Modular Structure of Proteins Flashcards
What is a protein sequence motif?
Simple secondary structures combine to form structural motifs or larger functional domains ( different from sequence motifs)
A protein sequence motif is a pattern of amino acids that are found in related genes or proteins
C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H a zinc finger sequence motif
What do motifs and domains refer to?
Motifs and domains are an independent order of structure
These can be identified within the overall tertiary or quaternary structure
They are an independent order of structure
Such units of protein structure are commonly found and are conserved across functionally related proteins but may not be related in sequence
What are the definitions of motifs?
A simple definition of a motif is a minimum arrangement of independently forming secondary structures combining recognisable folds across many different protein
OR
A combination of two or more secondary structures to form a recognisable localised folded arrangement of structure
What are domains?
Domains are functional units
Motifs are organised or combined into larger structural and functional domains
The difference between a motif and a domain is sometimes blurred
But domains more clearly define a functional unit than a motif but both are evolutionarily conserved and are modular in nature, for example, functional domains can often be found in exons
However, a domain can be defined as a more complex structure at the tertiary or quaternary level, often involving interaction between distant parts of a protein or motifs
A functional domain is typically larger and may or may not be a contagious segment of a single polypeptide chain
How many proteins motif are there and how are they linked?
Around 1400-1500 different structural motifs exist
They are recognisable in many different and unrelated proteins but confer functional properties with a few exceptions
A beta-alpha-beta(4)-alpha motif but that appears repeated twice within a TATA-binding protein each in opposite directions
What are some examples of common motifs
EF-hand-Ca2+ binding e.g. Calmodulin & Troponin-C resembles a helix turn helix but combines with a metal ion such as calcium
Greek Key motif consists of antiparallel beta-strands forming a beta-sheet but is one motif that is so common it isn’t generally associated with a specific function
Beta barrel-beta strands wrapped around to form a circular tunnel
Parallel strands of a beta-sheet interlinked with an alpha helix to form a beta-alpha-beta motif
What are DNA binding motifs? What are some examples?
DNA binding motifs- helices can be inserted into the major groove of DNA in a sequence specific manner
Helix loop helix- e.g. Max & Mad also Ca2+ binding
Helix turn helix- e.g. Cro, tryptophan & lac repressors
Leucine Zipper- e.g. GCN4
Zinc finger- e.g. hormone receptors
What are structural and functional domains?
One functional domain easily understood is represented in e.g. membrane-bound receptors
These come in several forms most commonly as bundles
Bundle of alpha-helices or less commonly lone helices or bundle of beta-sheets
The 7-transmembrane arrangement of alpha-helices is common
Found in rhodopsin, TSHr, many pharmacological receptors and also receptors for some polypeptide hormones
How are domains recycled?
Individual domains can be found in different proteins
Domain shuffling in the genome results in modular units of function being conserved but shuffled between genes
Mammalian phospholipase C contains 4 different recognisable domains
Each of these is found individually in other proteins
How are motifs related to transcription factors?
Proteins that bind to DNA and regulate transcription
There are many different transcription factors but they each contain a small number of conserved motifs which combine to form domains that interact with DNA
These motifs are conserved across all phyla (i.e. huge variety of eukaryotes and prokaryotes, ranging from bacteria and fungi to plants and animals)
These motifs form DNA binding domains that allow the regulatory function of their respective proteins
Why are alpha helices important in DNA binding?
An alpha helix can fit within the major groove of DNA- comprising the “recognition’ helix
The amino acid sequence of a DNA binding motif provides specificity
Different DNA binding domains & motifs present the binding helix using different arrangements of the structural motif
Describe the motif helix-loop-helix
Binds DNA only in the dimeric form
Exists as hetero (different monomers) and homodimers (identical monomers)
The central portion is made from overlapping helices that form a structure enabling 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
Describe the leucine zipper motif
This motif is formed from 2 contagious 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 below is cFos partnered with cJun
Describe the helix-turn-helix
Although the name suggests some similarity to the leucine zipper and helix-loop-helix motifs, the structural appearance of this motif is 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 eukaryotic DNA binding proteins e.g. CRO repressor and 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
Describe the 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
Mineralocorticoid
Oestrogen
Progesterone
Vitamin D receptors
