Amino Acids Protein Structure and Function Lecture 2 Notes: Protein Structure - Typical experimental procedures to identify protein structure and function include: (a) Solubilisation, purification, enrichment and protein identification (b) Structural and functional analysis (experimental), molecular interactions (c) Combinations of biochemistry, molecular and cell biology techniques (d) Prediction of structure and function, molecular interactions - The study of protein structure and function is challenging as they have a huge range of physical and structural properties (e.g. hydrophobic/hydrophilic, soluble/insoluble, impossible to predict accurately) and are easy to degrade and denature (e.g. do not stand heat or organic solvents). Each protein requires an individual experimental approach and the abundance in biological tissues greatly varies. side chain R H OH Ca 1 H - Total protein hydrolysis of proteins will yield a mix a- aminocarboxylic acids H O amino group carboxyl group - 20 most common amino acids exist. Others occur (rarely) as the post-translational products of enzymatic modifications. 10 amino acids (VLIFTMKRHW) are not synthesised in humans. - In amino acids there is a common central carbon (Ca) to which a hydrogen, NH2 (amine group) and COOH (carboxylic acid) are attached. Side chains ('R' groups) vary but have the same projection formula (Fischer projections, mirror images, measured via optical rotation). - All amino acids are chiral (except glycine). Chirality is determined by the position of the R group and measured by optical rotation. - If the amino group (NH2) is to the left of the central carbon, it is levorotatory (minus, L-amino acid). Natural amino acids are mostly amino acids whereas bacterial peptides often contain D-amino acids (amino group on right). N - The chemical nature, structural properties, size, polarity and ionization properties of the R group determine properties of the amino acids. Other properties vary also, such as absorption, fluorescence (mostly aromatic) and chemical reactivity (modifications). - There is a wide range of possible relationships between natural a-amino acids and a range of different properties and functions. However, physical and chemical versatility is not unlimited thus 'special cases' (i.e. rare/unnatural/altered amino acids) exist (e.g. presence of metal ions, post-translational modifications). - Special common amino acids include: (a) Cysteine (Cys) (b) Glycine (Gly) (c) Selenocysteine (Sec or U) (d) Proline (Pro) - Cysteine contains a thiol group, which can undergo redox reactions. Cysteine is formed by the oxidation of cysteine (two cysteine residues joined by a disulphide bond), which is a reversible reaction. Cysteine is evolutionarily stable/important (disulphide bonds). The disulphide bonds of cysteine are crucial to defining the structures of many proteins (stability
of structure, link different chains) or to stabilise irregular structures. Cysteine has a high affinity for heavy metals so proteins containing cysteine will bind metals (e.g. mercury, lead, cadmium and gold). - Glycine a very small and simple non-polar amino acid. The side chain comprises of only one hydrogen atom (i.e. it is the smallest amino acid) so can fit where other amino acids cannot. It is not chiral (not optically active). Glycine is evolutionarily stable/important as a