Protein Structure and Function

Introductory Biochemistry

Overview of Protein Structure and Function

  • Proteins are macromolecules whose function is determined by their structure.

Structure of Myoglobin and Hemoglobin

  • Myoglobin

    • Type: Monomer (1 subunit and 1 polypeptide chain)

    • Contains: 154 amino acids (aa) and 1 domain

    • Structural Organization: Has only tertiary structure

  • Hemoglobin

    • Type: Oligomer (4 subunits)

    • Each subunit: Contains 1 domain

    • Structural Organization: Has quaternary structure; specifically, a heterotetramer.

Red Blood Cells in a Capillary

  • Hemoglobin functions to bind O2 in the lungs and release it in the tissues.

Function of Myoglobin

  • Myoglobin serves several critical roles:

    1. Acts as a local reserve of oxygen (O2) during periods of intense exercise.

    2. Functions to store O2 in aquatic animals, allowing them to remain submerged for extended periods.

    3. Facilitates the diffusion of O2 through muscle tissue, enhancing oxygen delivery to muscle cells.

    4. Inactivates nitric oxide (NO) and scavenges reactive oxygen species (ROS) to protect tissues from oxidative stress.

  • Myoglobin is specifically classified as a cytoplasmic hemoprotein.

Protein-Ligand Interactions

  • Many proteins depend on their ability to reversibly bind small molecules termed ligands.

  • Affinity Concept:

    • The greater the affinity of Protein X for Ligand Y, the more of the complex XY will be present at any given concentration of Y or X.

  • Interactions:

    • The interactions that link protein X and ligand Y can involve various types, including hydrogen bonds, ionic interactions, hydrophobic effects, and van der Waals forces.

Ligand Binding Curves

  • Represents the relationship between binding sites being full and the concentration of protein.

  • Expression for binding equilibrium:
    X.Y⇌X+YX.Y \rightleftharpoons X + Y

  • The dissociation constant, Kd, is defined:
    Kd=[X][Y][XY]Kd = \frac{[X][Y]}{[XY]}

  • At a concentration where 50% of binding sites are occupied:

    • This is the point where Kd is reached.

Ligand Affinities

  • Comparative Affinity of Protein X for Ligands Y and Z:

  • If Kd for ligand Y is lower than that for ligand Z, it indicates:

    • Ligand Y has a higher affinity (lower Kd) compared to ligand Z (higher Kd).

  • Observations from binding curves:

    • Kd Y: lowest Kd (highest affinity)

    • Kd Z: highest Kd (lowest affinity)

Structure of Myoglobin

Detailed Structure

  • Hydrophobic Pocket

    • Located between helices E and F.

Significance of Heme Prosthetic Group

  • Myoglobin requires the heme group for its functional capability.

  • Structure Breakdown:

    • Consists of 154 amino acids, 8 alpha-helices, and irregular structures (loops).

    • The heme group is a prosthetic group essential for Myoglobin’s activity.

Heme Structure

  • Porphyrin Ring

    • Contains one Fe2+ iron ion coordinated between four nitrogen (N) atoms of the ring.

    • The two substituents at the bottom of the ring are polar propionyl groups while the rest are non-polar aliphatic groups.

    • Key feature: Heme is circular and planar.

Coordination Bonds of Heme

  • The Fe2+ ion in heme can form 6 coordination bonds:

    • 4 with nitrogen from the porphyrin

    • 5th with the globin protein.

    • 6th position occupied by the proximal histidine (HisF8) which is crucial for binding.

Mechanism of O2 Binding

Binding to the Heme Group

  • O2 binds to the Fe2+ ion through the 6th coordinate position, facilitated by the proximal histidine (HisF8).

  • The distal histidine (HisE7) assists in the binding of O2 to improve specificity.

  • The binding of heme to the polypeptide helps prevent the oxidation of Fe2+ which is essential for its proper function.

Binding Site Optimization

  • The design of binding sites in myoglobin is precise to enhance binding specificity and affinity, comprising:

    • His F8: Proximal histidine

    • His E7: Distal histidine

Specificity and Affinity in Heme Binding

  • Affinity Comparisons

    • When stripped of globin, carbon monoxide (CO) binds to heme with more than 20,000 times the affinity of O2.

    • Other ligands like cyanide (CN-) and hydrogen sulfide (H2S) also bind with high affinity.

  • When heme is attached to globin:

    • CO binds with only greater than 200 times the affinity compared to O2, suggesting that the presence of globin reduces the reactivity of heme towards CO, enhancing its specificity for O2.