BS2520 - Protein Structure and Function Lecture 3 Protein Structure and Function We are usually looking for protein sequence, structure, and function, or to repair/modify new functions. Typical experimental procedures: - Solubilisation, purification, enrichment, protein identification. - Structural and functional analysis, molecular interactions. - Combinations of biochemistry, molecular and cell biology techniques. - Predication of structure and function, molecular interactions. Challenges of studying proteins: - Huge variety of physical properties. - Procedures and tightly regulated. - Easy to degrade and denature. - Proteins do not stand heat, detergents, chaotropic reagents, or organic solvents. - There is a huge variety of structures. - Each protein often requires individual experimental approach to extraction, purification, testing, expression, and analysis. - The abundance in biological tissues varies. Properties and Classification of Natural Amino Acids - Total protein hydrolysis will yield a mix of a-aminocarboxylic acids. - There are 20 common amino acids. - Others can occur but they are the products of enzymatic modifications post-translationally. - There are 10 amino acids not synthesised in humans. - There is a central carbon attached to H, NH2, COOH. - The side chains, R, vary. - All amino acids are chiral, determined by the position of the R chain. Dextrorotatory means to the right. Laevorotatory means to the left, most amino acids are L-amino acids. Intrinsic metal atoms: - Side chains of His, Cys, Asp, Glu are excellent metal ligands. - Frequent metals in proteins are Fe, Zn, Mg, Ca.
Name Formula Abbreviations Name Formula Abbreviations Glycine O H2C" OH - NH Gly G Cysteine O "OH HS NH2 Cys C Alanine Valine HaC C H3C. OH NH2 CH3 O 'OH Ala A Val V Methionine O OH HaCo NH2 Lysine O OH Met M Lys K NH2 HAN NH2 Leucine H3C O OH CH3 NH2 Leu L Arginine HN H2N ZI NH2 O "OH Arg R Isoleucine H3C. SOH CH3 0 NH2 Ile - Histidine O `OH N ANH NH2 His H Phenylalanine OH NH- Phe F Tryptophan 0= HN OH Trp W NH2 Proline O= OH -NH Pro P Aspartic Acid OH Asp D O OH NH2 Serine HO 0 OH Ser S Glutamic Acid OH O Glu E NH2 HO SO NH2 O Asn N Threonine H3C OH C OH Thr T Asparagine O OH NH NH2 NH2 Tyrosine HO 0 OH Tyr Y NH2 Glutamine O `OH HAN SO NH Gin Q Special Amino Acids Cystine contains a thiol group which can undergo redox reactions. Cystine is formed by the oxidation reaction of cysteine, this is a reversible reaction. The disulphide bonds of cystine are crucial to the structures of many proteins. They have a high affinity for heavy metals, proteins containing cysteine will bind metals such as mercury, lead, cadmium, and gold. Glycine is a non-polar simple and small amino acid. The only side chain is a hydrogen. It is a non-chiral molecule. Selenocysteine is a cysteine analogue with a selenol group in place of the thiol group. It is not coded