moduel 4: Proteins

amino acid = AA

What does is structure influenced by and what does it determine?

• thermodynamics and chemical interactions drive folding

• folding determines function

levels of protein structure

• primary structure

• secondary structure

• tertiary structure

Primary structures

• linear AA sequence

• dictated by DNA

• contains “instructions” for folding

secondary structures

• folding of backbone only (not side chains)

• governed by:

  • peptide bond rigidity

  • H bonding

• structural constraints

  • peptide bond = partial double bond making structure rigid (planar)

  • only rotation allowed around

    • phi: N- C(alpha)

    • psi: C(alpha)-C

    • angles determine allowed conformations (Ramachandran plot)

• Types:

  • Beta sheets

  • Alpha Helix

Alpha Helix

• helical coil (3.6 residues/turn)

• stabilized by H bonds (i → i + 4)
  

• key features:

  • R-groups pt outward

  • has a dipole:

    • N-terminus → +

    • C-terminus → -
      

• AA effects:

  • alanine → stabilizes helix

  • proline → breaks helix (rigid kink)

  • glycine → too flexible
    

• structure depends on BOTH sequence + residue positioning

beta sheets

• extended zig-zag strands

• stabilized by inter-strand H-bonds

• still backbone drive (like a-helix), but diff geometrey

types:

• antiparallel (more stable)

• parallel

tertiary structures

• full 3D folding of entire pp

• driven mainly by side chain interactions

Hydrophobic effects and protein folding

• folding driven by entropy of water, not protein

  • water forms cages around phobic residues → entropy decreases

    • phobic residues limit number of H-bonds free H2O moelcules can make → thermodynamically unfavourable

      • causes water to surround residues to conserve H - bonds and reduce entropy

  • folding releases water → increases entropy (favourable)

• phobic residues → buried inside protein

• phillic residues → exposed to water

how do thermodynamics influence protein folding

• folding dec. protein entropy, and increases water entropy (net favourable)

forces involved in folding

• folding balances all forces

• forces include:

  • H bonds

  • electrostatic interactions

  • van der waals

  • phobic interactions

  • thermodynamic forces

  • cooperativity

why is folding a cooperative process?

• it is all or nothing (folding produces very little intermediates)

• not independant = formation of one interaction → stabilizes structure → makes next easier

  • ex. like zipper

    • few first teeth are hard to close

    • once started, rest zip up quixkly

• ensures fast, accurate and complete folding

• usually during folding of secondary structures

cooperative folding mechanism

• 1. Initial interactions (rate-limiting)

  • First hydrophobic contacts or H-bonds form

  • This reduces conformational freedom

• 2. Reduction in conformational space

  • Protein has fewer possible shapes

  • Easier to find correct interactions

• 3. Cascade effect

  • More interactions form rapidly:

    • Hydrophobic clustering

    • Hydrogen bonds (α-helix, β-sheet)

    • Electrostatic stabilization

• 4. Folding nucleus

  • Small stable core forms early

  • Acts as a template/scaffold for rest of folding

motifs

• small, recurring structure (ex. β-α-β loop)

• helps predict function

domain

• independently stable unit

• can function on its own

• proteins = modular

protein types

• fibrous

• globular

• membrane

fibrous proteins

• structural roles in cells and tissues

• structure: elongated/filamentous in shape

• some fibrous proteins are permanent and build to last and not be degraded/modified/regulated (ex. collagen and keratin)

• some are regulated (ex. actin and tubulin)

  • actin and tubulin form regulated fibrous but are not fibrous themselves

• EXAMPLES:

  • colalgen and keratin which both share coiled-coiled structural domain

globular proteins

• carry out chxm work in cell (ex. synthesis, transport and metabolism)

• structure: compact structures

  • tertiary structure of flobular portein determines function

  • phobic AA’s are at core of protein, phillic/polar AA’s on surface

• ex. myoglobin and hemoglobin

membrane proteins

• has high proportion of phobic AA

  • allows protein to interact with phobic acyl chains of the lipid bilayer

    • they do this by resting on top of lipid bilaer (partially buried in lipid membrane - these are called peripheral membrane [rpteons)

    • could also be integrated in lipid bilayer (integral membrane proteins)

• examples: ATP synthase and insulin receptor