Lecture 11. Test next week in class Protein structure. Collagen. Most abundant protein of vertebrates. Extracellular protein-insoluble fibers, great tensile strength Major component of connective tissues (bone, teeth, cartilage, tendon, ligament, etc.)
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Figure 8-30b X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (b) View along helix axis.
Figure 8-30c X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (c) A schematic diagram.
Figure 8-38a The 2D proton NMR structures of proteins.(a) A NOESY spectrum of a protein presented as a contour plot with two frequency axes w1 and w2.
Off diagonal peaks (cross peaks) occur from interaction of 2 protons that are <5 Å apart in space and whose 1D-NMR peaks are located where the horizontal and vertical lines cross through the cross peak intersect the diagonal.
Nuclear Overhauser Effect (NOE)
Figure 8-38b The 2D proton NMR structures of proteins.(b) The NMR structure of a 64-residue polypeptide comprising the Src protein SH3 domain.
Figure 8-39a Representations of the X-ray structure of sperm whale myoglobin. (a) The protein and its bound heme are drawn in stick form.
Figure 8-39b Representations of the X-ray structure of sperm whale myoglobin. (b)A diagram in which the protein is represented by its computer-generated Ca backbone.
Figure 8-39c Representations of the X-ray structure of sperm whale myoglobin. (c)A computer-generated cartoon drawing in an orientation similar to that of Part b.
Figure 8-43a The H helix of sperm whale myoglobin. (a)A helical wheel representation in which the side chain positions about the a helix are projected down the helix axis onto a plane.20
Figure 8-43c The H helix of sperm whale myoglobin.(c) A space-filling model, viewed from the bottom of the page in Parts a and b and colored as in Part b.
The completely unfolded protein is thought to be in the least stable form.
For most proteins, the native conformation is the most thermodynamically stable and the only form that is biologically active.
a-Helix-loop-a-helix motif binds DNA, sequesters calcium ion.
The aa motif
b) The bb motif; antiparallel
c) The bbbb “Greek Key” motif
d) The bab motif
Several bab motifs combine to form a superbarrel in the glycolysis enzyme triose phosphate isomerase (TIM barrel)
Structural elements of IgGs:
Naturally occurring immunoglobulins (IgG molecules) have identical heavy chains and light chains giving rise to multiple binding sites with identical specificities for antigen.
Antibodies are composed of:
V (for variable) regions - encodes the antigen binding activity
C (for constant) regions - encodes immune response signal/effector functions:
Complement fixation (activation of complement cascade)
Binding and activation of Ig receptors (transport from maternal source, activate immune system T cells to engulf, destroy foreign cells, particles, proteins)
Also binds bacterial Protein A, Protein G (used in purification)
Note: dashed lines indicate
interchain disulfide bonds
There is a conserved glycosylation site in the CH2 domain of IgG (purple region).
A carbohydrate is covalently attached here by postranslational modification.
IgG secondary/tertiary structure: multiple beta-sheet domains.
Termed “immunoglobulin domain”.
Repeated motif in many immune and receptor proteins.
Modes of Flexibility of IgG structure