Lecture 6: Medical Biochemistry, Higher Order Protein Structures

1. Higher Order Protein Structures
Lecture 6, Medical Biochemistry

2. Lecture 6 Outline
• Molecular forces involved in protein
structure
• Protein folding
• Structure and biosynthesis of collagen

3. Protein Native State
and Denaturation
A protein folded into its tertiary
structure under optimal conditions is
said to be in its “native state,” which
corresponds to its most thermo-
dynamically favorable arrangement
of atoms. Proteins can be denatured
(loss of their secondary and higher
structures) by changes in temperature,
pH, ionic strength, urea or detergents

4. Proposed Folding Pathway
Accessory
proteins?

5. O-H = 460
C-H = 410
C-C = 350
Bond kJ/m
Compare:

6. Non-covalent Molecular Forces
in Protein Structure and Folding
• Hydrophobic interactions: interactions between
hydrophobic amino acids is likely the largest
noncovalent force responsible for most protein
folding. Recall that water will tend to form a
solvation shell around free hydrophobic compounds,
which in thermodynamic terms, is a decrease in
entropy (and thus not favored). This drives
formation of hydrophobic regions of protein chains
to come together, the water shell is disrupted and
entropy increases.

7. Non-covalent Forces (cont)
• For hydrophobic interactions, calculations have
shown that 1/3 loss of water of solvations occurs
with formation of secondary structure; an additional
1/3 water of solvation is lost in the formation of
tertiary structure. This is a large source of the
energy that drives protein folding.
• Hydrogen Bonds - these have been discussed for
helix and sheet formation. Distance between the
donor and acceptor atoms are the most important
determinants for bond formation, 2.7-3.1 angstroms
are optimal (covalent bond is 1.0-1.6 angstroms)

8. Non-covalent Forces (cont)
• Electrostatic, or charge-charge interactions.
Predominantly found on the exterior
surfaces of proteins, interacting with the
water solvent. The strength of the ionic
forces are largely dampened by the high
dielectric constant of the surrounding water,
such that proximity to other charged groups
is likely the strongest attractive force for
charge-charge interactions

9. Non-covalent Forces (cont)
• Van der Waals interactions: Occur when molecules
or atoms which do not have covalent bonds between
them come so close together that their outer electron
orbitals begin to overlap. This can lead to changes in
the overall distribution of the electronic charges to
create a weak attractive force. Contact distance
ranges from 2.8 to 4.1 angstroms, so forces are
weak. However, in a folded protein, thousands of
individual interactions occur, thus providing a
significant cumulative stabilizing force.

10. Accessory Proteins for Folding
• In a test tube, protein renaturation of an
unfolded protein can take minutes, days or
never occur. Protein folding in the cell
occurs during protein translation (synthesis)
and generally takes only a few minutes for
formation of the native conformation. This
is primarily due to the inherent properties of
the protein, and is assisted by cellular
accessory proteins, examples of which
include:

11. Accessory Proteins (cont)
• Protein disulfide isomerase - catalyzes
formation of disulfide bonds
• Peptidyl Prolyl Cis-Trans Isomerases - this
class of enzymes, also called rotamases,
facilitates the conversion of Pro residues to
cis-conformations (originally made in a
trans conformation)

12. Accessory Proteins (cont)
• Chaperones - a large group of proteins, also
termed heat shock proteins and chaperonins,
their precise regulation and mechanisms of
action remain largely undefined. During the
folding process, they function to prevent
unfavorable protein interactions with other
potentially complementary surfaces (like
other proteins, carbohydrates, lipids, nucleic
acids, etc.) Many of these proteins are
ATPases (use hydrolysis of ATP as an
energy source).

13. Fibrous Proteins - Examples and
Characteristics
• Highly elongated proteins whose secondary
structures are the dominant structural motif
• Found in skin, muscle, tendon and bone and have
connective, protective and/or supportive
functions
• EXAMPLES: keratins (hair, nails, horn,feathers)
elastin (tendons); spider silk fibroin; collagens

15. COLLAGEN: Properties
• Most abundant protein in mammals
• example of a fibrous protein (in general,
these protein have repetitive secondary
structures, are poorly soluble, and cannot be
crystallized; other fibrous proteins include
elastin in tendons & keratins in hair and
nails)
• collagen composed of approximately 33%
glycine, 21% proline or hydroxyproline,
and 11% alanine

17. COLLAGEN: Properties (cont)
• Tropocollagen (the precursor form) is
composed of three polypeptide chains of
about 1000 amino acids each, wrapped in a
triple helix, rope-like coil
• Every third residue in each polypeptide in
this triple helix is a glycine. The glycines
from each strand interact with each other in
the central, shared interior of the helix
• Proline frequently follows glycine, and the
third residue can be any other amino acid
(X) found in collagen; a Gly-Pro-X motif

19. COLLAGEN: Properties (cont)
• Extensive post-translational modification of
prolines and lysines occurs
• Cross-linked fibrils of collagen form after
secretion and processing of tropocollagen
• Defects in enzymes involved in the collagen
biosynthetic pathway are responsible for
many diseases.

20. Synthesis of Hydroxyproline and
Hydroxylysine residues

22. Formation of collagen
cross-links: Mediated by
lysine modifications and
subsequent lysine-allysine
or allysine-allysine covalent
bond formation

23. Post-translational
processing of
collagen

24. Marfan syndrome is caused by mutations in the fibrillin gene; Fibrillin i
a large fibrous protein component of extracullar microfibrils, frequently