Trader Lecture 2 - Protein Structure and Function PDF

Lecture 2 Protein Structure and Function Prof. Trader Winter 2025 PharmSci 177/277 So far… We have talked a lot about small molecules and how their interaction with targets can have a therapeutic response. But what, more specifically are these targets? And how does...

Lecture 2 Protein Structure and Function Prof. Trader Winter 2025 PharmSci 177/277 So far… We have talked a lot about small molecules and how their interaction with targets can have a therapeutic response. But what, more specifically are these targets? And how does binding actually work? Don’t for get those amino acids! -Proteins are macromolecules made up of 20 common amino acid building blocks. -Don’t forget, you need to know all 20 of these! -You need to know the 1 and 3 letter codes for each amino acid -You should know the approximate pKa value of the side chains (i.e. what what pH are the side chains charged or neutral?) -The side chain functional groups is what makes each amino acid unique pKa values are lower than those observed for simple amino & carboxy groups Shifting of the pKa value for the amino group The pKa of the amine shifts from 10.6 for a typical amine, like methyl amine, to 9.6 for an amino acid. This is due to the close proximity of the positively charged amine to the negatively charged carboxylic acid. The strongly electronegative carboxylic acid group ‘pulls electrons’ from the positively charged amine, which makes it easier to remove a proton from the amine, thus lowering the pKa. The dashed red arrow shows the pulling of electrons toward the carboxylic acid group. Shifting of the pKa value for the carboxylic acid The pKa of the carboxylic acid shifts from 4.8 for a typical acid, like acetic acid, to 2.3 for an amino acid. This is due to the charge-charge repulsion between the positively charged amine and the build-up of partial positive charge on the departing proton of the carboxylic acid group. The double headed arrow (pink) shows repulsion between the two positive charges. pKa values allow you to know if charged amino acids are protonated or unprotonated in the cell pKa of Amino Acid Side Chains Right side of the equilibrium is closer to 7 Left side of the equilibrium is closer to 7 Titration of Histidine (H, His) -Polar side chains have pKa values that are important for protein function. -Notice the number of transitions equals the number of ionizable groups Levels of Protein Structure Primary Structure of Proteins Peptides and proteins are writing in the N-terminal to C-terminal direction Peptide One Letter Sequenceà YGGFM Practice Can you draw the following 3-mer peptides? AWG NH O O H N N OH H NH2 O Ala-Trp-Gly HO O OH OH SRY H 2N HN O HN O HN H 2N NH The Secondary Structure of Proteins The Secondary Structure of Proteins Beta Sheet Secondary Structure Beta Turn Secondary Structure Circular Dichroism (CD) Spectroscopy Tertiary Structure of Proteins Tertiary Structure of Proteins Cont. General Trends Polar residues are favored on the outer surface b/c this allows for Hydrogen- bonding with water Non-Polar residues are favored on the inside b/c this maximizes VDW and hydrophobic interactions The shape of the side chain is an important factor in protein folding. Proteins can be thought of as a ‘3D jigsaw puzzle’. Residues far apart in 1o structure can be close in the 3o structure. Tertiary Structure of Proteinsà Disulfide Links Tertiary Structure of Proteinsà Ionic Bonds Called salt bridges in proteins Tertiary Structure of Proteinsà Hydrogen Bonds Quaternary Structure of Proteins Quaternary Structure of Proteins- Example Post Translational Modifications “Posttranslational modifications (PTMs) are covalent processing events that change the properties of a protein by proteolytic cleavage and adding a modifying group, such as acetyl, phosphoryl, glycosyl and methyl, to one or more amino acids” PTM Chemistry But why do PTMs? Phosphorylationà Signal Transduction Glycosylationà Protein trafficking and Cell-Cell contacts Sulfationà Neuropeptides, intracellular transport Carboxylationà Enhances Ca2+ binding (unclear currently) Hydroxylationà Collagen folding Acetylationà Regulation, Localization Lipidationà Membrane Anchoring Disulfide--> Structural, redox activity