Protein Structure and Folding

Protein Structure and Folding Notes

Amino Acid Conformation

  • Conformationally Restricted Amino Acid: Proline (Pro) is the most conformationally restricted due to its cyclic structure.
  • Least Conformationally Restricted Amino Acid: Glycine (Gly) is the least restricted because it only has a hydrogen atom as its side chain.

Alpha Helix

  • Characteristics:
    • 3.6 amino acids per turn.
    • Hydrogen bond forms between the carbonyl oxygen of the nnth amino acid residue and the -NH group of the (n+4)(n + 4)th amino acid residue.
    • Right-handed helix.
    • Proline is typically not found in the α helix due to its conformational restriction.
  • Incorrect Statement: Glycine is NOT required every third amino acid residue in an alpha helix.

Beta Sheet

  • Characteristics:
    • Amino acid side chains are located both above and below the sheet.
    • β sheets have a pleated edge-on appearance.
    • Can exist in either parallel or antiparallel configurations.
    • Sheets can contain as few as two and as many as 22 polypeptide chains.
  • Incorrect Statement: Parallel β sheets containing fewer than five chains are NOT the most common.

Fibrous Proteins

  • Characteristics:
    • Usually contain only one type of secondary structure.
    • Usually exhibit structural or protective characteristics.
    • Have usually elongated hydrophilic surfaces.
    • Usually insoluble in water.
  • Incorrect Statement: Domains do NOT have a globular fold in fibrous proteins.

Collagen

  • Requirements for Structure:
    • Glycine every 3rd amino acid is essential for the triplet helix formation.
  • Statements:
    • The inability to hydroxylate proline results in the inability to synthesize collagen.
    • Hydrogen bonds between the ─OH groups of Hyp residues stabilize the helix.

Crystalline Proteins

  • Properties:
    • Many crystallized enzyme proteins remain catalytically active.
    • The diffractive pattern observed during X-ray exposure to the crystal can be used to calculate the electron density map of the crystalline protein.
    • The larger region indicating electron density within the electron density map, the more accurate the structure determination.

Prolyl Oxidase and Scurvy

  • In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in scurvy.

Tertiary Structure Stabilization

  • Amino Acid Combinations: Lys and Glu have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein.

Protein Digestibility

  • The low pH found in the gut can enhance the digestibility of dietary protein by causing protein denaturation.

Protein Folding

  • When folding a disordered polypeptide chain into a stable protein formation, the aggregation of hydrophobic regions in the protein occurs first.

Chaotropic Agents

  • Treatment of a protein with a high concentration of a chaotropic agent results in:
    • Nonpolar portions of the protein becoming more soluble.
    • The protein beginning to denature.

Beta Sheets: Parallel and Antiparallel

  • For β-sheets, the terms 'parallel' and 'antiparallel' refer to the 'direction' of the associated peptide strands.

Molecular Chaperone Proteins

  • Molecular chaperone proteins function by preventing premature folding by binding hydrophobic regions of the protein.

NMR Spectroscopy

  • Conventional one-dimensional NMR spectroscopy is generally NOT an effective tool for determination of protein structure because:
    • Proteins (including small proteins) have a high number of hydrogen atoms.
    • The NMR spectra exhibit high peak overlap.

Protein Structure Similarities

  • Proteins with the same function from a different species are likely to have similar motifs.
  • An effective protein motif is likely to be observed in multiple proteins.
  • Proteins with the same motifs are likely to perform similar functions.
  • False Statement: Proteins with the same function from different species are likely to be more similar in sequence than in structure.

Noncovalent Forces Stabilizing Protein Structure

  • Noncovalent forces that stabilize protein structure include:
    • The hydrophobic effect
    • Salt bridges
    • Electrostatic interactions with metal ions
    • Hydrogen bonding
  • Exception: Disulfide bridges are covalent bonds, not noncovalent forces.

RNase A Refolding Experiment

  • The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that 1° (primary) structure can determine 3° (tertiary) structure.

Chaperonins (GroEL/ES System)

  • Chaperonins such as the GroEL/ES system require ATP hydrolysis.

Protein Diseases

  • Protein diseases can be caused by:
    • Mutations affecting the 1° structure.
    • Mutations affecting the 3° structure.
    • Changes in the post-synthetic processing of proteins.

Protein Stability

  • A β sheet region made up of amino acids Val, Ile, Phe would be most stable.

Energetics of Protein Structures

  • Hydrogen bonds and maximum separation of amino acid side chains make the α helix and β sheet very stable and energetically favorable.

Chaperonins Function

  • A chaperonin helps fold some proteins in their lowest energy state.

Alpha Helix Structure

  • If a helix has hydrogen bonds between the carbonyl group from residue “nn” and the amino group of residue “n+6n+6,” it has more residues per turn than an α helix.

Protein Folding - Minimizing Energy

  • Orientating amino acid groups to maximize hydrogen bonding contributes to the minimization of energy that occurs with protein folding.

Creutzfeld-Jakob Disease

  • Creutzfeld-Jakob Disease is caused by the aggregation of a misfolded protein.

Protein Denaturation

  • Proteins can denature due to a change in:
    • pH
    • Temperature
    • Ionic strength

Protein Purification with Organic Solvents

  • Changing from water to an organic solvent in protein purification:
    • Proteins with hydrophilic groups on the exterior would denature and likely precipitate.
    • Proteins with exposed hydrophobic groups would maintain their structure and remain in solution.

Protein Refolding and Primary Sequence

  • Spontaneous refolding of proteins into their native state under physiologic conditions helped to solidify the connection between primary amino acid sequence and 3-D structure.

Molecular Chaperones

  • Molecular chaperones bind to unfolded or partially folded polypeptide chains to ensure that improper aggregation of hydrophobic segments does not occur.