L2 - Higher levels of protein structure Flashcards

1
Q

What is the next level of complexity after the secondary structure?

A

Super secondary structure or ‘motifs’

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2
Q

What is the super secondary structure or ‘motifs’?

A

These things are recognisable building blocks of proteins

They are stable subunits that fit together to form proteins

By understanding these, the variety of protein structures is not as great as once though – more tractable & understandable

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3
Q

What do motifs usually contain?

A

Motifs usually contain loops or turns
• Turns are short & defined by H bonds
• Loops are long & ill-defined

These nonregular secondary structures are not random or disordered
They are simply harder to describe

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4
Q

3 groups of loops/turns?

A

Beta-turn/bend

Omega loops

Disordered loops

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5
Q

Beta-turn/bend

A

Most often link beta-strands

Consist of 4 residues, 2 residues do not form H-bonds, 1 H-bond is formed per turn

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6
Q

Omega loops

A

Found in most large proteins

Is longer than a beta-turn but stable & functional

Compact globular entities which fill their internal empty spaces with side chains

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7
Q

Disordered loops

A

If it gets so big it becomes a disordered loop – we don’t understand the order

N & C termini plus internal linking secondary structure

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8
Q

Protein loops

A

Not defined by H bonding

Very variable & dependent upon local context & sequence

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9
Q

What are motifs?

A

Small definable elements of super secondary structure

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10
Q

4 examples of motifs

A

Anti-parallel beta-strand pair

Greek key

Helix bundle

Beta-alpha-beta motif

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11
Q

Anti-parallel beta-strand pair motif

A

A simple motif

Beta strands cannot exist by themselves

Has to have H bonds to stabilise it (in both directions)

H bonds are maintained by an antiparallel strand

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12
Q

Greek key motif

A

Sometimes the order of the beta strands isn’t always a simple meander – can be a Greek key motif

Is still antiparallel but it has a beta strand pair which has been inserted in-between the other 2

Due to the way it forms in 3-dimensional space

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13
Q

Helix bundle motif

A

The alpha helix is different to the beta structure as it folds by itself – doesn’t need to H bond to other alpha helices for stability

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14
Q

Beta-alpha-beta motif

A

The beta-alpha-beta motif is represented as 2 parallel strands with a helix in-between

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15
Q

What does super secondary structure tell us?

A

They tell us how bits of secondary structure are arranged in proteins relative to each other

There are defined ways in which secondary structure fit together – it is not random

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16
Q

How do secondary structures fit together?

A

They are quite limited & well defined with a limited number of interactions

17
Q

Why do beta sheets twist?

A

Because beta-sheets are formed from L-amino acids it has the effect of inducing a reproducible twist in the strands which then causes the whole sheet to bend

Can be as extreme as 30 degrees per residue in extended antiparallel beta-strand pairs

18
Q

How do beta-sheet twists affect folds?

A

Antiparallel = flat H bonds
Parrallel = less straight & weaker H bonds
Can be mixed together

Has a pronounced twist – propeller twist

Very few beta sheets are flat – most of them have some kind of twist

19
Q

Structure of thioredoxin in terms of beta sheets?

A

Thioredoxin is an essential protein which controls oxidation in the cell

It has a mixed anti-parallel & parallel beta sheet at its core which adopts a constant twist that looks like a propeller

20
Q

Do helix-helix interactions have limited angles?

A

Yes - alpha helices fit together in preferred conformations – not random

21
Q

What are the 3 conformations of helix-helix interactions?

A

Practically right angle (105 degrees)

Something in between (52 degrees)

23 degrees

22
Q

Conformation of helices in a 4 helix bundle

A

In a 4 helix bundle each alpha helix is about 23 degrees from each other – fit better together in this orientation

Makes life simpler for us – most helices fit in particular ways

Protein folds because they are stable molecules & these 3 ways are the most stable ways for the protein to fold

Restricts the variety

23
Q

Helix-strand interactions

A

The twist in the beta sheet can sometimes create a groove suitable for the side chains of the alpha helix to fit into

24
Q

What are motifs?

A

Motifs are small structures whose folding pattern is made up of simple & often recurring arrangements of secondary structure

Motifs are unlikely to exist alone & when added together form recognisable folds

25
What is a fold?
A fold is a complete structure able to exist either by itself or as part of a multi-domain protein Some proteins are made up of multiple different folds – these are called domains within a protein
26
Jelly (or Swiss) Roll Barrel
This is a fold as can sit by itself This is a beta barrel that isn’t just a meander – a complicated Greek key structure It is composed of lots of beta hairpins that fit together
27
What happens if a beta sheet folds around itself?
Beta-sheets can curl & form Beta-barrels Beta barrel is a fold
28
Beta rich structures can form large repetitive architectures such as:
- Sandwich - 3 Solenoid - 5 bladed propeller - Clam
29
Relationship between motifs and folds?
The same motifs can form different folds
30
Tertiary structure of proteins
Tertiary structure is composed of folds in which secondary structures are linked by turns, loops & disordered regions Larger proteins may appear to consist of 2 or more distinct folds thus referred to as domains of that protein
31
Hierarchy of protein structure
The hierarchy is defined by the rigidity of the peptide bonds & H bonds demands End up with either an alpha helix or a beta sheet as the secondary structure We then have a certain number of repetitive ways to fit them together to form motifs Can then see defined folds which either make up whole proteins or domains within proteins
32
What are domains?
A protein domain is a conserved part of a given protein sequence and tertiary structure that can evolve, function, and exist independently of the rest of the protein chain Function follows domains Helps us with evolution