Chapter 4. The Three-Dimensional Structure of Proteins Part 2. Chapter 4, Part 2: Learning Goals. Know the structures and functions of collagens, role of ascorbic acid (vitamin C) in collagen structure. Know globular protein structure and families.
Structure of Proteins
Left Handed, 3 aa/turn
Hyrdoxproline is necessary to keep some prolines in the “exo” form to allow the collagen triple helix to form.
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.
James Lind’s experiment could not be done today. Why?
Did he lack a control group?
Was there something else?
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
This figure has a flaw. Horizontal dimensions are OK, Verticals are off in two ways: different scale and globular form is way too small.
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?
Each Domain has a Distinct Function: Binding Ca++
Here alpha helix connects Alpha turn alpha are
two beta-structures common on some DNA
2 α and 2 β
This step must be done very slowly
Proteins folding follow a distinct path
Vacuoles Contain a Missfolded Protein – in Brain Tissue
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
Chaperones prevent misfolding
Chaperonins facilitate folding
Different Amyloid diseases depend on organ the fibers occur
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.
4. One of the largest unsolved puzzles in modern biochemistry: the details of how proteins fold.