Lecture 5 - Elements of protein structure Flashcards
Peptide bond features
In proteins and peptides, amino acids are joined together by peptide bonds
Peptide bond is planar, trans and has a dipole
Each protein is made up of at least one….
Protein (or polypeptide) chain
The amino acid residues in a polypeptide chain are numbered starting from the amino terminus to the carboxy terminus
Proteins may have anywhere from one to several chains
Proteins with one chain are the most common variety
Proteins are mostly globular therefore
The main chain has to double back and form a more compact shape
THis structure will turn out to be comprised of primarily alpha-helix, beta sheet and turns
Levels of protein structure
There are 4 levels - primary, secondary, tertiary and quaternary
Primary
Amino acid sequence of a protein
Secondary
3D arrangment of a protein chain over a short stretch of adjacent amino acid residues
What the primary structure does with residues adjacent to it
Tertiary
3D structure of a complete protein chain
Quaternary
Interchain packing and structure for a protein that contains multiple protein chains
Not all proteins have multiple chains so not all proteins have quaternary structure
This is how the chains pack together
Main chain atoms in a protein are…
N, C⍺, C’
Phi ɸ
Chain/rotation angles between N and C⍺
Psi Ѱ
Chain/rotation angles between C⍺ and C’
Phi and psi
These angles take on values ranging from 0 to +/- 180 degrees
Omega ⍵
The chain angle between C’ and N is called by the greek omega and is usually very close to either 180 degrees or 0 degrees (trans 180 or cis 0)
The rotation angle around the peptide bond is called omega - no free spinning around this bond because it has partial double bond character, usually around zero
Third main chain angle - angle of rotation around the peptide bond
Is trans
Protein 3D structure can be generally described by….
The rotation angles found around the bonds of the residues of the protein chain
Phi-Psi restrictions
Phi-psi angles have restrictions in their values because of steric hinderance due to collisions
Phi rotation can lead to O-O collision
Psi rotation can lead to NH-NH collisions
Steric hinderance between the hydrogen on the amide nitrogen and the carbonyl oxygen
Peptide bonds are mostly trans…
For a trans peptide bond, the C⍺ atoms are found on opposite sides of the peptide bond. In a cis peptide bond, the C⍺ atoms are found on the same side of the peptide bond. Steric crowding is increased for cis peptide bonds, very little rotation is allowed for the peptide bond
Look at alpha carbon to know if cis or trans
Proline is cis but the rest are pretty much trans
3D structure of a protein determines …
Function - side chains orientated by the 3D structure, side chains are what carries out the chemistry
Two dominant secondary protein structures
⍺- helix
Β-strand or beta-sheet
Alpha helix
Main chain spirals around like a spiral staircase
In helices, not the interaction between residues that are 4 apart in the protein sequence
In an alpha helice, what atoms hydrogen bond? How far apart are the N and O atoms in angstroms?
O and the hydrogen on the N, 2.9
Beta strand or beta sheet
Beta strand is a single strand and a bunch of strands form a beta sheet
Alpha helix key properties
3.6 residues/turn; 5.4Å/turn
d = 1.5Å/residue
spiral is “right handed”
side chains point out from the helix axis
dipole (are additive so that hydrogens are always pointing down in the same direction, this is because the bottom is more positive and the top is more negative)
ɸ=~-57,ψ=~-47
Some residues e.g. are “helix breakers” e.g., glycine (due to flexibility), proline (these examples don’t like it because its side chain binds back to the amino group
Beta sheet/strand key properties
Involves adjacent peptide chains, called b-strands, that have an extended structure that allows for hydrogen bonding between chains
Hydrogen-bonding occurs between adjacent chains
The chains often form a b-sheet, ≥ two b-strands
Typically 2 to 10 strands per sheet
Average strand length contains ~ 6 amino acid residues
Each strand may have up to 15 residues
Two types of interaction in a b-sheet: Parallel (2 independent main chains that are side by side, chains point from N to C terminus) and antiparallel (opposite direction)
Parallel and Antiparallel interactions
Usually between 6 and 15 amino acids in a strand
Arrow points from N terminus to C terminus
What are the key properties of a β-sheet?
- what bonding occurs between adjacent peptide chains (β-strands)?
- Are there parallel, antiparallel or both interactions?
- Where do side chains point?
- Hydrogen bonding occurs between adjacent peptide chains (β-strands)
- There can be parallel or antiparallel interactions
- Side chains point above and below the sheet
What are the key properties of a β-sheet?
- Chains often form a β-sheet with typically how many strands per sheet?
- what stretch of residues usually forms a β- strand?
- Chains often form a β-sheet with typically 2 to 10 strands per sheet
- Any NP-P-NP-P stretch of residues usually forms a β- strand
What is the strand length of a β-sheet?
ie. how many amino acid residues?
The strand length ~6 amino acid residues
Hydrogen bonds in beta vs alpha
Beta has interchain hydrogen bonds and alpha has intrachain hydrogen bonds
To find a main chain
Find a nitrogen and then the carbonyl carbon for one strand
Then find out the alpha carbon
Beta sheets: Number of strands, normal number of amino acids, maximum number of amino acids, what type of twist, silk repeating sequence, what direction do side chains point?
2-10, 6, 15, right handed, GSGAGA, up and down
Key properties of turns
hairpin like, involve usually 3 or 4 residues
high Gly, Pro content
important, almost 30% residues involved in turns
hydrogen bond, across the turn is common
more than 16 types, given Roman Numeral names
Type I, Type II are common types
Protein structural shorthand
Helices shown as spirals (or cylinders)
Strands shown as arrows, pointing from N to C
Turns and random coil*, shown as loops or rope- like stretches
Advantages of protein structural shorthand
Easily visualize the main chain path of protein
Identify elements of secondary structure
Allows an appreciation of proteins as 3-D objects
Allows comparison to other proteins
What residues are “helix breakers”?
Glycine is too flexible to adopt a helical structure
Proline always forces a turn because of its cyclic structure
Location of the peptide, phi and psi bonds?
Ca-C = psi N-Ca = phi C-N = peptide
