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Chapter 4
The Three-Dimensional
Structure of Proteins
Part 2
Chapter 4, Part 2: Learning Goals
1. Know the structures and functions of collagens,
role of ascorbic acid (vitamin C) in collagen
structure.
2. Know globular protein structure and families.
3. Know how de-naturation and re-naturation
works or sometimes doesn’t.
Collagen Triple Helix
Left Handed, 3 aa/turn
Prolyl-4-hyroxylase Hydroxylates Protein as
Procollagen
Hyrdoxproline is necessary to keep some prolines in the
“exo” form to allow the collagen triple helix to form.
Prolyl-4-hydroxylase is a Di-oxygenase can Catalyze
Two Reactions
Without Vitamin C, the iron of the first enzyme becomes oxidized
and Inactive. Ascorbate actually keeps the enzyme iron reduced
although this diagram does not show it.
Hydroxylysine Cross Links Collagen Triple Helix Strands
Iriquois showing Jacques Cartier how to make Cedar
Tea - a source of Vitamin C
James Lind’s experiment
could not be done today.
Why?
Did he lack a control
group?
Was there something else?
Newly Discovered Bond in Collagen IV
The Sulfilimine Bond
Between a hydroxylysine
and methionine
Vanacore, R, et al. 2009. A sulfilimine bond identified in collagen IV. Science. 325:13230. Sept 4, 2009
Sulfilimine Bond – Evolutionary Conservation
Human Serum Albumin (Mr = 64,500)
if it was:
This figure has a flaw. Horizontal dimensions are OK, Verticals are off in
two ways: different scale and globular form is way too small.
Structures of Myoglobin
What about “random coil” or “random
structure”?
Where is it in myoglobin? - go back to previous
slide, it represents 22% of the amino acids in
myoglobin!
Is it random? Yes and No!! Both are correct why?
Is it coil? Yes and No!! Both are correct why?
Heme in Myoglobin
Structures of some Small Proteins
A
Troponin has 2 Domains
Each Domain has a Distinct Function: Binding Ca++
Two Small Motifs
Here alpha helix connects
two beta-structures
Alpha turn alpha are
common on some DNA
binding proteins
Smaller Motifs into Large Motifs
Protein Families – Classes and Folds
All Beta Protein Families
Alpha/Beta Protein Families
Alpha + Beta Protein Families
Max Perutz and John Kendrew
Quaternary Structure of Hemoglobin
2 α and 2 β
Quaternary Structure: Symmetry
Polio Virus and Tobacco Mosaic Virus
A
Protein Stability and Folding
• A protein’s function depends on its 3D-structure
• Loss of structural integrity with accompanying loss of
activity is called denaturation
• Proteins can be denatured by:
• heat or cold
• pH extremes
• organic solvents
• chaotropic agents: urea and guanidinium
hydrochloride
Thermal and Chemical Protein Denaturation
Irreversible
Reversible
or Urea
Ribonuclease Refolding Experiment
• Ribonuclease is a small protein that contains 8 cysteines
linked via four disulfide bonds
• Urea in the presence of 2-mercaptoethanol fully denatures
ribonuclease
• When urea and 2-mercaptoethanol are removed, the protein
spontaneously refolds, and the correct disulfide bonds are
reformed
• The sequence alone determines the native conformation
• Quite “simple” experiment, but so important it earned Chris
Anfinsen the 1972 Chemistry Nobel Prize
Reversible Unfolding with Mercaptoethanol
CH3-CH2-SH
This step must be
done very slowly
Simulated Folding
Proteins folding follow a distinct path
Creutzfledt-Jakob Disease:
Human Spongiform Encephalopathy
Vacuoles Contain a Missfolded Protein – in Brain Tissue
Prions
Infectious proteins
Inherited and transmissible by ingestion, transplant,
& surgical instruments
PrPC, normal cellular prion protein, on nerve cell
surface
PrPSc, scrapie protein, accumulate in brain cells
forming plaques
Prion Miss-folding
PrPSc
PrPc
1
2
3
4
Lysosome
Endosome
5
6
7
8
PrP Folding
Chaperones prevent misfolding
Chaperonins facilitate folding
GroEL and GroES
Protein Folding  Alzheimer’s Disease, Type 2
Diabetes and Parkinson’s Disease
A
Amyloid Fibers Stabilized by F
Different Amyloid
diseases depend
on organ the
fibers occur
A
A
Summary of Forces Driving Protein Structure
1. hydrophobic interactions contribute strongly to protein folding
and stabilization  ultimately burring hydrophobic R groups with
at least two layers of secondary structure covering them up to
exclude water.
2. alpha and beta structures are usually in different layers. Their
R-groups generally do not allow mixing.
3. Secondary structure near each other (in primary sequence)
are usually stacked (except in quaternary structure).
4. beta structure is most stable when slightly twisted. The great
example being the beta-barrel (Fig 4-20) of many membrane
proteins.
5. Beta bends can not form knots.
Things to Know and Do Before Class
1. Know collagen structure and the role of vitamin C.
2. Structure of globular proteins, circular dichroism, and
the main idea of protein families (there are over 800).
3. Denaturation and Renaturation (or not) of proteins
4. One of the largest unsolved puzzles in modern
biochemistry: the details of how proteins fold.
5. Roles of Chaparones.
6. Be able to do EOC Problems 7-11 Problem 12 makes
you calculate the molecular weight of the DNP-aa in
the diagram.