modular structure of proteins

Question 1

describe the relationship between different structural levels of protein

Answer 1

Protein folding of primary structure produces secondary structures eg alpha helices and beta sheets & beta turns
•Secondary structure fold to produce tertiary structures
•and tertiary structures combine to form quaternary structures

Question 2

what does comparison of proteins tell us?

Answer 2

A comparison of proteins tells us thare are similar structures found in unrelated proteins- providing evidence of the parallel evolution and solutions to functional needs.

This in itself tells us that
There are other ways to think about structure other than simply the hierarchical of folding of primary, secondary structures, tertiary to quaternary structure

Question 3

give one way the formation of structure can occur

Answer 3

• One way the formation of structure can occur is a series of folds which occur.
• The combination of which leads to a specific structure. this sequence is sometimes described as a fold or folds. Combining structure through folds result in recognisable arrangements that can be observed in many proteins to form motifs. These may contribute to the formation of larger and more complex structures that have specific functions. These are called functional domains

Question 4

what can simple secondary structures ( folds) combine to form ?

Answer 4

structural motifs and larger functional domains

Question 5

what is a protein sequence motif

Answer 5

• A Protein Sequence motif is a pattern of amino acids that are found in related genes or proteins

Question 6

what is the difference between a sequence motif and structural motif?

Answer 6

• A sequence motif is a sequence of amino acids that may be conserved in related proteins but is quite different from a structural motif, where the structure may be similar but the underlying sequence of amino acids are entirely different.

Question 7

outline the characteristics of motifs and domains

Answer 7

Motifs and Domains are an independent order of structure
These can be identified within the overall tertiary or quaternary structure, and so are a feature of higher order structure.
They are an independent order of structure different from primary, secondary, tertiary and quaternary
A characteristic of Such units of protein structure are commonly found and are conserved across functionally related proteins but may not be related in sequence, nor a direct evolutionary pathway.

Question 8

define motif

Answer 8

combining secondary structures
• A simple definition of a motif is a minimum arrangement of independently forming secondary structures combining recognisable folds (arrangements) across many different proteins or…
• A combination of two or more secondary structures to form a recognisable localised folded arrangement of structure

Question 9

compare motifs and domains

Answer 9

• Motifs are organised or combined into larger structural and functional domains; such structures may also be called superstructures.
• 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. whilst they are both subject to evolutionary pressure they have evolved through different means and sometimes different selection pressures.
• Because both motifs and functional domains are coded ultimately by segments of our genes they are modular in nature and relate back to a heritable unit of genetic structure for example functional domains often but not always relate to a single exon within a gene

Question 10

define domain

Answer 10

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 contiguous segments of a single polypeptide chain
• a protein would comprise of multiple modular domains each with a different function for example SRC (pronounced SARK) kinase would have multiple domains, both kinase and regulatory domains each with different functions, the SH4 domain is unique to but the others are modular units combined elsewhere in different proteins

Question 11

what is a minimum arrangement of secondary structure combining folds & is a small structural unit that can be recognized in a variety of proteins.

Answer 11

motif

Question 12

what is a generally more complex structure that has a tertiary or quaternary structure of its own?

Answer 12

domain

Question 13

recall the concept of a protein motif

Answer 13

confer functional properties to the proteins they are found within, with a few exceptions
In some cases these are very narrowly defined for example some motifs relating to binding to nucleic acids such as a zinc fingers are quite distinct whilst some others confer relatively broad properties that contribute to a wide range of properties that are found in many functionally different proteins

Question 14

give examples common protein motifs

Answer 14

EF hand, Greek key, beta barrel and beta-alpha-beta

Question 15

describe the EF hand

Answer 15

The EF hand is a calcium binding motif found in for example in Calmodulin & Troponin-C , it resembles a helix turn helix but it combines with a metal ion in this case calcium shown as a green ball. There are 2 EF hands at either end of an alpha helix going into the page and away from us.
Calmodulin is part of the mechanism for sensing intracellular calcium levels and calcium binding to the EF hand results in a conformational change in the protein.

Question 16

describe the Greek key

Answer 16

Greek Key motif consists of a specific arrangement of beta strands within an antiparallel beta sheet but is one motif that is so common it isn’t generally associated with a specific function.

Question 17

describe the beta barrel motif

Answer 17

A beta barrel is an arrangement of beta strands rapped around to form a circular tunnel that looks somewhat like a wicker basket, the two images show it from the side and top, a similar structure to this is an alpha/beta barrel which is also surrounded

Question 18

describe the beta-alpha-beta motif

Answer 18

Parallel strands of a beta sheet are interlinked with an alpha helix to form a beta-alpha-beta motif.

Question 19

define DNA binding motifs

Answer 19

DNA binding motifs – helices can be inserted into the major groove of DNA in a sequence specific manner
Most DNA binding motifs –have one feature in common they are arranged to recognise specific sequences of bases.

Question 20

give 4 examples of motifs that have alpha helices inserted into the major groove of the DNA in a sequence specific manner

Answer 20

• Helix loop helix –e.g Max & Mad also but are also associated with Ca2+ binding
• Helix turn helix –e.g the Cro, tryptophan, & lac repressors
• The Leucine Zipper – e.g GCN4, a yeast transcription factor
• And fourth the Zinc Finger –e.g hormone receptors

Question 21

Membrane bound receptors are ?

Answer 21

functional domains.

these come in several forms but most commonly as Bundles of alpha helices or less commonly, lone helices or a bundle of beta sheets
they have the specific function of anchoring the protein in the membrane
The 7-transmembrane domain arrangement of alpha helices is common
found in rhodopsin, TSHr, many pharmacological receptors and also receptors for some polypeptide hormones

Question 22

what does domain shuffling result in ?

Answer 22

• Domain shuffling in the genome results in modular units of function being conserved but shuffled between genes

Question 23

give an example of where domain shuffling has occured.

Answer 23

• Mammalian phospholipase C contains 4 different recognisable domains.
• Each of these is found individually in other proteins troponin C, bacterial phospholipase C etc
• Since each of these are linked to a segment of the gene, Domain shuffling in the genome results in modular units of function being conserved but exchanged between genes

Question 24

describe the globin domain

Answer 24

Each chain of haemoglobin has a tertiary structure very similar to that of the single myoglobin chain, strongly suggesting evolution from a common ancestral oxygen-binding polypeptide

Question 25

what do transcription factors contain ?

Answer 25

• There are many different transcription factors but they each contain a small number of conserved motifs such as the helix turn helix etc, and other parts of the protein or other monomers.
• These combine to form domains that have specific functions such as DNA binding, dimerization and other regulatory functions
• These motifs are conserved across all phyla (ie huge variety of eukaryotes & prokaryotes, ranging from bacteria & fungi to plants and animals)
- These motifs form DNA binding domains that allow the regulatory function of their respective proteins

Question 26

which structure is important in DNA binding and why?

Answer 26

An alpha helix !! because it can fit within the major groove of DNA , this structure forms specific contacts with the DNA bases and is referred to as the “recognition” helix
The amino acid sequence of a DNA binding motif provides specificity - it is rich in basic amino acids like arginine and lysine
Different DNA binding domains & motifs present the binding helix using different arrangements of the structural motif:

• Helix loop helix – eg Max & Mad
• Helix turn helix –eg Cro repressor
• Leucine Zipper – eg cFos & cJun
• Zinc Finger – DNA binding motif containing zinc eg steroid receptors

Question 27

describe the helix-loop-helix motif

Answer 27

Binds DNA only in the dimeric form
Exists as hetero (different monomers) and homodimers (identical monomers) , this is a key characteristic of the regulatory transcription factors and their ability to combine in different forms allow different dimers to regulate different genes as a consequence of each monomer that comprises the dimer recognising a different sequence in the DNA
The central portion of the HTH is made from overlapping helices that form a structure enabling dimerisation , this dimerization domain forms a structure that resembles a twisted rope. Binding the two together.
The terminal part of the lower opposing helices contains basic amino acids that interact with the major groove of the DNA – giving rise to the b/HLH functional domain. The central part hold the recognition helices in place.
Examples include mad, max, myc, myoD some of which you’ll recognise as master gene regulators.

Question 28

leucine zipper motif

Answer 28

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. Since they are basic, they repel each other, opening the terminal ends and interact with the DNA major groove of the negatively charged DNA.
Heterodimerisation similarly expands the regulatory potential of leucine zippers the example on the right is cFos partnered with cJun

Question 29

describe the helix-turn-helix motif

Answer 29

Although the name suggests some similarity to the leucine zipper and Helix-loop-helix motifs the structural appearance of this motif quite different
It Consists of:
• two short helices orientated at right angles to each other & connected by a “turn” but this is not a beta turn
The motif is found in both prokaryotic and eukarotic DNA binding proteins eg CRO repressor, & homeobox proteins
CRO and Lambda are homodimers, CRO therefore recognises a palindromic sequence and by binding DNA represses transcription
Only the recognition helix interacts with the nucleotide sequence itself but other parts of the protein combines to form with the motif to form the DNA binding domain and like other DNA binding motifs the helix turn helix locates the recognition helix within the major groove

Question 30

describe the zinc finger motif

Answer 30

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. As with the others different parts of the dimer contribute to the DNA binding domain in addition to each of the motifs, whilst other parts of the dimer form different functional domains allowing regulation of transcription
Of note among the proteins that have zinc fingers include many of the hormone receptors such as
• Glucocorticoid, Mineralcorticoid oestrogen, progesterone, as well as Vit D receptors