Modular Protein Structure Flashcards
What is some evidence for parallel evolution (relating to proteins?)
A comparison of unrelated proteins with a similar structure
What is a protein sequence motif?
A pattern of amino acids that are found in related genes or proteins
What is a protein structure motif?
The structure of protein found in similar genes or proteins that don’t have similar primary structures
Where are motifs and domains commonly found?
Across functionally related proteins but may not be sequentially related?
What is a motif
Minimum arrangement Of independently forming secondary structures combining recognisable folds (arrangements) across many different proteins
What is a domain?
A more complex structure at the tertiary or quaternary level, often involving interaction between distant parts of a protein or motif
Both domains and motifs are what in nature?
Modular
What do domains often relate to?
A specific exon in a gene
How many different structural motifs exist?
1400-1500
What is an ef hand?
Ca2+ binding motif resembles a helix turn helix but combines with a metal ion.
Give two examples of ca2+ binding motifs
Calmodulin and troponin-C
What is calmodulin?
Part of a mechanism for sensing cellular calcium leads
What does the Greek key motif consist of?
Antiparallel beta strands forming a beta sheet
Why is the Greek key motif important?
It is such a common motif that isnt generally associated with a specific function
What is the beta- alpha- beta motif
Parallel strands of a beta sheet interlinked with an alpha helix. Beta strands are connected to an alpha strand which sits on top of the betas
What’s a beta barrel?
Beta strands wrapped around to form a circular tunnel
What is a DNA binding motif?
Helices inserted into the major groove of DNA in a sequence specific manner. Arranged to recognise specific DNA sequences
Give some examples of helix loop helix
Max and mad and ca2+ binding
Give some examples of helix turn helix
Cro, tryptophan and lac repressors
Give some examples of a leucine zipper
GCN4
Give some examples of a zinc finger
Hormone receptors
Give the most common example of a form of membrane bound receptors
Bundles of alpha helices
What is the most common arrangement of alpha helices in membrane bound receptors?
7-transmembrane arrangement
Where is the 7-transmembrane arrangement of alpha helices found?
Rhodopsin, TSHr pharmacological receptors and some polypeptide hormone receptors
What are the membrane bound receptor domains called in the extracellular region?
Ligand binding domain
Where are the membrane bound receptor domains in the transmembrane region?
Domain embedded in the lipid bilayer
What does genome shuffling in the genome cause?
Modular units of function being conserved but shuttled between genes
What are the four different genes founds in mammalian phospholipids C?
Troponin C
Bacterial phospholipase C
Synaptotagmin
Recoverin
How are myoglobin and haemoglobin similar and why?
Both have a tertiary structure, which suggests evolution from a common ancestral O2 binding polypeptide
What are transcription factors?
Proteins that bind to DNA and regulate transcription
What does each transcription factor contain a small number of?
Conserved motifs that combine to form domains that interact with the DNA
Are motifs different across phyla?
No, all conserved
What do DNA binding domains do?
Allow the regulatory function of their respective proteins
What is a recognition helix?
When an alpha helix fits inside the major groove of DNA
What does the amino acid sequence of a DNA binding motif provide?
Specificity
The helix-loop-helix motif only binds DNA in what form?
Dimeric
What are the two names for the dimers of the helix - loop - helix motif?
Heterodimer and homodimer
What is a homodimer?
Identical monomers
What is a heterodimer?
Different monomers
What is the central portion of the helix-loop-helix motif made from?
Overlapping helices that form a structure enabling dimerisation
What does the terminal part of the Lower opposing helices contain in the helix-loop-helix motif?
Basic amino acids that interact with the major groove of DNA- giving rise to the b/HLH functional domain
Give some examples of a helix-loop-helix motif
MAD, MAX, MYC, MYOD
What is the leucine zipper motif formed from?
2 contiguous alpha helices
What type of protein is the leucine zipper motif?
Dimeric
What do the dimers in the top stalk zip together to form?
A short coiled coil
How is the coil held together?
By hydrophobic interactions down opposing sides of the helix
What type of amino acids dominate the lower part of the helix
Basic
What does heterodimerisation do in the leucine zipper motif?
It expands with the regulatory potential of leucine zippers
What does the helix-turn-helix motif consist of?
Two short helices oriented at right angles to train each other - connected by a turn
Where is the helix-turn-helix found?
In both prokaryotic and eukaryotic DNA binding proteins
Give some examples of where the helix-turn-helix motif is found
CRO repressor and homeobox proteins
What is the CRO protein?
Homodimer
What does the CRO repressor do?
Recognises palindromic sequence and by binding DNA represses transcription
What is the zinc finger motif comprised of?
Alpha helix and beta sheet held together by non-covalent interactions with zinc
What does the alpha helix of each motif do with DNA in the zinc finger motif?
Knots with the major groove of the DNA and recognises specific DNA sequence
What hormones may have the zinc finger motifs in?
Glucorticoid
Mineral corticoid
Progesterone
Vitamin D
