supersecondary structure

Question 1

how man unique ways of creating protein folds are there and why

Answer 1

1,200, only so many ways of permuting alpha helices and beta strands and domain sizes are limited to 250 AAs
typical alpha helix is 10-20AAs

typical beta strand is 10AAs, so at most 25 secondary structures in a domain

Question 2

what are the common motifs

Answer 2

alpha motif
beta hairpin
greek key
beta-alpha beta

Question 3

describe alpha motif

Answer 3

helix-turn-helix motif
tightly joined alpha motifs common in DNA binding proteins
loosely joined alpha motifs common in calcium binding proteins

Question 4

what is an EF hand motif

Answer 4

loosely joined alpha motif
if you hold your right hand with palm facing towards you and stick your index finger and thumb out the index finger represents helix E and your thumb represents helix F, calcium would bind underneath your middle finger

Question 5

what is a beta hairpin

Answer 5

2 anti parallel beta strands connected by a turn

Question 6

what is a greek key

Answer 6

2 beta turns connected to eachother with one turned back on itself (4 antiparallel strands, 4 is connected to 1 which is connected to 2 which is connected to 3), end in C terminus on strand which is turned back on itself

Question 7

why are greek keys so common

Answer 7

24 ways of combining 2 beta hairpins, only 8 are observed, 2 of which are greek keys

Question 8

what is a beta alpha beta motif

Answer 8

a way of connecting parallel beta strands, strand then turn then helix then turn then strand

2 possible conformations;

right handed where alpha helix is close to the strand which it is connected to by C terminus

left handed helix is closer to strand which is connected to by N terminus

only right handed strands are observed

Question 9

what do lots of beta-alpha-beta-alpha motifs create

Answer 9

beta barrel/ TIM barrel

Question 10

what are the different classes of protein folds

Answer 10

all alpha class (helix to helix fold)

alpha/beta class (parallel beta strands with beta-alpha beta motifs)

beta class (anti parallel beta strands)

alpha+beta class (minor class containing discrete beta and alpha subdomains)

small domains held together by multiple disulphide bonds or metal ions

unstructured (not all parts of proteins are ordered)

collagen triple helices

Question 11

what are the different kinds of alpha class folds

Answer 11

anti parallel
antiparallel pair of two parallel
27 helices in double layer (used to design new drugs)

Question 12

what are different formations of alpha/beta protein fold

Answer 12

either
TIM(triose phosphate isomerase) barrel where alpha and beta alternate

or Rossman (open twisted) where one end of the alpha beta alternations is not alternating and one of the ends connects to somewhere in the middle via alpha-alpha or beta-beta motif