CHEM 237 - Protein structure

primary structure

linear chain of amino acid

linked by disulfide bonds

secondary structure

local conformation of polypeptide chain

partial double bond character C-N

coplanar

tertiary structure

3D arrangement

quaternary structure

arrangement of 2 or more polypeptide chainns

trans vs cis configuration

trans is more favoured

cis is sterically hindered

secondary structure elements

helix

sheets

b-turn

omega loops

random coiling

n

number of amino acids per turn

p (pitch)

distance helix rises in 1 turn

alpha helical structure

right handed

n = 3.6aa/turn

p = 5.4A/turn

h bonds between c=o

direction of alpha helix

N to C terminal

left handed helices

polyPro and polygly

n=-3

p = 9.4A

collagen structure

3 left handed helices

forms a right handed super helix

beta sheet structure

2 sheets of polypeptide connected by h-bond

antiparallel or parallel

antiparallel beta sheet

shorter and linear H-bonds

stronger

parallel beta sheet

H-bonds are bent and longer

weaker

important structural features of beta sheet

2+ strands of polypeptide bonded by H-bonds

parallel, antiparallel, or mixed

H-bond in antiparallel strands are linear

h-bond in parallel strands are not linear

strands are slightly twisted and puckered

amino acid chains point out at right angles

b-bulges occur when amino acids do not line up

strands have turns, loops, and helices

beta tight turns

antiparallel

random coil

non repetitive structure connect by beta turns

mobile fluctuating structure

fibrous protein structure

simple, repetitive AA sequence

long extended structure

many polypeptides

structural function

water insoluble

globular protein structure

complex AA sequence

spherical shape

polypeptide folds in on itself

enzymes

water soluble

a-keratin

primary sequence with heptad (7)

forms right handed a-helix

2 keratins form a left handed helix

coiled coils

in structural proteins

strong

flexible

extensible

a-keratin fiber

made up of smaller a-keratin chains

dimer - protofilament - microfibril

silk fibroin

regions of repeating ala-gly in primary sequence

forms b-sheet

collagen

fibrous protein

primary sequence of 3 aas: Gly, Pro, Hyl/Hyp

needs ascorbic acid (vitamin C)

tropocollagen

3 collagen chains wrapped around each other

right handed super helix

collagen fibre

many tropocollagen helices wound together

crosslinking enzyme strengthens fibres

globular proteins

complex primary and tertiary structure

secondary structure has globular formation with hydrophobic interior

myoglobin

globular

a-helices with turns and loops

mainly b-sheet

some are mixed

TIM barrel

most common enzymatic fold

closed circular 8-stranded sheet

active site cleft

active site cleft

reversing order of strands causes helices to pack on either side

creates cleft

super secondary structures

combination of secondary structures

mixed elements packed together

quaternary structure

proteins bound to other proteins

interactions are specific and reproducible

symmetrical

hemoglobin

carries O2

a2b2 structure

heterotetramer

transthyretin

a₂ homodimer

glutamine synthase

a₁₂

12 subunits arranged into dimer of hexamers

non covalent forces in protein folding

ionic interactions

dipole dipole interactions

hydrogen bonding

hydrophobic effect

ionic interactions

uses coulombs law

energy is inversely proportional to distance

strength of interaction ON protein < strength of interaction in protein core

dipole interactions

stronger dipoles = stronger interaction

a-helix have dipoles where NH and CO groups turn to make favourable interactions

hydrogen bonding

electrostatic and covalent interaction = strong

orientation is important = directional

important for determining structure inside proteins

hydrophobic effect

H2O in cathrate structures are more ordered than bulk water

entropically unfavourable

drives hydrophobic residues inside protein

drives protein folding

disulfide bonds

covalent interaction

adds stability to protein structure

steric effects

• important for backbone and sidechain to restrict conformations

non covalent interactions

cooperative

bonds are stronger together, breaking 1 bond will weaken all other bonds

many interactions altered simultaneously

proteins are easily denatured bc cooperative