Proteins

Learning Objectives
Primary, secondary, tertiary, and quaternary structure Structure of collagen, a fibrous protein

Location of polar and nonpolar residues in globular proteins

Myoglobin Hemoglobin and sickle-cell anemia

Primary Structure
Primary structure of a protein is the amino acid sequence of its polypeptide chain. For example, the primary structure of an antifreeze protein in one-letter code is:
DTASDAAAAAALTAANAKAAAELTAANAAAAAAATAR

A protein has tens to thousands of amino acid residues

100 amino acid residues may be combined in 20100 different sequences (the universe has 1079 atoms)

10130

The primary structure determines properties of a protein, while the amino acid composition is relatively not important (compare word atom and its anagram moat) Each protein consists of one ore more polypeptide chains

Protein Structure Levels

Figure 6-1.

Secondary Structure
Secondary structure refers to a spatial arrangement of the backbone without regard to the side chain conformations Fig. 6-7 -Helix. Backbone carbonyl C=O of residue i accepts an H-bond from the backbone N-H group of residue i+4

Secondary Structure
-sheets are stabilized by Hbonds between two parallel backbones Fig. 6-9 In the parallel sheet, the backbones extend in the same directions In the antiparallel -sheet, the backbones extend in opposite directions

Collagen
Depending on their overall shape, proteins are classified as either fibrous or globular The fibrous protein collagen is the most abundant vertebrate protein. It has numerous Gly, Pro, and hydroxy-Pro residues. Fig. 6-17

Collagen triple-helix fibers are the major stress-bearing components of connective tissues (bone, teeth, tendon) and the fibrous matrices of skin and blood vessels.

Collagen is a TripleHelix Protein

Side chains of certain Pro residues in collagen are hydroxylated with the help of an enzyme (prolyl hydroxylase) and coenzyme ascorbic acid (vitamin C). Lack of vitamin C results in scurvy because collagen cannot form fibers. The superhelical structure of collagen is formed of three collectively twisted polypeptide helices

Tertiary Structure
The tertiary structure of a protein refers to the folding of its secondary structure segments. The segments are joined by reverse turns, which usually occur on the surface of the protein. The 3D structures of proteins are studied experimentally by X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and theoretically by molecular modeling. > 75,000 3-D structures of proteins are deposited in the Brookhaven Protein Data Bank (http://www.rcsb.org).

Freely available programs (PYMOL, VMD, RASMOL, etc.) may be used to visualize 3D structures of proteins.

Visualization of Proteins
Atoms in proteins are tightly packed. Showing all atoms obscures internal details. Usually, only backbones are visualized. Fig. 6-29 -Helices are drawn as ribbons passing via C atoms.

Visualization of Proteins
-Sheets are drawn as flat arrows pointing toward the C-terminus.

Fig. 6-29

Visualization of Proteins
Proportions and arrangements of the secondary-structure segments vary in different proteins. Unfolding of a protein (denaturation) may require the free energy as small as 0.4 kJ/mol per residue.

Fig. 6-30

Location of Polar and Nonpolar Residues

Hydrophobic residues prevail in the protein interior. Hydrophilic residues prevail at the protein surface. This arrangement maximizes preferable interactions and minimizes non-preferable interactions of amino acids with water.

Figure 6-27

Myoglobin
Intracellular protein facilitating O2 transport in vertebrate muscle Contains a heme group that coordinates the central Fe (II) atom Fig. 7-1. Oxygen binds reversibly to the heme group in the protein

The Heme Group

Four nitrogen atoms (blue balls) coordinate the central Fe(II) atom (yellow ball). Oxygen molecule (red ball) reversibly binds to Fe(II).

Toxic compounds such as CO (carbon monoxide) and NO (nitric oxide) bind to the heme group with much higher affinity than O2. Every year, nearly 300 people in the United States die from CO.
Oxidation of Fe(II) to Fe(III) converts myoglobin to metmyoglobin. Oxidized forms of myoglobin and hemoglobin are responsible for the brown color of old meat and dried blood

Hemoglobin
Animals > 1 mm thick use circulatory system and oxygenbinding proteins to deliver oxygen to the interior tissues. Hemoglobin, the major component of erythrocytes, transports O2 from the lungs to respiring tissue that returns carbon dioxide (CO2).
In erythrocyte, carbonic anhydrase catalyzes the reaction CO2 + H2O H+ + HCO3-

Hemoglobin binds bicarbonate (HCO3- ) and carries it to lung

Hemoglobin
Figure 7-5

Hemoglobin is a tetramer consisting of two and two subunits The subunits are similar to each other and to myoglobin
Oxygen binding alters structure of the tetramer

Sickle-Cell Anemia
Hereditary disease caused by the recessive gene of hemoglobin variant in which -chain has Val6 instead of Glu6 in normal hemoglobin
VHLTPEEKSA... Normal -chain VHLTPVEKSA... Variant -chain

Fig. 7-18

Val6 fits into a hydrophobic pocket on another hemoglobin molecule

Sickle-Cell Anemia
Hemoglobin molecules polymerize and form fibers that cause erythrocyte deformation
Fig. 7-17

Fig. 7-18