modular structure of proteins Flashcards
(28 cards)
what’s evolutionarily significant about motifs and domains
commonly found and conserved across functionally related proteins
what is a motif
minimum arrangement of independently forming secondary structures combining recognisable folds/arrangements across many different proteins
what’s a domain
more complex structure, at the 3* or 4* level, often involving interaction between distant motifs on separate chains
what does an EF hand motif do
Ca2+ binding e.g. calmodulin and troponin C
what does a DNA binding motif do
helices can be inserted into the major groove of DNA in a sequence specific manner
where can a helix loop helix motif be found
Max, Mad, Ca2+ binding
where can a helix turn helix be found
Cro, trypt, lac repressors
where can you find a leucine zipper
GCN4
where are there zinc fingers
hormone receptors
what shape is a greek motif
antiparallel beta strands - so common that it’s not associated with a specific function
the domain represented in membrane bound receptors is the most easily understood functional domain - give an example
7 transmembrane arrangement of alpha helices in a G protein coupled receptor
where can you find a 7 TM arrangement of alpha helices
rhodopsin, TSHr, many pharmacological receptors, and also receptors for some polypeptide hormones
how many domains in PLC
4 - each found individually in other proteins eg troponin C, bacterial PLC, recoverin, synaptotagmin
Hb and myoglobin chains have a similar 3* structure - what does that suggest?
common ancestral O2 - binding polypeptide
why are alpha helices important in DNA binding
can fit within DNA major groove - AA sequence of a DNA binding motif provides specificity
what’s important about how the helix loop helix motif binds DNA
only binds DNA in the dimeric form, but can be hetero or homodimers
describe the structure of a helix loop helix motif
central portion formed from overlapping helices forms structure that enables dimerisation
the terminal part of the lower opposing helices contain basic AAs that interact w/ the major DNA groove, giving rise to a b/HLH domain
what is a leucine zipper motif formed from
2 contiguous alpha helices - it’a a dimeric protein formed from 2 pp chains
how do the dimers that make up a leucine zipper polymerise
dimers zip together in the top ‘stalk’ to form a short coiled coil
what holds together the coil in a leucine zipper
hydrophobic interactions down opposing sides of the helix
how is the regulatory potential of leucine zippers increased
heterdimerisation
how is a helix turn helix motif structured
consists of 2 short helices orientated at right angles to each other and connected by a turn
where is ‘helix turn helix’ found
pro and eu DNA binding proteins eg CRO repressor and homeobox proteins
what does the CRO protein do
homodimer that recognises palindromic sequences and represses transcription by binding DNA.
