Structural Degrees Flashcards
Why do some side chains adopt non-staggered positions?
energy differences between each rotamer is small –> adopt if protein function requires it.
Give an example of each; hydrophobic mix, polar on onside and hydrophobic on other, all polar.
citrate synthase, alcohol dehydrogenase, troponin c.
Describe coils and loops.
still adhere to allowed phi and psis.
L = ordered but less regular - mainly short (up to ~22 residues) & rigid or flexible.
C = elongated, unstructured irregular regions.
what is a domain?
independent structural unit with well defined hydrophobic core. Formed by different combinations of secondary structural elements and motifs.
What is a motif?
local rearrangement of secondary structure –> optimises interactions but minimises steric clashing (grouping of elements of secondary structure).
give the numbers for ridges into grooves.
Ridges formed by side chains spaced three residues apart make an angle of 45 degrees with helical axis.
Ridges formed by side chains separated by 4 residues make angle of 25 degrees.
Inclination of -20 (i.e. 25-45) between two helices packs them together.
What determines crossing angles?
backbone of protein chain.
describe the armadillo motif and beta propeller.
A = many helix loop helices B = several 1,2,3,4 antiparallel beta sheets.
which form reads CORN clockwise?
L form.
