The 3D Structure of Proteins Flashcards
What is the folding of a polypeptide determined by?
- The amino acid sequence.
- The molecular structure and properties of its amino acids.
- The molecular environment (solvent and salts).
Why is the peptide bond important?
- The peptide bond is a flat planar structure that has a fixed arrangement.
- Rotation about the carbon-nitrogen bond in the peptide link is restricted.
- This has a huge influence on the shape and structure of proteins, which in turn determine how they behave.
What do polypeptides adopt a structure based on?
Polypeptides adopt a structure based on energy minimisation.
- Each molecular structure has a specific energy state.
- The minimisation of this energetic state (the free energy of a molecule “G”) determines the most favourable conformation.
- The change in free energy upon folding is called ∆G.
- If change in free energy is positive that means it will not spontaneously fold and it will need an imput of energy from some other source or it will be maintained in that conformation.
What is the free energy of any conformation affected by?
It’s affected by the molecular environment :-
- Aqueous or lipid membrane.
- Other proteins or molecules (that the protein is interacting with), including salts and their ionic state.
- Changes in this environment can induce further conformational change (eg. a receptor binding to a ligand).
What two categories do the forces that determine the folding of a protein fall into?
- They fall into two categories: COVALENT and NON-COVALENT bonds.
- Weak, non-covalent bonds have 1/20th the strength of covalent bonds.
- However, their overall contribution is significant because the number of non-covalent bonds is far larger than covalent bonds.
List the four categories that non-covalent bonds fall into.
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CHARGED OR ELECTROSTATIC ATTRACTIONS:
* Falls off exponentially as distance increases, is affected by electrostatic environment (aqueous environment). -
HYDROGEN BONDS:
* transient non-covalent bonds. - VAN DER WAALS ATTRACTIONS - DIPOLE:
- These weak forces occur between two atoms in non-covalent interactions.
- They’re determined by their fluctuating charge, and are induced by the proximity of the molecules.
- The attraction at a close distance is balanced by the repulsion due to the proximity that is determined by the Van der Waals radius of an atom.
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HYDROPHOBIC INTERACTIONS:
* Hydrophobic interactions minimise disruption of water network.
Transient meaning - lasting only for a short time; impermanent.
Describe disulphide bonds, an example of covalent bonds.
- Disulfide bonds form between the side chains of two cysteine residues.
- The bonds form in an oxidative reaction forming very strong covalent bonds.
- The SH (sulfhydryl) groups from each cysteine cross link.
- This usually occurs in distant parts of the amino acid sequence, but occurs adjacently in the three-dimensional structure.
- Disulfide bonds can form on the same (intra-chain) or different (inter-chain) polypeptide chains (eg. insulin left).
Describe the orientation of amino acid side-chains in α helices and β sheets.
- Hydrogen bonding occurs between the carbonyl and amide groups of the polypeptide backbone.
- The variable side chains protrude outwards from both molecules (providing the properties of the helix or sheet), the helical α helix and the planar β sheet and participate in folding of the secondary structure.
Give an example of a tertiary structure.
The seven transmembrane domain of the thyroid stimulating hormone receptor.
Give an example of a quaternary structure.
The combining of the four chains of haemoglobin, comprising of 2 α and 2 β chains.
What happens to the protein in protein misfolding?
- Firstly, the function of the misfolded protein is almost always lost.
- Secondly, misfolded proteins often have a tendency to self-associate and form aggregates (eg. Huntington’s, Alzheimer’s, Parkinson’s disease, etc.)
- Other misfolded proteins result in cellular processing that lead to their degradation.
How does protein misfolding occur?
- Somatic mutations in the gene sequence leading to the production of a protein unable to adopt the native folding.
- Errors in transcription or translation leading to the production of modified proteins unable to properly fold.
- Failure of the folding machinery.
- Mistakes of the post-translational modifications or in trafficking of proteins.
- Structural modification produced by environmental changes.
- Induction protein misfolding by seeding and cross-seeding by other proteins.
Somatic cells meaning - all body cells of an organism apart from the sperm and egg cells.
Describe the protein misfolding in Alzheimer’s disease.
- In Alzheimer’s disease, the proteolytic cleavage of Amyloid Precursor Protein (APP) is observed.
- APP has multiple functions but is involved in G-protein signalling.
- In alzheimers there is a cleavage of APP at 40 residue to form a protein called β-amyloid.
- In a normal molecule the APP anchors the protein in the membrane (green part) and the APP accumulates and mis-folds to form beta sheets.
- In alzheimers disease the β-Amyloid (Aβ) accumulates.
- Miss folding of this protein results in a planar arrangement and polymerisation.
- This can form fibrils of mis-folded protein (amyloid fibrils).
- β-Amyloid (Aβ) fibres are formed from stacked beta sheets in which the side chains interdigitate.
Proteolysis meaning - It is the breakdown of proteins into smaller polypeptides or amino acids.
Amyloid precursor protein - It is an integral membrane protein expressed in many tissues and concentrated in the synapses of neurons. Its primary function is not known, though it has been implicated as a regulator of synapse formation, neural plasticity and iron export.
Fibrils meaning - Any of various threadlike fibers or filaments that are constituent parts of a cell or larger structure.
Describe the protein misfolding in Cystic Fibrosis.
- In Cystic Fibrosis, the most common mutation is a deletion of Phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regulator (CFTR) .
- This ΔF508del leads to the misfolding of the protein whilst it is still in the ER.
- This is recognised by the cellular machinery that identifies and processes misfolded protein.
- This results in ubiquitination, trafficking of the misfolded protein to the proteasome and degradation.
Ubiquitination meaning - The addition of ubiquitin to a substrate protein is called ubiquitination or less frequently ubiquitylation. Ubiquitination affects proteins in many ways: it can mark them for degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein interactions.
Describe infectious proteins.
- Prions are misfolded proteins (PrPSC) that interact with other normal proteins (PrPC).
- Through this interaction, they induce misfolding of the normal protein and polymerisation Oligomers form fibrils of misfolded protein.
- This process is reliant upon the concept of energy minimisation, ∆G.
- It is a dynamic process brought about by the interaction of molecules, resulting in a more stable, aggregated structure.
Prions meaning - an infectious protein particle similar to a virus but lacking nucleic acid; thought to be the agent responsible for scrapie and other degenerative diseases of the nervous system.
