From Amino Acids to Proteins Peptide Bonds

Amino Acids & Proteins Part II

Dr. Kevin Ahern From Amino Acids to Proteins Peptide Bonds

In RibosomesAlpha Carboxyl Alpha Amine Primary Protein Structure

• Linear sequence of amino acids • Joined by Peptide Bonds • Translated from mRNA using Genetic Code • Synthesis begins at amino end and terminates at carboxyl end • Ultimately determines all properties of a protein Polypeptides Alternating Orientations of R-groups A simple view

Peptide Bond Peptide Bond Free Carboxyl Group Amino Terminus Peptide Bond

Carboxyl Terminus

Peptide Bond Peptide Bond Free Alpha Amine

Alternating Orientations of R-groups Peptide Bonds Chemical Character

Double Bond Behavior

Alpha Carbons Usually Trans-oriented Separated bulky groups Proteins Alpha Carbons Trans Steric Hindrance

Separated bulky groups

Interacting Bulky Groups

Alpha Carbons Cis Polypeptides Multiple Peptide Bond Planes

Free Rotation Phi and Psi Angles Peptide Bond Phi Angle Omega Angle

Psi Angle Peptide Bond Ramachandran Plot Bond Angles

Primary Angles of Stability Secondary Structure Alpha Helix Secondary Structure Alpha Helix

Hydrogen bonds stabilize structure Hydrogen bonds stabilize structure Secondary Structure Hydrogen Bonds Beta Strands / Beta Sheets

Anti-Parallel Parallel Beta-Sheet Interactions Secondary / Supersecondary Structures Ramachandran Plot Labeled Secondary Structure Fibrous Proteins

• Collagen • Connective tissue • Keratin • Hair / nails • Fibroin • Silk Collagen Partial Sequence

Primary Structure Hydroxyproline Proline in Helix Abundant Glycine Occasional Lysine Structural Proteins

Keratins Fibrous 50 in Humans Intermediate Filaments of Cytoskeleton Hair, nails, horns Fibroin

Silk Beta sheets Repeating glycines Secondary Structure Types

Alpha Helix Beta Strands / Beta Helix Reverse turns (5 types)

310 Helix Secondary Structure Tendencies of Amino Acids

High Propensity for Alpha Helices

High Propensity for Reverse Turns High Propensity for Beta Strands Amino Acid Hydropathy Soluble vs. Membrane Bound Proteins

Hydrophobic Amino Acid Bias Inside

Hydrophilic Amino Acid Bias Outside

Hydrophobic Amino Acid Bias In Bilayer

A folded enzyme’s active Oh little protein molecule And starts to catalyze You're lovely and serene When activators bind into With twenty zwitterions like Its allosteric sites Cysteine and alanine

Some other mechanisms Your secondary structure Control the enzyme rates Has pitches and repeats By regulating synthesis Arranged in alpha helices And placement of phosphates And beta pleated sheets

And all the regulation The Ramachandran plots are That's found inside of cells Predictions made to try Reminds the students learning it To tell the structures you can have Of pathways straight from hell For angles phi and psi

So here’s how to remember And tertiary structure The phosphate strategies Gives polypeptides zing They turn the GPb's to a's Because of magic that occurs And GSa's to b's In protein fol-ding Reverse Turns Tertiary Structure Folding and Turns Beta Strands

Alpha Helices

Random Coil Turns Folding of a Globular Protein Unfolding of a Globular Protein Forces Stabilizing Tertiary Structure

Hydrogen Bonds

Figure 2.41 - Hydrogen bonding in liquid water Wikipedia Forces Stabilizing Tertiary Structure

Disulfide Bonds (Covalent) Forces Stabilizing Tertiary Structure Denaturing/Unfolding Proteins

Break forces stabilizing them Mercaptoethanol/dithiothreitol - break disulfide bonds Detergent - disrupt hydrophobic interactions Heat - break hydrogen bonds pH - change charge/alter ionic interactions Chelators - bind metal ions Denaturing/Unfolding Proteins Folding of a Globular Protein Energetics of Folding Protein Structural Domains

Leucine Zipper - Prot.-Prot. and Prot.-DNA Helix Turn Helix - Protein-DNA Leucine Zipper Zinc Fingers

SH2 Domains - Protein-Protein Pleckstrin Homology Domains - Signaling (Membrane)

Leucine Zipper Zinc Finger

SH2 Domain Helix-Turn-Helix Pleckstrin Domains Folding Errors Prion Replication Model Amyloids and Disease

Amyloids - a collection of improperly folded protein aggregates found in the human body. When misfolded, they are insoluble and contribute to some twenty human diseases including important neurological ones involving prions. Amyloid diseases include (affected protein in parentheses) -

•Alzheimer’s disease (Amyloid β)

•Parkinson’s disease (α-synuclein)

•Huntington’s disease (huntingtin),

•Rheumatoid arthritis (serum amyloid A),

•Fatal familial insomnia (PrPSc) Protein Processing

Chaperonins - Proper folding - environment for hydrophobic sequences

GroEL / GroEL-GroES

Proteasomes - Degradation to oligopeptides of about 8 amino acids each Role of Ubiquitin

Flag for protein destruction by proteasome Intrinsically Disordered Proteins

Not all proteins folded into stable structures Intrinsically Disordered Proteins (IDPs) have regions favoring disorder IDP regions tend to lack hydrophobic residues Rich in polar amino acids and proline IDPs may favor adaptation to binding another protein IDPs may favor being modified IDPs may be more involved in signaling and regulation Non-IDPs more involved in catalysis and transport

Metamorphic Proteins May adopt more than one stable structure Lymphotactin - monomeric receptor. Binds heparin as dimer Protein Structure

• Primary – Amino Acid Sequence • Secondary / Supersecondary – Repeating Structures – short range forces • Tertiary – Folded structures – longer range interactions My Old Enzymes (To the tune of "Auld Lang Syne") Metabolic Melody Copyright © Kevin Ahern

Whene’er my proteins go kaput If they are past their prime. The cells will act to soon replace All of my old enzymes

They know which ones to break apart Ubiquitin’s the sign A marker for pro-TE-a-somes To find the old enzymes

These soon get bound and then cut up In pieces less than nine More chopping yields the single ones Building blocks from old enzymes

So in a way the cell knows well Of father time it’s true Amino acids when reused Turn the old enzymes to new