Modular Structure of Proteins Flashcards
When does the free energy of any conformation change?
The free energy of any conformation is affected by the molecular environment:
- Aqueous or lipid membrane.
- Other proteins or molecules including salts.
- Changes in this environment can induce a further conformational change -for example a receptor binding a ligand.
What determines the most favourable conformation of polypeptides?
Each molecular structure has a specific energetic state
The minimisation of this energetic state (the free energy of a molecule “G”)
the change in free energy upon folding is called ∆G
What is a motif?
-A combination of two or more secondary structures to form a recognisable folded arrangement, that appears across many different proteins.
What is a domain?
A combination of motifs that come together to carry out a function. A more complex structure at the tertiary or quaternary level, often involving interaction between distant parts of a protein or motifs.
4 examples of motif
- EF hand - Ca2+ binding - Found in Troposin C & Calmodulin
- Greek Key - Series of antiparallel beta strands
- Beta barrel - beta strands wrapped around to form circular tunnel
- Beta-alpha-beta motif - 2 betas and alpha in the middle.
DNA binding motifs
helices can be inserted into the major groove of DNA in a sequence specific manner
4 DNA binding motifs
- Helix loop helix – eg Max & Mad also Ca2+ binding
- Helix turn helix –eg Cro, tryptophan, & lac repressors
- Leucine Zipper – eg GCN4
- Zinc Finger – eg hormone receptors
What does domain shuffling result in?
Domain shuffling in the genome results in modular units of function being conserved
Where do alpha helices fit?
Alpha helices can fit within the major groove of DNA
How is specificity achieved in DNA binding motif?
The amino acid sequence of a DNA binding motif provides specificity
Helix-loop-helix motif
Binds DNA only in the dimeric form
Exists as a hetero (different monomers) and homodimers (identical monomers)
The central portion formed from overlaping helices form a structure that enables dimerisation
The terminal part of the lower opposing helices contain basic amino acids that interact with the major groove of the DNA – giving rise to the b/HLH functional domain
Examples include mad, max, myc, myoD
Leucine zipper motif
This motif is formed from 2 contiguous alpha helices and like the HLH, is a dimeric protein formed from two polypeptide chains
The dimers “zip” together in the top “stalk” to form a short “coiled-coil”
The coil is held together by hydrophobic interactions down opposing sides of the helix
As in the b/HLH basic amino acids dominate the lower part of the helix (forming a motif) and interact with the DNA major groove
Heterodimerisation expands the regulatory potential of leucine zippers the example right is cFos partnered with cJun
Helix-turn-helix motif
Although the name suggests some similarity to the leucine zipper and Helix-loop-helix motifs the structural appearance of this motif quite different
Consists of:
two short helices orientated at right angles to each other & connected by a “turn”
The motif is found in both prokaryotic and eukarotic DNA binding proteins eg CRO repressor, & homeobox proteins
The CRO protein is a homodimer
CRO recognises palindromic sequence and by binding DNA represses transcription
Only the recognition helix interacts with the nucleotide sequence itself and like other DNA binding motifs it locates within the major groove
Zinc finger motif
This motif is an alpha helix and a beta sheet held together by non-covalent interactions with zinc
The diagram shows a dimer with 2 motifs on separate polypeptide chains each containing two zinc atoms stabilising the recognition helix and loop structure
The alpha helix of each motif interacts with the major groove of DNA and recognises a specific DNA sequence
Of note among the proteins that have zinc fingers include many of the hormone receptors such as
Glucocorticoid, Mineralcorticoid oestrogen, progesterone, Vit D receptors.
