protein primary structures

how to stabilize an alpha helix

• hydrophobic interactions

• energetically efficient use of hydrogen bonds

• maintain optimal pH and temp

how to destabilize an alpha helix

• bulky R groups

• get rid of hydrogen bonds

• extreme pH, high temp

oppositely charge R groups 3 amino acids away from each other form…

ionic interactions

nonpolar R groups that are 3 amino acids away are close enough in 3D space to form…

hydrophobic interactions

van der Waals interactions can support formation through

bulky side groups (R groups)

Beta sheets

made up of multiple beta strands, can be parallel or anti parallel

Pro B sheets

• large R groups

• anti-parallel: short distance hydrogen bonding, stronger than parallel

• hyrophobic interactions stabilize beta sheet stacking

Anti Beta sheets

• repulsion

• proline and glycine found in B turns but not sheet itself

Beta turns

• 4 AA sequence for tight 180degree turn

• 1st and 4th residues - between carbonyl oxygen and amide hydrogen

• proline at position #2

  • cis confirmation

  • frequently bent due to bonding of side chain and main chain backbone

• glycine at position #3

  • small side chain allowing it to be small and flexible

Beta sheets in spider silk

• the beta sheets of fibroin are stacked on top of each other

• side chains are pointing toward and away from you

• silk does not stretch because it is in the extended confirmation

• flexible, can bend because sheets are held together by non-covalent interactions

globular proteins

• made up of alpha-helices, B-sheets, B-turns, and disordered segments

primary protein structure

the sequence of amino acids (from N to C terminus)

secondary structure

describes how a local region of the polypeptide folds (due to interactions between A.A. residues)

different representations of proteins

Ribbon Diagram, Surface Contour, and Space-filling

Common secondary structures form because they optimize _________ and they minimize __________ between atoms!

main-chain hydrogen bonds, steric clashes

Alpha helices

• Hydrogen bond every 4th amino acid

• R groups oriented externally (since they are bulky!)

  • Interactions can form to stabilize alpha helix

• Energetically efficient use of hydrogen bonds (almost every peptide bond forms a hydrogen bond, each alpha helix turn is supported by 3-4 hydrogen bonds = stable)

ionic interactions

can form between 4th amino acids R groups to stabilize

hydrophobic interactions

can also form between relevant 4th residues to stabilize helix 

tertiary structure

• overall 3D shape of entire protein (fiber vs globular)

Quaternary structure

• overall structure of 2 or more polypeptides interactions

motifs

• folding pattern involving two or more types of secondary structure

Domains

• part of a polypeptide chain that is independently stable/able to move. Domains can contain motifs

Based on thermodynamics, main idea is that…

folding is favorable! (-ΔG )

chaperone

a protein that helps other proteins fold correctly

Levinthal’s Paradox

• takes way too long to try every combination so there are steps to folding (secondary structure form first)

• some proteins need the help of chaperones