A protein’s 3 dimensional conformation is called :
The native fold
What are some favorable interactions in proteins?
- Hydrophobic effect
- Hydrogen bonds
- London dispersion
- Electrostatic interactions
The structure of the protein is partially dictated by the properties of the peptide bond. The resonance causes the peptide bonds to be :
Less reactive compared to esters, for example
– to be quite rigid and nearly planar
– to exhibit a large dipole moment in the favored trans configuration
What are phi and psi angles ?
- f (phi): angle around the a-carbon—amide nitrogen bond
- y (psi): angle around the a-carbon—carbonyl carbon bond
- In a fully extended polypeptide, both y and f are 180
What does a Ramachandran plot show ?
• A Ramachandran plot shows the distribution of f and y dihedral angles that are found in a protein
➔ shows the common secondary structure elements
➔ reveals regions with unusual backbone structure
Why does glycine fall out of the Ramachandran plot ?
it is too small and flexible
Describe 2 regular and 1 irregular arrangement in protein secondary structure
- The a helix – stabilized by hydrogen bonds between nearby residues
- The b sheet – stabilized by hydrogen bonds between adjacent segments that may not be nearby
- Irregular arrangement of the polypeptide chain is called the random coil
Which AAs are strong helix formers ?
Small hydrophobic residues such as Ala and Leu
Which AAs break the alpha helix and why ?
- Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible
- Gly acts as a helix breaker because the tiny R-group supports other conformations
Does the helix have a charge ?
- The a helix has a large macroscopic dipole moment
- Negatively charged residues often occur near the positive end of the helix dipole
( the peptide bond has a strong dipole moment – Carbonyl O negative – Amide H positive)
What’s the difference between parallel and antiparallel beta sheets ?
- In parallel b sheets the Hbonded strands run in the same direction resulting in bent H-bonds (weaker) (> 5 residues)
- In antiparallel b sheets the H-bonded strands run in opposite directions resulting in linear H-bonds (stronger)
When do beta turns occur ?
whenever strands in b sheets change the direction
What are the 2 major classes for protein tertiary structure ?
Fibrous and globular (water or lipid soluble)
When does quarternary structure occur ?
It results from interactions between two or more polypeptide chains.
What is protein denaturation?
Loss of structural integrity with accompanying loss of activity
What is the basis of numerous human diseases?
Protein misfolding (prions)
How do prion and amyloid proteins escape the proteases and chaperones of the quality control systems?
- Alternatively folded precursor proteins have surface structures that are not recognized by the chaperones and proteases.
- A second possibility is that amyloids forms aggregate more quickly than they can be degraded or refolded.
- Most abundant chaperones and proteases in cells do not appear to act on aggregates, fibril formation will not be easily reversed once initiated.
In an a-helix, the R groups on the amino acid residues are found where?
on the outside of the helix spiral.
