8-10 proteins

X- ray diffraction

discovery of repetitive 3D structural features

alpha helices, beta pleated sheets

X ray Crystallography, Nuclear magnetic resonance and cryto- electron microscopy

3D structure with atomic resolution

Peptide bond configurations

• Trans

• Cis

Trans

2 Alpha carbon atoms of adjacent residues that are on opposite sides of the peptide bond

no steric clashes between adjacent residues

Cis

2 alpha carbon atoms of adjacent residues are on the same side of the peptide bond

Proline

• Nitrogen aton of backbone is bonded to its sidechain

• in a polypeptide has no NH

unfolded peptides and proteins

the relative probability of the proline peptide bonds in trans and cis are 2/3 trans, 1/3 cis

infolded proteins

proline peptide bonds are in cis

the enzyme: proline cis/trans isomerase converts them from cis to trans

what determines backbone conformation

• dihefral angles:

1) (𝜔) close to 180

2) (𝜙) phi rotation around the NC bond

3) (𝜓) psi rotation around CC bond (c’ is carbonyl c)

Ramachandran plot

graph describing backbone conformation

tertiary structure stabilized by:

• van der waals interactions

• ionic interactions

• H- bonds

protein folding (structure formation) driver by the hydrophobic effect

• entropy driven effect

• folding occurs when of gain of entropy upon folding of soluble (water) overcomes the loss of conformational entropy of protein

• Hence in a water- soluble protein- hydrophobic residues mainly in the centre and hydrophilic residues to dominate the surface

ribonuclease

break down RNA - smaller components by clearing phosphodiester bonds between nucleotides

Oxgen binding

• Requires a Prosthetic group

• controls the position of Fe 2+ with porphyrin ring