Proteins, DNW

"Amino Acids, Peptides and Proteins: Chemistry, Structure and Function"

Polyamides

Nylon (polyamides) from condensation polymerisation, e.g.

nH₂N-(CH₂)₆-NH₂ + nClOC-(CH₂)₄-COCl → (-HN-(CH₂)₆-NH-CO-(CH₂)₄-CO-)_n (nylon 6,6 with amide bond in bold) + 2nHCl

Aramids e.g. Kevlar

Amino acids

Amino acids
All naturally-occurring amino acids have the (S) configuration, except cysteine which is (R):
(because of its C-S side chain, which unlike all other side chains, has a higher priority than the CO₂H group)

Proteins

Protein structure

Protein structure, Protein folding, Protein structure prediction, Membrane protein
Keratin, especially β-keratins (a kind of scleroprotein [AKA fibrous protein], thus a type of quaternary structure alongside globular proteins)
π-π stacking interactions
Ubiquitin (PDB 1UBQ ubiquitin), Proteasomes

Amino acids by polarity and structure

Chemical polarity of amino acids: F A M I L Y V W - hydrophobic, D E H K N Q R S T - polar, G P C - special
Proline (Pro, P) is special:

It's a secondary amino acid (AKA imino acids, although this nomenclature is disputed)

It's conformationally locked (backbone dihedral angle φ fixed to about −75°) → very rigid, loses less conformational entropy upon folding, found in turns

More protein structure

Primary structure

Primary structure: sequence of amino acid backbone (plus cross-linking such as disulfide bonds)

Secondary structure

Secondary structure: alpha helices, beta strands (plus rare others)

Tertiary structure

Tertiary structure: three-dimensional structure (full set of atomic coordinates in 3D space) - determined by protein crystallography or protein NMR

all α-structures (αα) - buffers, triggers, allostery
- calbindin - (2 × EF hand) mops up loose Ca²⁺
- myoglobin - baby brother of haemoglobin - 8 helices, haem group binds Fe and thus O₂
all β-structures (ββ) - hard-as-nails brick walls → rigidity
- viral capsids
- plastocyanin
- antibodies

Quaternary structure

Quaternary structure: arrangement of multiple folded protein molecules in a multi-subunit complex - XRD again

Ramachandran plots

Ramachandran plot

UV-Vis spectroscopy can be used to determine protein concentration - aromatic amino acid side chains (K, Y, W, H) absorb UV

Supersecondary structure

Supersecondary structure
- EF hand - chiral, right-handed enantiomer only (with one exception). Aspartic acid residues bind Ca²⁺ (important in calcium signaling) in loop between two alpha helices.
- Beta hairpin - major structural unit, two beta strands antiparallel
- βαβ motif - two beta strands parallel, chiral (alpha helix either above or below plane of beta strands), only right-handed enantiomer found in nature
- Coiled coil - left-handed(!) - HPPHPPP repeat gives 3.5 not 3.6 residues per turn, so hydrophobic seam slowly curves - myosin, keratin
- Polyproline helix?
- Collagen helix?

Plastocyanins - Cu redox centre converts between Cu(I) and Cu(II), coordination geometry of Cu is not optimal for either oxidation state, making neither favoured and thus interconversion facile. Structures: PDB 3BQV, PDB 1PNC.