Protein Structure and Function

Protein Structure and Function

• Proteins are essential components of cells; their shapes, functions, and responses to the environment determine cellular behavior.

Review of Basic Concepts

• The pKa of a group is the pH at which it is 50% protonated.
• A group is primarily protonated at pH values lower than its pKa.
• Carboxylic acids are considered acidic due to their low pKa, meaning they are deprotonated at neutral pH.
• Basic groups have a high pKa.
• Elements towards the upper right of the periodic table are more electronegative.
• Peptide bonds form via dehydration reactions and have a partial double bond character, contributing to their planar nature.
• Cysteines can be oxidized to form disulfide bonds - a process favored in oxidizing environments, such as the extracellular space; reducing environments, like the cytosol, prevent disulfide bond formation.
• Hydrogen bonds have lengths between 1.6 and 2.0 Angstroms.
• Van der Waals forces between nonpolar groups are weak; the aggregation of hydrophobic domains in proteins is driven primarily by entropy of water molecules, not by Van der Waals forces.
• All amino acids, except glycine, are chiral and exist in the levorotary (L) form in all known life.

Levels of Structural Organization

• Proteins have four levels of structural organization:
  • Primary: Amino acid sequence
  • Secondary: Alpha-helices, beta-sheets, and loops
  • Tertiary: Entire polypeptide chain, bundles of helices and sheets, domains
  • Quaternary: Multiple subunits folded into a complex

Amino Acids

• Dihedral angle: The spatial arrangement of amino acids is defined by three dihedral angles:
  • Φ (phi): angle along the N-Cα bond
  • Ψ (psi): angle along the Cα-C bond
  • Ω (omega): angle along the C-N bond

Peptide Bond

• Dihedral angles in a polypeptide:
  • The Ω angle is always 0 or +180 degrees.
  • Analyzing Φ and Ψ angles reveals preferred conformations:
    • Alpha-helix combinations
    • Beta-sheet configurations
    • A less common structure called Lα (left-handed alpha-helices)
  • The trans conformation of Ω is favored due to steric hindrance between consecutive side chains.
  • Proline's unique structure allows for a cis conformation because it is anchored to the backbone.

Secondary Structure

• α-helix:

  • Forms due to hydrogen bonding between the backbone NH and C=O groups.
  • Contains 3.6 residues per turn, with each residue spanning 100 degrees of rotation.
  • Consecutive α-helix turns are separated by 5.4 Angstroms.
  • Almost exclusively right-handed.
  • Amphipathic helices have hydrophobic residues on one side and hydrophilic residues on the other.
  • Fully buried helices consist of hydrophobic residues, and fully exposed helices are composed of hydrophilic residues.

• β-sheet:

  • Also forms through hydrogen bonds between backbone NH and C=O groups.
  • All potential hydrogen bonds are satisfied, except for the flanking strands at the sheet ends.
  • About 20% of beta-sheets are mixed parallel and anti-parallel, the other 80% are purely one type or the other.
  • β-sheets are not flat, but pleated.

Disulfide Bonds

• Ribonuclease:

  • Contains disulfide bonds.
  • Illustrates Anfinsen's experiment, which suggested that primary sequence determines structure (current understanding is more nuanced).

• Insulin:

  • Also contains disulfide bonds.

• Immunoglobulins:

  • Chains are held together by disulfide bonds.

Protein Carriers

• Cholesterol:

  • Transported by high-density lipoprotein (HDL) and low-density lipoprotein (LDL) particles.
  • Apolipoproteins within these particles play a crucial role.

• Solute Lipid Carriers (SLC family):

  • Transport carboxylic acids and small molecules.

• Myoglobin (Mb) and Hemoglobin (Hb):

  • Transport oxygen.

Hemoglobin

• Oxygen-carrying team:

  • Hemoglobin: carries oxygen (transport function).
  • Myoglobin: stores oxygen (repository function).

• Saturation curves:

  • Myoglobin: exhibits a parabolic curve, indicating simple binding.
  • Hemoglobin: displays a sigmoidal (S-shaped) curve, reflecting cooperative binding between heme units in the tetrameric structure.

• Hemoglobin and oxygen:

  • Hemoglobin's affinity for oxygen increases with rising oxygen pressure.
  • Oxyhemoglobin: Hemoglobin with bound oxygen.
  • Deoxyhemoglobin: Hemoglobin without bound oxygen.
  • HbO2 is a stronger acid than Hb.
  • In acidic environments, Le Chatelier's principle dictates that the equilibrium shifts towards the weaker acid (Hb), releasing oxygen - an adaptation crucial for oxygen delivery to tissues with high oxygen consumption.

• Crystal structures:

  • X-ray diffraction structures solved by Perutz and Kendrew (1961 Nobel Prize).
  • Myoglobin (Mb): contains seven helical chains, with heme nestled in the middle, secured by histidines; prolines create bends between helices.
  • Hemoglobin (Hb): similar amino acid sequence to Mb; its structure prevents oxidation of Fe(II) to Fe(III), which would render the molecule incapable of binding oxygen.

This quiz explores the fundamental concepts of protein structure and function, including key principles like pKa, peptide bonds, and molecular interactions. Understand how proteins interact within cellular environments and the significance of structural features in their functionality. Test your knowledge on the essential roles that proteins play in biological systems.