Properties of 20 Amino Acids - Lecture Slides | BCH 5505, Exams of Biochemistry

Download Properties of 20 Amino Acids - Lecture Slides | BCH 5505 and more Exams Biochemistry in PDF only on Docsity! Amino Acids 9/19/2005 BCH 5205 (c) M.S.Chapman 1 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 1 Properties of the 20 Amino Acids BCH 5505: Structure and Function of Enzymes © Michael S. Chapman, FSU, 1994-05 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 2 What do I need to know? For my future? For the Test? (The same). Names, abbreviations. Properties: Hydrophobicity Acidity (approximate pK's) "Reactive" groups Hydrogen bonding properties Likely conformation Special interactions Special functions To understand these, you will probably need to know the covalent structures. 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 3 1. Hydrophobic (non-polar) residues Usually interior of proteins away from water. Hydrocarbon: do not contain polar atoms. 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 4 Alanine Abbr.: Ala A Hydrophobic Polyalanine models: Used early in structure determinations when not possible to fit the sequence. The smallest side chain with a Cβ to show where the side chain would be. 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 5 Glycine Abbrev. Gly, G "Abnormal" φ, ψ angles: Many more φ, ψ combinations are possible. Ramachandran plot almost symmetrical. Cα is symmetrical (non-chiral) E(φ,ψ) = E(−φ,−ψ) Each region expanded, because H << C. As a result, Gly associated with Sharp turns Flexibility Lower vdW barriers Switching rotamers W/in rotamers Non-Gly Gly +180 0 -180 -180 0 + 180 ψ φ 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 6 Other hydrocarbon side chains Valine, Val, V Leucine, Leu, L Isoleucine, Ile, I Amino Acids 9/19/2005 BCH 5205 (c) M.S.Chapman 2 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 7 Methionine Sulfur is not very reactive. 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 8 Phenylalanine Hydrophobic. Abbreviated: Phe F Aromatic Delocalized π electrons ⇒ occasional stacking w/ other aromatics: Face to face Edge on Separation = 3.4 A 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 9 Proline, Pro, P Saturated 5 membered ring: 4th C (Cδ) substitutes for peptide H: i.e. side chain re- connects with main chain N. Not aromatic Where is Cα? What restrictions are there on backbone torsion angles? This one is constrained according to the pucker of the ring. Which angle is this? 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 10 Proline, Pro, P φi constrained to ~ - 60° What does this mean for protein structure? Not much Preferred angle anyway What else is restricted? ω (as it is in all residues) ψi-1 – new concern Pro Cγ replaces H Unless Ri-1 = H (Gly) ψi-1 restricted to ~ + 120° φi CH C'i N C'i-1 CH2 CH2 CH2 C i-1α Ri-1 ψi-1 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 11 Effects of Proline upon protein structure ψi-1 restricted to ~ + 120° What structures are allowed? α-helix stops w/ residue preceding Pro “Helix-breaking” amino acid Often found at turns 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 12 Acids and Bases in Proteins A review Amino Acids 9/19/2005 BCH 5205 (c) M.S.Chapman 5 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 25 Perturbation by Charge, continued Consider: HA---Y+ A----Y+ + H+ Stabilized right-side; No effect on left Net effect: Change equilibrium (constant); favor dissociation; lower pK If Y had –ve charge – opposite effects Should be able to figure out effects of… Neighboring anions & cations On charged & uncharged acids & bases HA A- + H+ (Cationic base) BH+ B + H+ (Uncharged base) 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 26 Perturbation by Dielectric Opposite charges are most easily separated in a high dielectric (e.g. water) Shielding reduces the attraction HA A- + H+ in low dielectric (protein interior): Products less favored than in low dielectric Dissociation decreased pK raised BH+ B + H+ Both sides charged Equally affected by dielectric No effect on pK 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 27 Perturbation by Dielectric - examples 4 5 6 7 8 9 0 10 20 30 40 50 60 70 80 Dielectric pK pK tris pK acetic acid Acetic acid CH3COOH CH3COO - + H+ HA A- + H+ Charged states differ pK perturbation possible Tris (HOCH2)3NH3 + (HOCH2)3NH2 + H + BH+ B + H+ Positive charges both sides of equilibrium No pK perturbation 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 28 What makes a good acid-base catalyst? Acid pK lower than substrate Proton prefers to be on substrate than protein Base pK higher than substrate Proton prefers to be on amino acid than substrate Regeneration: Catalyst needs to be returned to starting state Acid needs to regain proton If from substrate… Favored w/ pK higher than substrate Overall rate depends on both protonation & deprotonation Want both favored Matched pKs for isoergonic proton transfer 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 29 Acid-base catalysis continued If an acid catalyst regains its proton from solvent… Favored if pK > than water Again, need to balance needs of proton donation and proton acceptance Similar arguments for catalytic bases Best catalysts have pKs nearly matched with substrates and possibly solvent pKs usually close to 7 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 30 Properties of the Amino Acids Continued Amino Acids 9/19/2005 BCH 5205 (c) M.S.Chapman 6 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 31 Aspartate, Asp, D Hydrophilic: usually surface. pK = 3.9 At neutral pH: charged or protonated? Charged… Sometimes binds cations: ions, salt-bridges In catalysis would it be a general acid or base? Conjugate base predominates (accepting proton) Poor acid, as small concentration of proton donor Poor catalyst as pK very different from neutral Unless shifted by several pH units Rare, but important examples – Staph. nuclease Conformation of χ2 – see homework 1 Planar 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 32 Glutamate, Glu, E Hydrophilic: usually surface. pK = 4.2; Like Asp, usually charged, Base in catalysis, but poor Salt bridges Conformation like Asp, but Long chain ⇒ floppy ⇒ sometimes invisible 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 33 Arginine, Arg, R Hydrophilic: usually surface. pK = 12.5 ~ Always charged. Floppy: rarely see end. Unless salt-bridged: to Glu, Asp. Functional rôles: Never (?) catalytic – pK too far from 7.5 Anion binding, especially in substrates Carboxylates, e.g. lactate in LDH Sugar phosphates e.g. rubulose 1-5 bis-phosphate in RuBisCO DNA/RNA binding proteins – very prominent. 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 34 Lysine, Lys, K Hydrophilic: usually surface. pK = 10.5 99% (pH = pK + log[B]/[HA]) Floppy: rarely see end. Unless salt-bridged: to Glu, Asp. Binds anions. Functions like Arg Occasionally: a catalytic base, e.g. RuBisCO: Not a great acid-base catalyst Needs shift of ~ 3 pH units to be optimal 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 35 Histidine, His, H Catalytically, most important type of residue Full of surprises Name sounds like base Actually acid (pK = 6.1) But (of course) catalyzes like base Usually proton acceptor 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 36 His: Resonance & Titration N NH NH N N N Almost as good Favored state (NeH) Never seen NH NH + H+ Titrating between uncharged “His” singly protonated “HisH+” At pH 7.5 [HisH+] ≈ 200 [His] But easily changed w/ pK perturbation (1 or 2 units) Amino Acids 9/19/2005 BCH 5205 (c) M.S.Chapman 7 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 37 His: Most common acid-base catalyst pK is well matched w/ many substrates / water Rapid protonation and deprotonation Reaction & regeneration Only small perturbations are needed Base Acid Many examples: e.g. Lactate dehydrogenase 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 38 His: Metal ligand N NH Lone pair electrons sometimes donated to metal ions E.g. Mg++ Zn++ in SOD Fe++ in heme proteins Requires de-protonated His Metal ion helps shift pK Only then does [His] >> [HisH+] 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 39 His: Proton shuttling N N H N N H O OH Asp (for example) O O + H+ Protonation at Nε & Nδ have similar energies Proton shuttling Effect is large movement of proton Important in several enzymes, e.g. serine proteases 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 40 Polar Amino acids Uncharged, but contain: Electronegative/positive atoms. Dipoles. Capable of hydrogen bonding. Hydrophilic or Hydrophobic? Hydrophilic Inside or Outside? More often outside If inside, usually H-bonded 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 41 Serine, Ser, S; Threonine, Thr, T R-group does not usually deprotonate. (pK >> 14) pK irrelevant for most "polar" amino acids. Exception: Serine proteases - oxygen covalently links to substrate. H-bond donor & acceptor. Lone pairs on oxygen. OH's sometimes phosphorylated (Ser, Thr, Tyr). 9/19/2005 Amino Acids, BCH 5205 (c) M.S. Chapman 42 Tyrosine Abbreviations: Tyr; Y pK = 10 Lower than Ser, Thr Aromatic group Sometimes an acid Proton donor at physiological pH Very occasionally phenolate ion Else similar to Ser, Thr H-bonding Phosphorylation