Biochemistry_S7-8

Chapter 4: The Three-Dimensional Structure of Proteins

Overview

• Focus on the three-dimensional structures of proteins and their significance in biological functions.

Chapter Outline

• 4-1: Protein structure and function

• 4-2: Primary structure of proteins

• 4-3: Secondary structure of proteins

• 4-4: Tertiary structure of proteins

• 4-5: Quaternary structure of proteins

• 4-6: Protein-folding dynamics

Structure of the Peptide Bond

• Peptide Bonds:

  • Formed between amino acids; consists of 3 covalent bonds (Cα—C—N—Cα).

  • Resonance effects lead to rigidity and planarity in the bond, creating a dipole moment.

Peptide Conformation (Figure 4.1)

• Visualization of the amide plane and orientations of peptide bonds.

Peptide C—N Bonds

• Rotation Limitations:

  • Six atoms of the peptide lie in a single plane, characterized by a partial double-bond character of the C—N bond that restricts rotation.

Primary Structure of Proteins

• Definition: The linear chain of amino acids in a protein, extending from the N-terminus to the C-terminus.

• Free amino and carboxyl groups define structural ends.

• Each amino acid influences the third-dimensional conformation and functionality of the protein.

• Example: A single amino acid change can result in conditions like sickle-cell anemia.

Protein Structure Complexity

• Proteins have diverse conformations due to the flexibility of amino acids.

• Native Conformation: Defined as the biologically active 3D shape of the protein.

Four Levels of Protein Structure

• Primary Structure (1°): Sequence of amino acids.

• Secondary Structure (2°): Local folded structures stabilized by hydrogen bonds, including alpha helices and beta sheets.

• Tertiary Structure (3°): Overall 3D structure of the protein.

• Quaternary Structure (4°): Assembly of multiple polypeptide chains or subunits.

Secondary Structure Details

• Hydrogen Bonds: Stabilize various structures; includes alpha helices and beta-pleated sheets.

  • Alpha Helix:

    • Simplest form, maximizes hydrogen bonding (3.6 residues per turn, 5.4 Å pitch).

    • Right-handed coil with all R groups projecting outward.

• Beta Sheets:

  • Organized into strands that can be parallel or antiparallel, stabilized by hydrogen bonds.

  • Beta Turns: Connects segments of β sheets, typically involves 4 residues with a 180° turn.

Supersecondary Structures

• Result from combinations of α and β structures; include motifs like:

  • αβ Units: Parallel strands connected by α helices.

  • αα Units: Two antiparallel α-helices.

  • β-Meander: Antiparallel β sheet formation.

Protein Tertiary Structure

• Overall 3D arrangement determined by weak interactions and covalent bonds among side chains.

• Influenced by hydrophobic/polar interactions and disulfide bonds.

Types of Proteins

• Fibrous Proteins: Long, strand-like structures, insoluble, provide strength.

• Globular Proteins: Spherical, more soluble, often function as enzymes.

• Membrane Proteins: Embedded in hydrophobic lipid membranes.

• Intrinsically Disordered Proteins: Lack stable tertiary structures.

Collagen Structure

• Found in connective tissues; organized in a triple helix providing great tensile strength.

• Characterized by a repeating sequence that includes proline and glycine residues.

Determination of Tertiary Structure

• X-ray Crystallography: Creates a structural model from diffraction patterns of X-rays.

• Nuclear Magnetic Resonance (NMR): Analyzes protein structure in solution.

• Cryo-Electron Microscopy (cryo-EM): Allows observation of proteins in a near-native state frozen in ice.

Protein Quaternary Structures

• Assembly of multiple subunits; characterized by noncovalent interactions such as hydrogen bonds and hydrophobic interactions.

• Allosteric Proteins: Exhibit conformational changes that affect function based on subunit interactions.

Denaturation and Refolding

• Denaturation refers to the loss of 3D structure due to factors like pH changes, heat, detergents, or chemicals.

Myoglobin and Hemoglobin

• Myoglobin: Single polypeptide chain that stores oxygen.

• Hemoglobin: Tetramer that transports oxygen in the bloodstream.

• Binding properties: Hemoglobin demonstrates positive cooperativity in O2 binding.

• Differences in functions and binding affinities between myoglobin and hemoglobin provide insight into their roles in oxygen transport and storage.

Each imaging technique for determining tertiary structure has its advantages and disadvantages:

1. X-ray Crystallography

   • Pros:

     • High resolution, often down to atomic-level details.

     • Provides information on the arrangement and orientation of atoms in the protein.

   • Cons:

     • Requires protein crystallization, which can be a limiting factor as not all proteins crystallize easily.

     • May not represent the protein's natural state, as proteins might behave differently when crystallized.

2. Nuclear Magnetic Resonance (NMR)

   • Pros:

     • Can study proteins in solution, providing insights into their natural behavior and dynamics.

     • Useful for smaller proteins (typically < 50 kDa) and allows observation of conformational changes.

   • Cons:

     • Limited to smaller proteins due to the complexity of spectra for larger molecules.

     • Lower resolution compared to X-ray crystallography, and data interpretation can be challenging.

3. Cryo-Electron Microscopy (cryo-EM)

   • Pros:

     • Can analyze large macromolecular complexes and proteins in close to their native state without crystallization.

     • Increasingly high resolution with advances in technology.

   • Cons:

     • Generally lower resolution compared to X-ray crystallography.

     • Sample preparation can be complex, and data collection may require sophisticated equipment.