Proteins - Lecture Five Flashcards
Elements of Protein Structure
Primary structure
Amino acid sequence of a protein
Secondary structure
3D arrangement of a protein chain over a short stretch of adjacent amino acid residues
Alpha helix and beta-strands/sheet
Tertiary structure
3D structure of a complete protein chain
Quaternary structure
Interchain packing and structure for a protein that contains multiple protein chains
Why are proteins mostly globular?
So the main chain has a double back to form a more compact shape
What are the main chain atoms in a protein
Carbon, nitrogen and calcium
Phi angle
Rotation angle around the N-Ca bond
Psi angle
Rotation angle around the Ca-C’ bond
Phi angle restriction
Can lead to O-O collisions
Psi angle restriction
Can lead to NH-NH collisions
Steric hinderance in Phi-Psi restrictions
Between the hydrogen on the amide nitrogen and the carbonyl oxygen
Alpha Helix key properties
3.6 residue/turn, 5.4Å/turn
Spiral is right handed
Side chains point out from the helix axis
Dipole
Phi angle (Φ) = ~57˚
Psi angle (ψ) = ~47˚
Some residues are ‘helix breakers’ e.g. glycine and proline
Beta structure
Involves adjacent peptide chains, called beta strands, that have an extended standard that allows for hydrogen bonding between chains
One beta-sheet =
Two beta-strand
Average beta-strand length
~6 amino acid residues and can have up to 15 residues
What can NP-P-NP-P stretch of residues form?
B-strand
Beta-structure in silk
-Gly-Ser-Gly-Ala-Gly-Ala
Turns key properties
Hairpin-like and usually involves 3 or 4 residues High in Gly and Pro content Almost 30% residues involved in turns Hydrogen bond across the turn is common More than 16 types of turns Type I and II are common
Why can proteins be challenging to display?
Lots of atoms Detailed internal cavities Complicated shapes All elements of protein structure Alpha-helix, B-strands, turns and loops
Space-filling models of protein
Good for overall shape but can’t see inside and can’t see elements of structure
Protein structure shorthand
Helices shown as spirals (or cylinders)
Strands shown as arrows, posing from N to C
Turns and random coil shown as loops and rope-like stretches. Random coil is a stretch of protein structure that does not fit in any of the standard groups
Protein structure shorthand advantages
Easily visualise the main chain path of proteins
Identify elements of secondary structure
Allows an appreciation of proteins a 3D objects
Allows comparison to other proteins
