Protein structure

1
Protein structure function
Proteins are the most versatile macromolecules in
living systems, and serve crucial functions in
essentially all biological processes
Chapter 3 Outline
3.1 Proteins are built from a repertoire of 20
amino acids 3.2 Primary structure amino acids
linked by peptide bonds form polypeptide
chains 3.3 Secondary structure polypeptide
chains fold into regular structures such as
alpha helix, beta sheet, turns loops 3.4
Tertiary structure water-soluble proteins fold
into compact structures with nonpolar
cores 3.5 Quaternary structure polypeptide
chains can assemble into multisubunit
structures 3.6 The amino acid sequence of a
protein determines its three-dimensional
structure
2
Secondary structure (1) alpha helix
1951, predicted by Pauling Corey, 6 years
before it was seen!
ball stick, side
end view
ribbon
space-filling core
3
alpha helix stabilized by hydrogen bonds
CO group of residue n forms H-bond with NH group
of Residue n 4
4
Ramachandran diagram for helices
Screw sense right-handed (clockwise)
or left-handed (counterclockwise) Both
conformations allowed, right-handed energetically
more favorable, and essentially always in proteins
(N ?-C)
(CO ?-C)
5
Ball stick model of alpha helix
6
Ribbon and cylindrical depiction
Residues related to each other by a rise of 1.5 Å
and a rotation of 100 degrees. 3.6 aa residues
/ turn Pitch 5.4 Å(1.5x3.6)
7
Ferritin, an iron storage protein
75 alpha helix
Helical content of proteins ranges widely
8
Super helix alpha helical coiled coil
Can be as long as 1000 Å, very stable
Helical cables in these proteins serve a
mechanical role, forming stiff bundles of fibers
Found in myosin and tropomyosin in muscle,
fibrin in blood clots, keratin in hair, quills,
claws, hoofs, horns intermediate filaments
(cytoskeleton or internal scaffolding of cells)
9
Ramachandran diagram for (2) beta strand
structures
Beta strand is a fully extended polypeptide chain
Red shows sterically allowed conformations
10
Structure of a beta strand
Also predicted by Pauling Corey
Side chains are alternately above and below plane
of backbone
Distance between adjacent aa 3.5 A Contrast to
1.5 A for alpha helix
11
Antiparallel beta sheet
Strands linked by H-bonding between opposite
amino acids
12
Parallel beta sheet
Strands linked by H-bonding of an aa on one
strand to two different aa on the adjacent strand
13
Structure of mixed beta sheet
14
A twisted beta sheet, ball stick model
15
A twisted beta sheet, schematic model
Rotated 90 degrees
16
Fatty acid-binding protein
Rich in beta sheets
Arrow pointing to carboxyl- terminal end
17
Reverse turn, hairpin bend
H-bond
18
(omega, ?) Loops
Part of antibody
Surface loops interact with other molecules
19
Tertiary structure, myoglobin
O2 carrier in muscle, 1st protein in atomic
detail, 153 aa, X-ray crystals
20
Tertiary structure, myoglobin, schematic
Mainly alpha helices, total 8 helices (75 of
main chain)
Prosthetic (helper) group to bind O2 Heme group
is protoporphyrin IX, central iron atom
21
Distribution of aa in myoglobin
Surface, mainly charged aa. Interior,
mainly hydrophobic aa
Yellow hydrophobic aa Blue charged aa White
other aa
Cross-section
22
Porin inside out
Membrane protein
23
Protein domains (single polypeptide)
CD4 cell surface protein (immune system), four
similar domains
Protein to which HIV attaches
24
Quaternary structure, dimer
Cro protein of bacteriophage lambda
Dimer of identical subunits
25
Quaternary structure, tetramer
Human hemoglobin, two alpha(red) two
beta(yellow) subunits, 4 heme groups
26
Quaternary structure, complex
Coat of rhinovirus (common cold) 60 copies of
4 different subunits, 3 outside, red, blue, green
27
EM of rhinovirus
28
Amino acid sequence determines 3D-structure
Bovine ribonuclease, 1950, C. Anfinsen work
Denature renature
4 disulfide bonds 124 amino acids
29
Reducing disulfied bonds
beta-mercaptoethanol, reduced
oxidized
30
Denaturing agent, urea
31
Denaturing agent, guanidinium chloride
32
Denaturing agent, beta mercaptoethanol
33
Ribonuclease reduction denaturation
34
Reestablishing correct disulfide pairing
Scrambled conformation, from oxidation in 8 M
urea, only 1 activity, (105 possible pairings)
Urea removed before trace of mercaptoethanol added
, full activity restored. Process driven by
decrease in free energy
35
Relative frequency of aa in secondary structures
36
Alternative conformations context
Tertiary interactions (between residues far
apart) affect secondary structures
alpha helix
beta strand
Same aa sequence
37
Transition folded to unfolded
Sharp transition
38
50 / 50 mixture at halfway
39
Finishing touches covalent modifications
Proteins covalently modified to augment function
40
Hydroxyproline
Hydroxylation of proline residues in polypeptide
Stabilizes fibers of collagen in bone
connective tissue. Scurvy vitamin C deficiency,
leads to insufficient hydroxylation
41
gamma-Carboxyglutamate
Carboxylation of glutamate residues in
polypeptides
Carboxylation of glutamate in prothrombin (clottin
g protein) Vitamin K deficiency leads
to insufficient carboxylation, and hemorrhage
42
Carbohydrate to asparagine residues
Addition of sugars makes proteins more
hydrophilic, and more interactive with other
proteins
43
Phosphorylation of serine, threonine, tyrosine
Triggered by hormones, and growth
factors. Phosphorylation is reversible, thus
acts as, reversible switches for regulating
cellular processes
44
Green fluorescent protein (GFP)
Internal rearrangement and oxidation of
Ser-Tyr-Gly fluorescence
45
Fluorescence in embryo cell
Four-cell embryo of C. elegans. (cells
outlined) Protein, PIE-1 labeled with GFP