S ASC Answer to Practice Problem Draw the chemical structure of the tripeptide Ala – Ser – Cys at pH 7. Answer the following with regard to this tripeptide: 1. Indicate the charge present on any ionizable group(s). 2. Indicate, using an arrow, which covalent bond is the peptide bond. 3. What is the net, overall charge of this tripeptide at pH 7? __________ 4. What is this peptide called using the one-letter code system for amino acids? ______ S ASC

Structure and Function Proteins: Three Dimensional Structure and Function

Ribbon diagram Space-filling model Figure 4.3

Levels of Protein Structure Figure 4.1

Resonance structure of the peptide bond Figure 4.5

Planar peptide groups in a polypeptide chain Figure 4.6

Trans and cis conformations of a peptide group Figure 4.7 Nearly all peptide groups in proteins are in the trans conformation

Rotation in a peptide Figure 4.8 phi psi N-Ca Ca-C

Ramachandran Plot Figure 4.9

Secondary Structure of Proteins

The alpha helix Figure 4.10

The alpha helix Figure 4.11

An amphipathic alpha helix Figure 4.12

Amphipathic alpha helices are often found on the surface of a protein Figure 4.13

The beta sheet Parallel Figure 4.16

The beta sheet Parallel Figure 4.16 N N N

The beta sheet Antiparallel Figure 4.16

The beta sheet Antiparallel Figure 4.16 N N N

Side chains alternate from one side to another The beta sheet. Side chains alternate from one side to another Figure 4.17

Levels of Protein Structure Figure 4.1

Reverse turns Figure 4.19 Type II b turn Type I b turn

Reverse turns Figure 4.19 Type II b turn Type I b turn

Tertiary Structure of Proteins

Supersecondary structures, often called “motifs” Figure 4.20

Domain folds in proteins Figure 4.25

Figure 4.24

Quaternary Structure Figure 4.26

Protein Folding and Stability

How do proteins fold and unfold? The information for proteins to fold is contained in the amino acid sequence. Can proteins fold by themselves or do they need help?

Protein folding proceeds through intermediates

Intermediates in protein folding Figure 4.37

Heating proteins will unfold or “denature” the molecule. Figure 4.31

Anfinsen’s protein folding experiment Figure 4.35

Protein Folding A cell can make a biologically active protein of 100 amino acids in 5 seconds. If each amino acid could adopt 10 different conformations this makes 10100 different conformations for the protein. If each conformation were randomly sampled in 10-13 seconds it would take 1077 years Therefore protein folding must not be a random process.

Energy well of protein folding Figure 4.36

Forces driving protein folding: Hydrophobic effect Hydrogen bonding Charge-charge interactions Van der Waals interactions

Molecular Chaperones (Chaperonins) Some proteins don’t spontaneously fold to native structures. They receive help from proteins called chaperonins Best characterized chaperonin system is from E. coli. GroEL / GroES chaperonin system (GroE chaperonin) These chaperonins bind to unfolded or partially folded proteins and prevent them from aggregating. They assist in refolding the proteins before releasing them.

GroE Figure 4.38

Chaperonin-assisted protein folding Figure 4.39

Three-dimensional structures of specific proteins 1. Collagen, a fibrous protein 2. Myoglobin and Hemoglobin, O2 binding proteins 3. Antibodies

Collagen is a fibrous protein found in vertebrate connective tissue. Collagen has a triple helix structure, giving it strength greater than a steel wire of equal cross section.

21% Proline + Hydroxyproline The repeating unit is Collagen is 35% Glycine 21% Proline + Hydroxyproline The repeating unit is Gly – X – Pro (HyPro) The interior of a collagen triple helix is packed with Glycines (red)

4-Hydroxyproline and 5-Hydroxylysine residues Figure 4.41 and 4.43

Allysine and lysine residues form cross-links in collagen Figure 4.44

Allysine residues form cross-links in collagen Figure 4.44

Hemoglobin and Myoglobin bind oxygen Figure 4.46 Heme Histidines Protein

Red blood cells (erythrocytes)

Myoglobin is monomeric and binds oxygen in the muscles Figure 4.44 Heme Histidines Protein

Hemoglobin is tetrameric and carries oxygen in the blood Figure 4.48

His 64 Fe2+ O2 Heme His 93 Whale Myoglobin Figure 4.51

Oxygen binding curves of hemoglobin and myoglobin Page 124 Y = Fractional oxygen saturation of myoglobin Mb = Concentration of myoglobin molecules without bound oxygen MbO2 = Concentration of myoglobin molecules with bound oxygen Mb + MbO2 = total concentration of myoglobin molecules

Oxygen binding curves of hemoglobin and myoglobin Figure 4.52

Oxygen binding induces protein conformational changes Figure 4.53

Hemoglobin binds 2,3-Bisphosphoglycerate at an allosteric site. 2,3-Bisphosphoglycerate lowers the affinity for oxygen. Figure 4.54

CO2 and H+ bind to hemoglobin and decrease oxygen affinity. Figure 4.55

Antibodies are proteins of the vertebrate immune system. Antibodies specifically bind to foreign compounds (antigens) Figure 4.57

Binding of three different antibodies to an antigen Figure 4.59