Lecture 5 - Elements of Protein Structure Flashcards
In proteins and peptides, amino acids are joined together by
peptide bonds
Levels of protein structure
Primary
Secondary
Tertiary
Quaternary
Primary structure
Amino acid sequence (chain)
Secondary structure
Local 3D stretch of residues
Tertiary structure
(3D) structure of a complete
protein chain
Series of helices connected by loops
Global fold
Quaternary structure
More than 1 protein chains packed together
Φ phi angle
angle around the N–Ca bond
Ψ psi angle
angle around the Ca–C’ bond
Protein structures Begin to fold when
Amino acid residues emerge from the ribosomes
Fold locally then globally
How do the protein structures fold?
Do it themselves
Rotate around the flexible bonds that connect them.
Some bonds can be flexible or rigid
Main chain bonds
N (in peptide bond)
Cα (sidechain attached to it)
C’ (carbonyl carbon. Attached to the double bonded oxygen)
C’
carbonyl carbon.
Attached to the double bonded oxygen
Main chain bond angles:
Φ phi angle
Ψ psi angle
How much rotation there is around the single bonds.
0 - 180 & -180 - 0
To figure out the orientation of a peptide and what direction its going. Look for…
amide nitrogen (H and Cα attached)
Peptides move from
amino terminus to the carboxyl terminus
Bond between amide nitrogen and Cα
Phi Φ angle
Single bond free rotation
Bond between Cα to C’
Psi Ψ angle
Residue 1
Phi 1
Psi 1
When a protein is completely flat
All angles are 180 degrees
Peptide bonds
Stiff
Rigid
Not very flexible
Phi and Psi restrictions
Steric hinderance
rotate around Phi and Psi bonds, collisions can occur
If rotate around the Phi Φ angle
2 oxygens will collide
o has vanderwaal radius, certain distance that can’t get any closer
If rotate around the Psi Ψ angle
Amide Nitrogens (NH) will collide.
The combination of all the rotation and twists around the flexible peptide bond leads to…
3D structure which in turn leads to its function.
Amino acid sequence leads to…
structure
Secondary structures
α helix (right hand turn)
β - strand/sheet (4 main chains)
Dominates tertiary protein structures.
Side chains point out from helix axis
α - helix and β - strand/sheet difference
Internal hydrogen bonding in helices
In beta, hydrogen bonding are across main chains
α-helix properties
Find amide nitrogen
Find Cα (has sidechain)
H bond (interaction between NH and C’) stabilizes helix and promotes helical formation.
Spiral right handed
Side chains point out from helix axis
Dipole (NH has partial positive charge and carbonyl has negative charge)
α-helix properties
residues / turn
turns
d =
- 6 residues/turn;
- 4Å/turn
1.5Å/residue
The carbonyl residue of 1 interacts with amide nitrogen (NH) of residue 5
Carbonyl residue = n
Amide Nitrogen residue = n + 4
α-helix Φ angle (phi) and Ψ angle (Psi)
Φ = ~ - 57 degrees Ψ = ~ - 47 degrees
Helix breakers residues
Glycine Proline (restrictions. Sidechains binds to themselves)
β structure
Extended structure that allows hydrogen bonding to occur on adjacent strands (another main chain by it)
Two types of interactions within (parallel and antiparallel)- arrows always from amino (N) to carboxy end (C)
Example Silk
β - sheet
Contains 2+ β strands
Typically 2-10
Multiple strands
β strands
6 amino acid residues long on Average
Can have up to 15 residues
Single chain
Parallel
Arrows pointing in same direction (always from amino (N) to carboxy end (C))
Hydrogen bonds on angles
Antiparallel
Arrows pointing in opposite direction (always from amino (N) to carboxy end (C))
Carbonyl Oxygen pointing down and underneath amide hydrogen pointing up.(vice versa)
Hydrogen bonds straight up and down
β structure properties
Extended more than helix Pleated (main chains up and down) All strands can twist Sidechains point above and below Any stretch of protein residues that can alternate in polarity (non polar, polar) forms a beta strand (be apart of beta structure).
Silk
Beta structure Model with 4 chains Sequence is Gly-Ser-Gly-Ala-Gly-Ala etc Antiparallel Flexible (because of hydrophobic interactions) Extended
β turns key properties
hairpin like
3-4 residues
high Gly Pro content
30% residues involved in turns
h bond, across the turn
Type I, Type II are common types
more than 16 types, given Roman Numeral names
