Protein structure Flashcards
(37 cards)
Describe where you would expect to find polar and nonpolar amino acids in a folded globular protein.
- proteins are compact, there is no empty space inside a protein (in a folded, globular protein)
- polar side. chains (usually contain groups made of “O” and “N” are charged, can form hydrogen bonds) are exposed on the surface of the protein
- non-polar side chain (mostly composed of carbon, thw aliphatics, aromatics_ are buried in the protein (disulfide bonds are also in the core)
Describe were you would expect to find Gly and Pro in a folded protein.
- glycines always tend to occur in regions where the polypeptide is turning around, Gly has no side chains so is flexible
- Prolines also found in turns, Pro’s side-chain is fixed onto its backbone, has a restrictive geometry, can only be found in certain structures
List the overall features of folded proteins.
- proteins are compact: there tends to be no empty space inside proteins because of close packing of backbone & side chain atoms
- water is generally excluded from the interior of proteins
- nonpolar/hydrophobic side chains are usally located inside the protein
- Polar/hydrophilic side chains are usually located on the outside of the protein
Explain why protein folding is said to be cooperative.
- protein folding is co-operative (all-or-none)
- Transitions between two states occur (folded and unfolded)
- folded and unfolded states are in equilibrium
- protein folding is reversible
- generally, if any part of a protein is disrupted, interactions with the rest of the protein structure are disrupted and the remainder of the structure will be lost. Conditions that disrupt an part of the structure will lead to the whole protein unravelling.
Explain how Christian Anfinsen’s experiments showed that under appropriate conditions protein folding is reversible.
- native state, catalytically active
- addition of urea and mercaptoethanol
- unfolded state, inactive, disulphide cross-links reduced to yield Cys residues
- removal of urea and mercaptoethanol
- native, catalytically active state. Disulfide cross-links correctly re-formed.
Describe the role of disulfide bonds in protein folding.
- oxidation in the presence of urea gave ‘mixed’ disulphides (scrambled), only a small fraction would have the pairing correct (105 different ways to arrange 8 cysteines), only the correct pairing can stabilise the native structure
- adding a trace of BME reduces scrambled disulphides and then the protein can refold correctly
- under appropriate conditions protein folding/refolding is reversible
- protein folding is reversible (all the ‘info’ is in the sequence)
- disulphide bonds don’t direct folding
- folding directs disulphide bond formation
- disulphide bonds increase the relative stability of the folded state over the unfolded state
(lock on the correct folded state)
Describe how cellular conditions are not ‘ideal’ for protein folding.
- Although a polypeptide should be able to fold unassisted under “ideal” solution conditions
- conditions in the cell can make folding slow or impossible:
1. molecular crowding: cells are concentrated solutions of proteins, lipids, nucleic acids, carbs and so “inappropriate” interactions with other molecules can occur before the protein can even fold itself
2. Nascent polypeptide may misfold as it comes off the ribosome in translation. The polypeptide chain grows by sequential addition of amino acid residues to the C-terminal end of the chain. Misfolding may occur because the sequence is not complete.
Explain the role of protein folding chaperones in ‘protecting’ unfolded proteins from ‘misfolding’.
- Chaperones dont fold the protein - they help avoid misfolding
- they bind to partially folded or unfolded polypeptides and protect them from misfolding
- they bind to temporarily exposed hydrophobic regions preventing them from interacting with the wrong partners
List the forces drive protein folding and which chemical groups and amino acid type are involved in each interaction.
Explain the thermodynamic basis of the hydrophobic interaction.
List the different regions of a Ramachandran plot.
- The backbone conformation (determined by phi & psi angles) can be completely described in terms of a ramachandran plot:
- on the x-axis is the phi
- on the y-axis is the psi
- each dot represents one amino acid in the folded protein
- not all psi and phi pairings are equally probable; there’s definitive clusters
- if all phi/psi pairings were equally probable then the whole graph will be filled with dots evenly
The plot shows the distribution of phi and psi angles, specifically:
1. shows the common secondary structure elements
2. shows the presence of unusual backbone structure
Theoretical plot:
- white areas are where there is steric hindrance = disallowed region (residue not usually found there with those particular angle combinations)
- Blue regions are compatible with covalent geometry of a protein - where steric hindrance is lowest
- Dark blue regions are regular structures at those angles
Regions of the plot (left–>right & top–>bottom):
- beta region = beta sheets
- L region = left-handed turns
- alpha region = alpha helices
-D region = disallowed region
Note:
- not all residues in beta region are beta sheets and etc.
- all residues are subject to steric hindrance that favours the alpha, beta or L regions even if they are in irregular structures like random coils
SUMMARY:
- The ramachandran plot is a “quality control” report for the protein structure determination
- can estimate helical residues by counting turns
- can compare ribbon length between helices and strands
- in proteins, the only allowable (phi,psi) pairings are alpha, beta and L
- All protein structure is made up of residues with either alpha, beta or L (phi, psi) angles
- certain repeated (phi, psi) angles are stabilised by a repeating backbone-backbone hydrogen bonds
- these are the regular structures - two are very common - alpha helix and beta sheet
Describe how hydrogen bonding helps make proteins compact. Identify different hydrogen bonding interactions in a protein
- the atoms of a hydrogen bond can approach much closer than a VDW interaction due to covalent character of the hydrogen bond
- this increased the compactness and stability of a protein
> Different hydrogen interactions in a protein:
- Backbone-backbone
- Backbone-side-chain
-side-chain-side-chain
*Note-hydrogen bonds should always be described donor to acceptor
List the structural properties of alpha-helices
- any polar group buried in the protein must form a hydrogen bond - charged groups included although rarely present
- Hydrogen bonds - Alpha helix
1. Helix is right-handed
2. H bond between NH residue and C=O residue
3. All NH and C=O residues (except 4 at each end) form favourable “internal” H bonds
4. A macrodipole of an alpha helix arises because each peptide bond has a small dipole, and when all those dipoles line up in the helix, they add up into one large directional dipole — positive at the N-terminus and negative at the C-terminus.
> Sequence affects helix stability:
- not all polypeptide sequences adopt alpha helix structure
- small hydrophobic residues such as Ala and Leu are strong helix formers
- Glycine acts as a helix breaker cuz its tiny R group doesn’t contribute to helix stability
- Proline acts a helix breaker as it lacks NH hydrogen donor
- Attractive or repulsive interactions between side chains 3-4 amino acids apart will affect formation - so the helix will form if oppositely charged residues are 3-4 residues apart in sequence enabling salt bridge formation
🧂 Salt Bridge
Type: Non-covalent electrostatic interaction
Occurs Between:
- A positively charged side chain (e.g. Lys⁺ or Arg⁺)
- And a negatively charged side chain (e.g. Asp⁻ or Glu⁻)
Example:
Lysine (–NH₃⁺) interacting with Glutamate (–COO⁻)
🔗 Disulfide Bond (Bridge)
Type: Covalent bond
Occurs Between:
- Two cysteine residues’ side chains (–SH groups)
- Forms a –S–S– bond (oxidation reaction)
Example:
Cys–SH + HS–Cys → Cys–S–S–Cys
Explain why alpha-helices are often ‘amphipathic’.
Amphipathic character - have both hydrophobic and hydrophilic character but seperated on different faces of the helix (ever one of these helices have a hydrophobic face and hydrophilic face - shown on a helical wheel diagram)
Draw a simplified helical wheel diagram.Read amino acid sequences to identify heptad repeat patterns
Helical wheel = single helix, looking at residue orientation.
Heptad repeat = recurring 7-residue pattern, often in coiled-coil interactions between multiple helices.
Explain the difference between a beta-strand and a beta-sheet.
> a beta sheet consists of two or more beta-strands. the The strand is the element
- the planarity of peptide bond and tetrahedral geometry of alpha carbon create a pleated sheet-like structure
- sheet-like arrangement of backbone amides in different strands
- side chains protrude from sheet, alternating
> A beta strand is either parallel or antiparallel to neighbouring strands, sheets can be pure or mixed
- twisted sheets are abundant
- hydrogen bonds between NH and C=O of neighbouring strands:
–> antiparallel more stable, outer NH & C=O of a sheet are not hydrogen bonded
List the structural properties of beta-sheets.
- multiple consecutive regions in beta region of plot
- stabilised by hydrogen bonds between adjacent segments that may not be nearby in the sequence
- planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet like structure
- sheet-like arrangements of backbone amides in different strands
- side chains protude from the sheet and alternate
Explain how a beta-sheet can have hydrophilic and hydrophobic face.
Read amino acid sequences to identify alternating sequence patterns.
Draw a diagrams illustrating hydrogen bonding in antiparallel and parallel beta-sheets.
- In parallel B-sheets, the H-bonded strands run in the same direction
> H bonds between strands are bent (weaker) - In antiparallel B-sheets, the H-bonded runs in opposite directions
> H bonds = between strands are linear (stronger)
List the structural properties of reverse turns.
- turns occur frequently whenever strands in B-sheets change the direction
- 180 turn is accomplished over four amino acids
- the turn is stabilised by a hydrogen bond from a carbonyl oxygen of position 1 to aide hydrogen of position 4 in the turn (i and i+3)
proline in position 2 (i+1) or glycine in position 3 (i+2) are common in beta turns
> BETA TURN properties:
- beta-turns reverse direction of main chain
- abundant, mostly on surface, redirect backbone (particularly for beta-sheets)
- consist of 4 residues
- residues i+1 and i+2 have different angles
- a hydrogen bond between NH of the fourth (i+3) and carbonyl of the first stabilises the turn
- proline often in position i+1
Type 1 vs 2
🧠 Simple way to remember:
Type I: Common and “regular” - proline at second residue
Type II: Needs GLYCINE due to tight steric constraints at POSITION 3, proline at second residue too mostly
🔁 Quick tip:
To identify a β-turn in a sequence or structure:
Look for 4 residues forming a loop
See if there’s a hydrogen bond from the carbonyl of residue 1 to the amide of residue 4
Check the residue at position 3 → if it’s glycine, suspect Type II
Read amino acid sequences to identify where turns are likely.
Define regular and irregular structures.
- Beta sheets and alpha helices are abundant elements of regular secondary structures
- Regular structure is defined as residues that have repeating psi/phi angles
- Beta-turns are simple way of reversing the main chain, a hydrogen bond also stabilises them, each residue in the turn performs a different structural role and has different psi/phi angles (irregular)
- irregular structure often links regular elements and is termed “loop” or “random coil”
Identify regular and irregular structures from structural information.
🔁 What is a reverse turn?
A reverse turn (or β-turn) is a way for the protein backbone to make a sharp U-turn.
It involves 4 amino acids: we label them as i, i+1, i+2, i+3.
The turn allows the protein chain to fold back on itself compactly.
💡 What’s special about a Type II turn?
In Type II β-turns:
The i+2 residue needs to bend in a way that gives it a positive φ (phi) angle.
Most amino acids can’t do that easily, because it would cause their side chain to crash into the carbonyl oxygen of the i+1 residue.
