Concise Notes on Protein Secondary Structures

Protein Secondary Structure

Proteins: Three-Dimensional Structure (Chapter 6)

Protein Secondary Structure (Part 1)

• Unlike most organic polymers, protein molecules adopt a specific three-dimensional conformation.

• This structure can fulfill a specific biological function

• This structure is called the native fold

• The native fold has many favorable interactions within the protein

Favorable Interactions in Proteins

• Hydrophobic effect

  • Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy.

  • Predominate in protein folding

• Hydrogen bonds

  • Interaction of $N-H$ and $C=O$ of the peptide bond leads to local regular structures such as $\alpha$-helices and $\beta$-sheets.

  • Occur within protein

• Van der Waals interactions

  • Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein

• Electrostatic interactions

  • Long-range strong interactions between permanently charged groups

  • “Salt-bridges” (ionic interactions), especially buried in the hydrophobic environment, strongly stabilize the protein.

  • Ionic interactions within the protein are maximized

Levels of Protein Structure

• Primary structure: Amino acid sequence in a polypeptide chain.

• Secondary structure: ($\alpha$-helix)

• Tertiary structure: One complete protein chain ($\beta$ chain of hemoglobin)

• Quaternary structure: The four separate chains of hemoglobin assembled into an oligomeric protein

Peptide Bonds and Conformation

• Peptide Bonds Assume Trans Conformation

• The Peptide Bond Is Rigid and Planar

  • 3 covalent bonds separate the $\alpha$ carbons of adjacent amino acid residues: C$\alpha$ —C—N—C$\alpha$

  • The N—C$\alpha$ $and$C$\alpha$ —C bonds can rotate

  • The peptide bond is a resonance hybrid of two structures

    • Resonance between the carbonyl oxygen and the amide nitrogen

    • Less reactive

  • Partial negative charge and partial positive charge sets up a small electric dipole

  • There is no rotation around the bond

Extended Conformation of Polypeptide

• 6 atoms of the peptide group lie in a single plane

• Partial double-bond character of $C—N$ peptide bond prevents rotation, limiting range of conformations.

Torsion Angles of Polypeptide Backbone

• Torsion angles ($-180 \sim +180^\circ$)

  • $\phi$ (phi) = dihedral angles around the $C_{\alpha} – N$ bond

  • $\psi$ (psi) = dihedral angles around the $C_{\alpha} – C$ bond

• Many $\phi$ and $\psi$ values are prohibited by steric interference

• $\phi$ and $\psi$ cannot both = 0 degrees

• In a fully extended polypeptide, both $\phi$ and $\psi$ are 180° (1st and 4th atoms farthest away)

Ramachandran Plot

• Ramachandran plot for L-Ala residues

  • Dark blue represents conformations that involve no steric overlap and thus are fully allowed

  • Medium blue indicates conformations allowed at the extreme limits for unfavorable atomic contacts

  • Lightest blue indicates conformations that are permissible if a little flexibility is allowed in the dihedral angles.

  • Yellow regions are conformations that are not allowed.

Protein Secondary Structure

• Secondary structure = describes the spatial arrangement of the main-chain atoms in a segment of a polypeptide chain

  • Regular secondary structure = $\phi$ and $\psi$ remain the same throughout the segment

  • Common types = $\alpha$ helix, $\beta$ conformation, $\beta$ turns, random coils

$\alpha$ Helix

• $\alpha$ helix = simplest arrangement, maximum number of hydrogen bonds

  • Backbone wound around an imaginary longitudinal axis

  • R groups protrude out from the backbone (roughly perpendicular with the helical axis)

  • Each helical turn = 3.6 residues, $\sim 5.4 \text{Å}$

    • Pitch = distance the helix rises along axis per turn

length per amino acid $= (5.4 \text{Å per turn}) / (3.6 \text{amino acids per turn}) = 1.5 \text{Å}$

Handedness of the $\alpha$ Helix

• Right-handed:

  • R groups protruding away from the helical backbone

  • Most common

• Extended left-handed:

  • Theoretically less stable, not observed in proteins

Intrahelical Hydrogen Bonds

• Between hydrogen atom attached to the electronegative nitrogen atom of residue n and the electronegative carbonyl oxygen atom of residue n + 4

• Confers significant stability

• Optimal distance between donor and acceptor atoms for H bonds

Amino Acid Sequence Affects Stability of the $\alpha$ Helix

• Amino acid residues have an intrinsic propensity to form an $\alpha$ helix

• Interactions between R chains spaced 3–4 residues apart or nearest neighbors can stabilize or destabilize $\alpha$ helix

  • Charge, size, and shape of R chains can destabilize

  • Formation of ion pairs and hydrophobic effect can stabilize (3–4 residues apart)

Proline and Glycine Occur Infrequently in an $\alpha$ Helix

• Proline = introduces destabilizing kink in helix

  • Nitrogen atom is part of rigid ring

  • Rotation about $N—C_{\alpha}$ bond not possible

• Glycine = high conformational flexibility, take up coiled structures different than $\alpha$ helix

Summary: Sequence Affects Helix Stability

• Not all polypeptide sequences adopt α-helical structures

• Small hydrophobic residues such as Ala and Leu are strong helix formers

• Pro not found in α helices because the no rotation around the N-Cα bond

• Gly not usually found in α helices because the tiny R-group allows many other possible conformations

• Attractive or repulsive interactions between side chains 3–4 amino acids apart will affect formation

Propensity of Amino Acid Residues to Take Up an $\alpha$-Helical Conformation

• $\Delta\Delta G^\circ$ is the difference in free-energy change, relative to that for alanine, required for the amino acid residue to take up the $\alpha$-helical conformation. Larger numbers reflect greater difficulty taking up the $\alpha$-helical structure.

The $\beta$ Conformation Organizes Polypeptide Chains into Sheets

• $\beta$ conformation = backbone extends into a zigzag

  • $\beta$ strand = single protein segment

  • $\beta$ sheet = several strands in $\beta$ conformation side by side

• Side chains protrude from the sheet alternating in up and down

Adjacent Polypeptide Chains in a $\beta$ Sheet Can Be Antiparallel or Parallel

• H bonds form between backbone atoms in different strands

• Antiparallel = H-bonded strands run in opposite direction

  • Occur more frequently

  • Linear H-bonds (stronger)

• Parallel = H-bonded strands run in the same direction

  • Bent H-bonds (weaker)

Connecting Adjacent $\beta$ Strands

• $\beta$ turns = connect ends of two adjacent segments of an antiparallel $\beta$ sheet (occur frequently whenever strands in $\beta$ sheets change the direction)

  • 180° turn

  • Involves 4 residues

  • Hydrogen bond forms between first and fourth residue

  • Pro (residue 2) and Gly (residue 3) often occur in $\beta$ turns

Secondary Structure Conformations are Defined by $\phi$ and $\psi$ Values

• Ramachandran Plot: visual description of combination of $\phi, \psi$ that are permitted in a peptide backbone and that are not permitted due to steric hindrance

$\phi$ and $\psi$ Values from Known Proteins Fall into Expected Regions

• Glycine frequently falls outside the expected ranges