Bonev - Protein structure Flashcards
What are two reasons as to why we want to know and understand protein structure?
- Understand their function
- Infer the function of unknown proteins with similar structure
When does the secondary structure form?
Spontaneously at the ribosome immediately after translation
How is it stabilised?
Hydrogen bonds between the NH and CO of the backbone
Where are the hydrogen bonds in the alpha helices structure?
Between the carbonyl oxygen of one amino acid, and the amide hydrogen of another amino acid four residues further down
Where are the hydrogen bonds in the beta sheets?
Between adjacent strands of the beta sheet. Carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid on an adjacent strand.
How many residues are present per turn in alpha helices?
3.6
What is the angular increment per residue?
100º
What is the helical pitch?
5.4Aº
What type of domain is usually found at plasma membrane proteins?
Alpha helices
For beta sheets, which way do the side chains point?
Outwards
What do beta barrels consist of?
Antiparallel strands
How is the backbone able to change direction?
Due to beta-turns. These are also needed for a closed barrel strucutre.
Beta barrels are common folds in outer membrane proteins. What places are they found?
Bacteria, mitochondria, and chloroplasts
Proline (P) and Glycine (G) are present in many proteins with beta sheets and are found in barrels. What is their purpose?
Proline = found in the second position of beta-turns and facilitates the reversal of the the direction in the turn
Glycine = found in the third position of the turns, smallest amino acid which allows greatest flexibility
What is meant by torsional flexibility at the peptide bond?
It refers to the ability of the peptide bond to rotate around two specific angles, known as the phi and psi angle
What does the phi angle represent?
Represents the rotation around the bond connecting the nitrogen atom (N) of one amino acid to the alpha carbon (Cα) atom of the same amino acid
What does the psi angle represent?
Represents the rotation around the bond connecting the alpha carbon (Cα) of one amino acid to the carbonyl carbon (C) of the next amino acid
What is the purpose of Ramachandran plots?
Ramachandran plots display the possible combinations of phi and psi angles that are energetically favorable and allowed for protein structures. It can show the possible secondary structures to be produced.
Ramachandran plot has the psi angle on the y-axis (left), phi angle on the x-axis (bottom). Beta sheet normally top left, left a helix in middle right, and right a helix bottom left
What is the supersecondary structure made up of?
Multiple secondary structures. They come together and interact, often stabilising each other when they come close.
What is an EF hand?
A Ca2+ binding motif from calmodulin acting as a binding site for calcium