W4 3D structure of proteins Flashcards
Folding of a polypeptide chain is determined by
The amino acid sequence
The molecular structure and properties of Its amino acids
The molecular environment (solvents & salts) - hybridisation of DNA depends on molecular environment (solvents, salts + proteins)
Classification of AA
Charged:
Asp (-ve and acidic as O at terminal end)
Glu (-ve and acidic as O at terminal end)
Lys (+ve and basic as amide +ve)
Arg (+ve and basic as amide +ve)
Non-polar: Ala Val Phe Pro Ile Leu Met
Polar: Ser Thr Tyr (aromatic) His (aromatic + charged basic AA) Trp (aromatic) Cys Asn Gln
Glycine seperate (nonpolar)
Classification guide
Secondary Amine NH and Carbonyl C=O groups = polar
Hydroxyl OH = polar
Hydrocarbon = Non-polar Hydrophobic
Polypeptides adopt a structure based on: Energy minimisation
Each molecular structure has a specific energetic state
The minimisation of this energetic state (the free energy of a molecule “G”) determines the most favourable arrangement of the atoms (confirmation)
The change in free energy upon folding is called ∆G (if ∆G -ve then spontaneously folds)
Energy minimisation
Aqueous or lipid membrane
Other proteins or molecules including salts and their ionic state
Changes in this environment can induce a further conformational change for example a receptor binding a ligand
Bonds determining folding
Weak non-covalent bonds have 1/20th strength of covalent bonds
But the overall contribution is significant because non-covalent bonds are far larger in number
Covalent bonds disulphide bonds
Bonds form in an oxidative reaction
The SH groups from each cysteine cross link .
Usually occurs in distant parts of the primary sequence but adjacent in the three-dimensional structure.
Can form on the same (intra-chain) or different (inter-chain) polypeptide chains eg insulin left
PS, SS, TS + QS
Primary structure
covalent bonds forming polypeptide chain – i.e. order of amino acid residues joined by peptide bonds
Secondary structure
regular folded form, stabilised by hydrogen bonds – e.g. alpha helices, beta sheets and beta turns
Tertiary structure
overall 3D structure, stabilised by hydrogen bonds, hydrophobic, ionic and Van der Waal’s forces, and sometimes by intra-chain covalent (disulphide) bonds
Quaternary structure
organisation of polypeptides into assemblies, stabilised by non-covalent and Covalent bonds (as for Tertiary) and sometimes by inter-chain covalent (disulphide) bonds
Orientation of amino acid side chains
The orientation of amino acid side chains in alpha helices and beta sheets is outward
Hydrogen bonding occurs between the carbonyl and amide groups of the polypeptide backbone
We know the variable side chains protrude outwards from both molecules, the helical alpha helix and the planar beta sheet and participate in folding of the secondary structure
Protein mis-folding and disease
Firstly, the function of the mis-folded protein is almost always lost or reduced
Secondly mis-folded proteins often have a tendency to self-associate and form aggregates
Huntingtin Htt (Huntington’s)
Amyloid-beta Ab (Alzheimer’s)
prion protein (PrPSc)
alpha-synuclein (Parkinson’s disease)
Serum amyloid A (AA amyloidosis)
islet amyloid polypeptide IAPP (Type 2 Diabetes) and many more
Other mis-folded proteins result in cellular processing that lead to their degradation
Cystic fibrosis
Reasons for protein mis-folding
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 and +ve ∆G
Mistakes of the post-translational modifications or in trafficking of proteins
Structural modification produced by environmental changes (heated so denature)
Induction protein mis-folding by seeding and cross-seeding by other proteins
Protein folding and mis-folding and disease Amyloid hypothesis
In Alzheimer’s disease proteolytic cleavage of Amyloid Precursor Protein (APP) is observed
APP has multiple functions but is involved in G-protein signalling
Cleavage of APP results in a @40 residue peptide beta amyloid
In the intact molecule this anchors the protein in the membrane APP accumulates & mis-folds to form beta sheets
In Alzheimer’s disease the beta-Amyloid (A-beta) peptide accumulates
Mis-folding of this protein results in a planar arrangement and polymerisation
As they behave aberrantly, aggregate = oligomers
This can form fibrils of mis-folded protein (amyloid fibrils)
beta-Amyloid (Abeta) fibres are formed from stacked beta sheets in which the side chains (above + below) interdigitate
Protein folding and mis-folding 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) (while still in the ER)
∆F508del leads to mis-folding 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 to the proteasome and degradation. Thus never reaches cell membrane so the patient is unable to handle Cl- ions and salt
70% of Caucasian CF patients harbour this mutation
Induced protein mis-folding
Mis-folded proteins (PrP^SC) that interact with other normal proteins (PrP^C)
Through this interaction they induce mis-folding of the normal protein and polymerisation
Oligomers form fibrils of mis-folded 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 (accumulation of insoluble fibres)
