3D structure of proteins

Question 1

Describe how the properties of amino acids are determined b y their structure

Answer 1

• The non-polar or hydrophobic amino acids such as alanine, valine etc contain a special case that of methionine.
• The polar amino acids such as serine, threonine, etc contains the aromatic amino acids tyrosine histidine and tryptophan. It also includes that of Cysteine. Glycine is usually in a group of its own but can be found included in the non-polar amino acids.
• Histidine is sometimes also considered as a charged basic amino acid.

Question 2

Describe bonds in amino acid

Answer 2

• Each repeating unit of the polypeptide chain is joined by a peptide bond. The variable side chain R is usually arranged in a trans conformation.
• The peptide bond is thus a planar structure with the rotational freedom within the molecule found around alpha carbon.
• Delocalised electrons of the N-CO make the bond ridged, with the Oxygen (red) and Hydrogen (white) atoms on opposite sides lying in the same plane
• Glycine is a special amino acid in that the R group consists of a single hydrogen which allows greater flexibility of the peptide back bone.
• Rotational freedom of the bonds allows huge variation in the conformation of the peptide chain. This freedom favours the formation of structural arrangements, such as alpha helices and beta sheets.

Question 3

Describe energy minimisation

Answer 3

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 (conformation).
The change in free energy upon folding is called ∆G.
The free energy of any conformation is affected by the molecular environment.
o Aqueous or lipid membrane.
o 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.

Question 4

Describe non-covalent bonds

Answer 4

• 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.
o Charge or electrostatic attractions
• Falls off exponentially as distance increases, affected by electrostatic environment (aqueous environment).
o Hydrogen bonds (transient non-covalent bonds).
• Occurs between polar groups like the carbonyl (C=O) and amide (NH) groups of the backbone.
o Van der Waals attractions – dipole
• These weak forces occur between two atoms in non-covalent interactions. Determined by their fluctuating charge. Attraction at a close distance is balanced by repulsion due to proximity that is determined by the Van der Waals radius of an atom. Van der Waals forces are induced by proximity of molecules.
o Hydrophobic interactions
• (Water is a polar molecule) hydrophobic interactions minimise disruption of water network – i.e. the fourth weak force.

Question 5

Describe covalent bonds

Answer 5

• 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 e.g. insulin left

Question 6

Describe protein misfolding and disease

Answer 6

• The function of the mis-folded protein is almost always lost or reduced.
• Misfolded proteins tend to self-associate and form aggregates
o Huntingtin Htt (Huntington’s).
o Amyloid-beta Ab (Alzheimer’s).
o Prion protein (PrPSc).
o alpha-synuclein (Parkinson’s disease).
o Serum amyloid A (AA amyloidosis).
o Islet amyloid polypeptide IAPP (Type 2 Diabetes)
• Other mis-folded proteins result in cellular processing that lead to their degradation.
o Cystic fibrosis

Question 7

Describe several reasons as to why a protein can misfold

Answer 7

o Somatic mutations in the gene sequence leading to the production of a protein unable to adopt the native folding.
o Errors in transcription or translation leading to the production of modified proteins unable to properly fold.
o Failure of the folding machinery.
o Mistakes of the post-translational modifications or in trafficking of proteins.
o Structural modification produced by environmental changes.
o Induction protein misfolding by seeding and cross-seeding by other proteins.

Question 8

Describe AD

Answer 8

On image

Question 9

Describe CF and Prions disease

Answer 9

On image.

• Mis-folded proteins (PrPSC) that interact with other normal proteins (PrPC)
• 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.
• PrPc protein is seen in the lower left and the green alpha helices mis fold to form a beta sheet this in turn induces other PrPc proteins to mis-fold and aggregate.