Ile, Met, and Phe largly occur in
the interior of the protein away from the aqueous solvent layer
2. The charged polar residues Arg, Lys, His, Asp, and Glu are
largely located at the surface in contact with aqueous solvent
3. The uncharged polar groups Ser, Thr, Asn, Gln, Tyr and Trp are
usually on protein surface and are also found inside of the protein
where they are always hydrogen bonded.
Forces which stabilize the protein structure:
Ionic interactions: Little contribution towards stability of native
structure
Dipole-Dipole interaction: Week forces but contribute to stability
Hydrogen Bonding Forces: Very important role in 3o structure
Hydrophobic Forces: Very Important contribution
Disulfide bonds: Very important
Techniques used for the determination of three dimensional
structure
1. Circular Dichroism:
2. X-ray crystallography
3. NMR spectroscopy
Circular Dicroism (CD): When polymers of optically active
monomers are exposed to circularly polarized light, the
absorptivty is different for right and left-circularly polarized
light.
The difference in the molar absorptivity varies with the wave
length of the light.
The CD spectra obtained for various secondary structures gives a
characteristic pattern.
X-Ray Crystallography:
When a beam of X-ray of a given wave length falls on a crystal, the xrays are diffracted by the electrons of various atoms of the crystal. The
diffracted X-rays are recorded on a photographic film or x-ray film by
producing a pattern of spots with various intensities.
By analysis of the x-ray diffraction pattern, spacing between different
atoms of the molecule can be determined.
X-ray diffraction pattern can give an idea about the electron densities in
three dimensional space.
Many proteins have been crystallized and their structures have been
determined by x-ray diffraction pattern.
Originally the process of calculations for atomic lattices from the
diffraction pattern was very laborious but now through the
development of computer software it has become more feasible.
NMR Spectroscopy:
Nuclear magnetic resonance is a manifestation of nuclear spin angular
momentum of atomic nuclei.
Only certain atoms including 1h, 13C, 15N, 19F and 31P posses the spin which
can give rise to NMR signals.
Nuclear spin generates a magnetic dipole which can either be in the direction
of an applied static magnetic field (parellel, low energy level) or in anti-parallel
direction (high energy level).
When a suitable frequency of electromagnetic energy is applied at the right
angle of the nuclei aligned in the magnetic field, it can absorb some energy and
go to high energy level.
The absorption spectrum thus obtained reflect the nature of the nuclei and its
immediate electronic environment.
With the advent of two dimensional NMR, distance dependent coupling of
nuclear spins in nearby atoms through space (nuclear Overhause effect,
NOSY) or the coupling of the nuclear spins of the atoms connected by covalent
bonds (total correlation spectroscop, TOSY)can be measured.
Supersecondary structures:
Also called motifs or simply folds
Particularly stable arrangement of several elements of secondary
structure and connection between them
Some simple motifs:
1. b-a-b loop and a-a corner can create layers in which the
inner sides are shielded from water.
2. b-hairpin motif
3. b-barrels: Twisted b sheet conformation are more stable and
they roll up to form b-barrels.
The b barrel (a single domain of a hemolysin
From bacterium S.aureus
Quaternary Structure:
Many proteins have multiple polypeptide subunits. It may be
heteromeric (with different types of mono-meric subunits) or a
multimer of same kind of subunits.
The repeating structural units in a multimeric protein is called
protomer.
Identical subunits of a multimer proteins are generally arranged in a
few ways of symmetric patterns.
Cyclic symmetry: involving rotation around a single axis
Dihedral symmetry: Two fold rotational axix intersects an n-fold
(4fold in picture) axis at right angle.
Other complex rotational symmetries are possible e.g. icosahedral
symmetry
The quaternary structure of deoxyhemoglobin
Coat proteins of poliovirus