MT1 BIOC 450 xtra info - secondary/ tertiary structures

properties of alpha helix, beta strands and such

where does methylation occur?

alpha amino of Lys, Arg or His

Lys 48

proteosomal degradation

lys 63

Dna repair, endocytosis, signalling

range of ionic interaction

2.4 to 4 A

typical distance H-bond

2.6-3.2 A

H bonds are

• geometry dependent

• distance dependent

Phi angle

Looks along N- Calpha bond

Psi angle

looks along Calpha-C’ bond

proline Phi/ Psi angles

• Phi restricted to -70

• Psi restricted to -30 and 140

Alpha helix phi/psi

• phi= -57

• psi=-47

H bond pattern of right handed alpha helix

i → i+4

rise alpha helix

1.5 A /residue → compact

pitch of alpha helix

3.6 residues, 5.4 A

alpha helix residues

5-40 residues

diameter alpha helix

5 A

stabilisation of alpha helix

• non polar and vdW interactions

• H bonds- but weaker

electric properties

• all peptide units point in the same directions

• +0.5 at N-term, -0.5 at C term

Amino acid prefered N-term alpha helix

• Asp

• Glu

Amino acid prefered C-term alpha helix

• Lysine

• Arginine

Amphipathic alpha helix

• polar/ non polar residues face opposite directions

• same-type residues appear every 3-4 positions

• generally found on protein surfaces

good helix formers

• Ala

• Glu

• Leu

• met

—> non polar, no charges, stabilising, no hindrance

poor helix formers

• Pro

Polar amino acids and alpha helix

compete with main chain (backbone) H bonds

Beta-branched aa in alpha helix

• Ile, Thr, Val

• destabilize helices bc of hindrance

Anti parallel Beta strand phi and psi

phi= -139

psi= +135

parallel Beta strand phi and psi

phi= -119

psi= 113

good sheet makers

all bulky stuff

• Tyr, Trp, Val, Ile, Phe, Thr

turns

• structured and classified by their dihedral angles

Beta turn H bond pattern

• 2nd is pro, 4th is gly

• i→ i+3

gamma-turn H bond pattern

• i → i+2

most common chi conformation

• gauche + conformation

• -60 degree

chi 1 is

between N and C/O gamma

other common chi configuration

• trans conformation

rare chi conformation

• gauche-

• R group between CO group and N → steric hindrance

motifs

• combination of a few secondary structure elements

• not stable when isolated, generally

common motids

• helix-turn-helix

• beta-hairpin

• greek key

• beta-alpha-beta

ex of helix-turn-helix

homeodomain TF → interacts with major groove of DNA

ex of Beta-hairpin

erabutoxin

ex of greek key

• beta sandwich (dimer) in IgG constant domain

ex of beta-alpha-beta

triose phosphate isomerate, glyolysis enzymes

domains

• 40-350 residues

• separate parts of the proteins but in same chain

• independent functional units

disulfide bonds

• present in reducing environment, extra cellular

• golgi, Er, outside

coiled coil - Leucine zipper

• helices interwine around each other

• left handed supercoil

• heptad repeat, every 4th is a leucine (leucine zipper)

• leucine zipper forms hydrophobic core of dimer

4 helix bundle

• all alpha

• helices pack in ridge and grooves model

Beta-propeller

• neuraminidase

• membrane protein, glycosylase activity to propel the virus

Beta barrels

• only membrane beta barrel is found in gram-negative bacteria

• porin-trimer , interacts with outside to get in nutrients

Alpha/beta proteins

• TIM barrel

• horseshoe fold

• rossman fold