Properties of amino acids in proteins

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1 Properties of amino acids in proteins one of the primary roles of DNA (but not the only one!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated in linear polymers We build ~20,000 different kinds, based on the number of identified genes in the human genome, ranging from small (29 aa) to large (34,000 aa)

2 Proteins are the workhorses of the cell Enzymes, signaling and transport, and structural support Eukaryotic cell (~10-30 µm) Proteins (~3-5 nm, or more) Trypsin - digests proteins (247 amino acids) Myoglobin - transports oxygen (154 amino acids) Titin - a muscle protein (34,000 amino acids!)

3 Proteins are made of amino acids Side chain (R group) α carbon Amine group Carboxyl group this is a trans peptide bond (cis also possible but unlikely)

4 Peptide bond formation -process takes place at the heart of the ribosome in its peptidyl transferase center (PTC) Ribosome (not to scale! more on this later)

5 Basic protein structure Backbone Amino acid (Phenylalanine) Side chain Polypeptide

6 Secondary structure ɑ-helix: i i+4 hydrogen bonding; there are also 310 helices (i i+3) and π helices (i i+5) β-sheets: two directions, anti-parallel (top) and parallel (bottom) Pauling, Corey, Branson. The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain. (1951) PNAS. 37:

7 Secondary structure ɑ-helix: i i+4 hydrogen bonding; there are also 310 helices (i i+3) and π helices (i i+5) β-sheets: two directions, anti-parallel (top) and parallel (bottom) Pauling, Corey, Branson. The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain. (1951) PNAS. 37:

8 Secondary structure backbone ɸ-ψ dihedral angles define secondary structure Ramachandran plot of all crystal structures of proteins β-sheets left handed ɑ-helices right handed ɑ- helices

9 Basic protein structure Backbone Side chain Amino acid (Phenylalanine) Polypeptide Surface representation Cartoon representation beta-sheet alpha-helix

10 From Primary to quaternary structure Primary structure Secondary structure Tertiary structure Quaternary structure α helix Hydrogen bond β pleated sheet β strand Hydrogen bond Transthyretin polypeptide Transthyretin protein forms from interactions along the backbone (contrast with RNA/DNA)

11 Amino acids have chirality They are not identical to their mirror image, have two forms L-amino acids D-amino acids -all ribosome-synthesized proteins use L amino acids, most enzymes distinguish between L/D amino acids (D tastes sweet!), etc. - WHY? one hypothesis: circularly polarized radiation favors one enantiomer over the other in comet dust (more L-amino acids than D have been observed in meteorites!)

12 Another possible source of homo-chirality mixture starts 50/50, but ends with one overwhelming the other Strong fluctuations combined with efficient self replication lead to one state quickly dominating over the other Noise can play a critical role in creating asymmetric outcomes! Jafarpour, Biancalani, Goldenfeld. Noise-Induced Mechanism for Biological Homochirality of Early Life Self-Replicators. (2015) PRL 115: See more possibilities here: The Origin of Biological Homochirality

13 Diversity of amino acids Side-chains (R groups) give amino acids a wide range of properties humans use typically 20 amino acids, can synthesize many but others are essential (must come from diet) Essential: Phe, Val, Thr, Trp, Ile, Met, Leu, Lys, His Non-essential: Ala, Arg, Asp, Cys, Glu, Gln, Gly, Pro, Ser, Tyr, Asp

14 Nonpolar amino acids Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) 14

15 Polar amino acids Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) 15

16 Charged amino acids Acidic (negatively charged) Basic (positively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) 16

17 Single Mutation Disease Sickle-cell hemoglobin Normal hemoglobin Primary Structure Secondary and Tertiary Structures β subunit Exposed hydrophobic region β subunit α β α β Quaternary Structure Normal hemoglobin Sickle-cell hemoglobin β α β α Function Molecules do not associate with one another; each carries oxygen. Molecules crystallize into a fiber; capacity to carry oxygen is reduced. Red Blood Cell Shape 10 µm 10 µm 17

18 Ionization states AH + B A - + BH + ph = - log10([h3o + ]) ph of pure water is 7 (varies in different cells) Ka = [H3O + ] [A - ] / [AH] pka = - log10 Ka ph = pka + log10 ([A - ] / [AH]) Henderson Hasselbalch equation - gives the ratio of protonated to deprotonated molecules as a function of the current ph and the molecule s pka

19 Ionization states ph = pka + log10 ([A - ] / [AH]) Glu - ph > pka - deprotonated Ionizable amino acids amino acid pka (model) Asp (D) 4.0 Glu (E) 4.4 Arg (R) 12.0 Lys (K) 10.4 His (H) 6.3 Cys (C) 9.5 Tyr (Y) 10.0 ph < pka - protonated Histidine is a special case! Glu

20 Calculating ionization states Empirical approaches - fast, use a well-developed scoring function Ex: PROPKA Poisson-Boltzmann equation solvers Ex: H++ Free energy calculations - (relatively) expensive! pka = ph - ΔG/[kTln(10)]

21 The Proton as an Ion Water dissociates very slightly 2 H2O H3O + + OH - Water Hydronium Hydroxide ph = -log10([h3o + ]) = 7 pure water pka H2O = ph log10 ([OH - ] / [H2O]) = 7 (-7) = 14

22 Water is very good conductor: Proton hopping Grotthuss mechanism (proton hopping) The proton has a very high diffusion constant in water (D = 6 x 10-9 m 2 /s ) because it can move along the hydrogen bond connecting two water molecules without the water molecules moving. Hydronium cation Ice has a high electrical conductivity despite the fact that the water molecules do not move in the solid. mobility in ice is ~100x greater! (at the same temperature)

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