Elements of protein structures Flashcards
What are the four levels of protein structures?
Primary - linear sequence of amino acids
Secondary - 3D arrangements of a protein chain, includes a-helix and B-sheets
Tertiary - 3D structure of a complete protein chain
Quaternary - interchain packing and structure for a protein containing multiple polypeptide chains
What is the phi angle in main chains of proteins?
phi angle is the rotation around the N — C alpha bond
Defined as 180 degrees
What is the psi angle in main chains of proteins?
psi angle is the rotation around the C alpha — C’ bond
Defined as 180 degrees
What are Phi-Psi restrictions?
Phi-Psi angles have restrictions in their values because of steric hindrance
Phi rotation can lead to O — O collision
Psi rotation can lead to NH — NH collision
What is the third main chain angle?
w - omega
Angle of rotation around the peptide bond
Trans and Cis peptide bonds
Most peptide bonds are trans, omega is 180 degrees and C alpha are found on opposite sides
In a cis peptide bond the C alpha atoms are found on the same side of the peptide bond, omega is 0 degrees - steric crowding increased
What is the structure of a secondary protein?
Dominated by two canonical structures
B-strand or B-sheet (beta)
a-helix (alpha)
What is the alpha helix?
The main chain spirals around the central axis like a spiral staircase
Hydrogen bonding between the carbonyl of residue ‘n’ and the N-H residue of ‘n+4’
Hydrogen bonds help stabilise a-helix structure
What are the key properties of a-helix?
3.6 residues turn
Spiral is right handed (turns to the right)
Side chains point out from the helix axis - helps stabilise a-helix
Some residues are ‘helix breakers’ e.g. glycine and proline
Helix dipole exists +ve at N terminal, -ve at carbonyl terminal
What are helix wheels?
Structures that can help illustrate helix side chain arrangements
3.6 residues per turn, one full turn in 360 degrees
In an a-helix each amino acid side chain is separated by 100 degrees
What is the Beta-structure?
Stretches of residues with a more extended structure than the a-helix
Hydrogen bonding occurs between adjacent strands - stabilises
Adjacent chains can form B-sheet > two B-strands
Average strand length contains ~ 6 residues, may have up to 15
What are the properties of B-structures?
Extended, pleated, ‘B-pleated sheet’
Sheets not planar, pleated with R-handed twist
Side chains point above and below sheet
Any NP-P-NP-P stretch of residues commonly will form a B-strand due to the direction that the side chains point in
Key properties of turns
Needed to form globular proteins, involves 3 or 4 residues
High Gly, Pro content
Often have H-bond across width
Type I and II very common, more than 16 different types
Can turn sharply due to arrangement of Phi and Psi terminals
Why are glycine and proline high in content in turns?
Small chains make glycine very flexible - lots of conformational freedom
Proline is too rigid for helices but has built in turn because of the bonding between R-group and amino group
