proteins: amino acid chains dna polymerase from e. coli standard amino acid backbone: carboxylic...

Proteins: Amino Acid Chains

DNA Polymerase from E. coli

Standard amino acid backbone:

Carboxylic acid group, amino group, the alpha hydrogen and an R group

(L)-alanine, the natural form

Importance of Chirality in Biological Systems

(L)-thalidomide is an effective sedative for expectant mothers while (D)-thalidomide causes severe birth defects

(L)-

Hydrophobic Amino Acids

Non-polar side chains that interact very weakly with water.

What type of bonding forces might contribute significantly for these AAs?

Polar Amino Acids

Where might these AAs be located in a polypeptide?

Amino acid side chains readily interact with water

Charged Amino AcidsAlways charged under physiological pH

What is the predicted pKa values for these acids and bases?

Ionizible Amino Acids at Physiological pH Values

Cysteine (Cys)

Histidine (His)

Imidazolium ion

Thiol group

Are these oxidation/reduction reactions?

Thiolate anion

pKa Values of Ionizable Amino Acids

ca. pKa

3

4

4

6

8

9

10

10

12

Disulfide Bond Formation

Polypeptide stabilization

Oxidation/reduction reaction

Amino Acid Coupling via Dehydration Synthesis

What is the Nucleophile, Electrophile and Leaving Group in this reaction?

Levels of Polypeptide Organization

A polypeptide Primary Structure: Amino Acid Order or Sequence

Coding convention: N- to C-terminus from left to right

Bond Length Indicates a Hybrid Bond Number of ca. 1.5

C-N single bond 1.45 ÅC=N double bond 1.25 Å

Peptide resonance

Peptide Bond Forms a Planar Unit

Steric hindrance favors trans configuration

Rotation in a Polypeptide Restricted to the Cα

Phi Psi

Ramachandran Diagram Shows Permitted Angles in Green

- 60

+120

What is phi and psi?

• What is the environmental condition favorable for a polypeptide to form an alpha helix?

• Where in the polypeptide would an α-helix be located?

α-Helix is a Coiled Polypeptide: Secondary Structure

Hydrophobic Strip Formed on the Surface of alpha-Keratin

n + 4 Hydrogen-Bonding Scheme for an Alpha Helix

Ribbon Depiction of Ferritin: an Iron Storage Protein

Beta-Sheet Polypeptide: Secondary Structure

Antiparallel

Parallel

Which configuration would be more stable?

Is the distance of 7 Å reasonable?

What do the green spheres represent?

What is the green spheres orientation relative to the β-sheet?

What is a favorable environment for beta-sheets formation?

Beta-Sheet Backbone

Beta-Sheet Configurations: Super-Secondary Structure

Twisted-Sheet

Beta-Barrel Reverse Turn

CD4 Surface Protein in HIV with Four Similar beta-Sheet Domains

Alpha-Helix Configuration: Super-Secondary Structure

• Common motif in DNA-binding proteins

Overall Configuration of a Single Polypeptide: Tertiary Structure

Oxygen Transporter in Muscles: Myoglobin

• Polypeptide Amino Acid Distribution: charged (blue), hydrophobic (yellow) & other (white)

Space-Filling Model of Myoglobin

Cross-Sectional ViewSurface

Overall Configuration of Multiple Polypeptides: Quaternary StructureBall and Stick

Ribbon Representation

α-Keratin – primary component of wool, hair and nails• Parallel alpha double helix with 7 AA 1,4 hydrophobic strip• Rich in cysteine residues that can form disulfide bridges• 2 right-handed double helices coil in an anti-parallel fashion to form a left-handed super-helix: a coiled-coiled protein• Length of ca.1000 Å

What causes the hardness of the fibrous protein keratin?

Hydrophobicity Scale

Free energy change in transferring from an organic to aqueous solution

Hydrophobic Effect In Protein Folding

Minimizing H2O-nonpolar interactions

Protein Folding by Progressive Stabilization of Intermediates

• All conformations are not

sampled

• Exergonic process

• Hydrophobic interactions

a major driver

• Chaperonin-assisted protein folding

Chapter 4 Problems: 1-5, 7, 10, 11, 12, 13, 23, 29, 35, 37, 51, 55 and 57