The 3D structure of a protein Flashcards
Folding of polypeptide chain is determined by the
Amino acid sequence
Molecular structure Properties of amino acid Molecular environment (solvents & salts)
Basic amino acid structure
Tetrahedral
R chain conferring determines physiochemical properties
Acidic amino acid
Polar molecule
Proton donor Negative charge (COO-)
Basic amino acid
Polar molecule
Proton acceptor Positive charge (NH3+)
Non-polar, hydrophobic amino acids
Hydrocarbon side chain therefore neutrally charged
Polar
OH side chains
Secondary NH groups Carbonyl C=O side chain
Peptide bonds
Flat and planar
Rotational freedom around the alpha carbon Allows huge variation in the conformation of the peptide chain Favours formation of structural arrangements like alpha helices and beta sheets Rigidity is caused by delocalized electrons around the region of the peptide bond Significant delocalization gives the group a partial double bond character
Energy minimisation
Each molecular structure has a specific energetic state
Minimization of this energetic state determines the most favourable confirmation (arrangement of atoms in space)
The free energy of a molecule is: G
The change in free energy is called: delta G
The free energy of any conformation is affected by the molecular environment:
Aqueous or lipid membrane Other proteins or molecules including salts and their iconic state Other change in environment e.g. receptor binding to ligand
Bonds determine folding
Weak non-covalent bonds have 1/20th strength of covalent bonds However there are usually more non covalent bonds than covalent therefore contribution is significant Disulphide bonds: Bond forms in an oxidative reaction SH groups from each cysteine cross link
Protein misfolding and disease
Function of misfolded protein always lost Often have a tendency to self associate and form aggregates Eg. Amyloid-beta(Alzheimer’s) Also result in cellular processing that lead to their degradation: Cystic fibrosis
Why can mis-folding occur
Somatic mutation Errors in transcription and translation Failure of the folding machinery Mistakes in post translational modification Structural modification Proteins cross-seeding and seeding by other protein
Disulfide bonds form between the side chains of two cysteine residues
Oxidative reaction
SH groups from each cysteine cross link Occurs in different parts of the primary sequence but adjacent in the 3D structure Can form in the same (intra-chain) or different (inter-chain) polypeptide chains
Alzheimer’s
Proteolytic cleavage (breakdown of peptide bond) of amyloid precursor protein (APP) is observed
APP is involved in G protein signalling Cleavage results in a 40 residue peptide beta amyloid In the intact molecule, this anchors the protein in the membrane, APP accumulates and misfolds to form beta sheets Beta amyloid accumulates Mis folding results in a planar arrangement and polymerisation This forms fibrils of mis folded protein (amyloid fibrils) Beta amyloid fibres form from stacked beta sheets in which the side chains interdigitate
Cystic fibrosis
Deletion of phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regulator (CFTR)
This leads to mis folding of the protein whist in the ER This is recognized by the cellular machinery that identifies and processes misfolded protein This results in ubiquitination, trafficking to the proteasome and degradation
induced protein mis-folding
Prions: Misfolded proteins that interact with normal proteins
Through this interaction they induce mis folding of the normal protein and polymerisation Oligomers form fibrils of mis folded protein The process is reliant upon the concept of energy minimization Dynamic process as it is brought about by the interaction of molecules resulting in a more stable aggregated structure
