module 5: protein structure & analysis

In an x_y helix, there are x _ and y _ per ring

residues, atoms

α-helix aka

3.6₁₃ helix

α-helix has _ hydrogen bonding

i+4→i

α-helix is _ Å per residue & _ Å per loop

1.5, 5.4

α-helix has _° turn per residue & _ Å radius

100, 2.3

α-helix Φ = _° & Ψ = _°

60, 45

3₁₀ helix is _ Å per residue & _ Å per loop

2, 6

3₁₀ helix has _° turn per residue & _ Å radius

120, 1.9

3₁₀ helix Φ = _° & Ψ = _°

49, 26

π-helix aka

4.1₁₆ helix

π-helix is _ Å per residue & _ Å per loop

1.15, 4.7

π-helix has _° turn per residue & _ Å radius

88, 2.8

π-helix Φ = _° & Ψ = _°

55, 70

separation methods

pH extremes: 8M urea, 6M guanidium HCL, high [salt]

S-S cleavage methods

ox. by performic acid or sulfhydryl compound + alkylating agent

sulfhydryl compounds

2-mercaptoethanol, DTT

alkylating agents

iodoacetate, 3-bromopropylamine

Edamn reagent

phenyl-N=C=S

carboxypeptidase A

all but Pro, Asp, Glu, & Lys

carboxypeptidase B

Arg & Lys

carboxypeptidase Y

all

trypsin

Arg & Lys

chymotrypsin

Phe, Tyr, Trp, & ~Leu

clostripain

Arg

endopeptidase Lys-C

Lys

staph. protease

Asp & Glu

CNBr

Met

hydroxylamine

Asn-Gly @ pH = 9

selective hydrolysis

Asp-Pro @ pH = 6