Bi515, Chapter 4

The Three Dimensional Structure of

Proteins
Dr. Clark
9/13/10
Do Chapter 4 problems: see syllabus for 5th edition,
4th edition: 1,5 and 6 (in class), 10 is optional
 Breeze

Peptide bond is rigid and planar

 Breeze

Peptide bond is rigid, but other

single bonds are not
 Link to
Structure
Tutorials,
Protein
Architecture,
alpha helix

H-bonds four residues away

 Link to
Structure
Tutorials,
Protein
Architecture,
alpha helix

H-bonds four residues away

 Interactions between R groups of alpha helix,
3 residues apart
Stabilizing
+ next to -
2 aromatics
Destabilizing
polar, bulky
same charge
Pro (constrained) or
Gly (too flexible)
Amphipathic helix?
Beta-Sheet
Beta-Sheet
 Beta-Sheet

Click here for link to

Structural Tutorials,
Protein Architecture, beta
sheet II Amphipathic beta sheet?
 -turns

4 residues in 180 degree turn, usually contain gly and pro, 1 H-

bond between first and fourth amino acid in turn (see Structural
Tutorial)
• Burial of hydrophobic groups is a powerful
stabilizing force in protein structure.
• Why? (think back to last week’s lecture)
Supersecondary structures = motifs/folds:
particularly stable arrangements of
elements of secondary structure
 Tertiary Structure (final folding
of one polypeptide)
• Tertiary interactions generally form the core of a
protein, and determine to a great extent its
function. In fact, we often classify proteins into
• groups based on tertiary structure: fibrous or
globular
• Long range interactions
• Disulfide bonds
• Domains (substructures, usually have identifiable
functions)

Link to structural tutorials

Constructing larger motifs from smaller ones
Shown here are 2 using -helix and -sheet
 Domains vs. motifs:
Domains are for larger polypeptides that
fold into 2 or more stable, globular
regions

Different domains generally have different functions within a protein

 Group Exercise
1 2 3 4 5 6 7 8 9 10
Ile-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-
11 12 13 14 15 16 17 18 19 20
Ala-Met-Cys-Lys-Trp-Glu-Ala-Gln-Pro-Asp-
21 22 23 24 25 26 27 28
Gly-Met-Glu-Cys-Ala-Phe-His-Arg

1. Where would you predict bends or -turns?

2. Where might intrachain disulfide bonds be formed?
3. Assuming the sequence is part of a larger globular
protein, indicate the probable location (external
surface or interior of the protein) of Asp, Ile, Thr, Ala,
Gln, Lys.
Lehninger, Ch4 #6
 Quaternary Structure
• Interactions between polypeptides
• Fibrous (e.g. keratin protein in hair,
collagen in joints) or globular (myoglobin,
hemoglobin)
 Fibrous protein (e.g. keratin)

Link to coiled coil

(structural tutorial,
tertiary structure
fibrous...)

This protein belongs to a family of structural proteins called Intermediate Filaments.

 Fibrous protein (e.g. keratin)

Link to coiled coil

(structural tutorial,
tertiary structure
fibrous...)

This protein belongs to a family of structural proteins called Intermediate Filaments.

keratin

Hair, skin, nails, hooves

Alpha-Keratin: Perms and Straightening
 Collagen triple helix

Fibrous protein found in connective tissue (tendons, bone, etc.) of

animals. Coiled coil like keratin.
 Collagen triple helix

Fibrous protein found in connective tissue (tendons, bone, etc.) of

animals. Coiled coil like keratin.
Silk is made up of layers
of the protein fibroin
Globular Protein: Myoglobin
Globular Protein: Myoglobin
 Heme in myoglobin and
hemoglobin
Coordination to
His

Heme

Coordination to
oxygen

Heme
 Quaternary Structure
• Proteins that are composed of more than a
one polypeptide are said to possess
quaternary structure.
• Each polypeptide is called a subunit
• Protein classified by subunits: whether
identical or different and how many, e.g.
homodimer, heterotetramer (dimer of Hemoglobin (F4-23b)

heterodimers = Hb), multimer

• Binding interfaces between subunits
• (see structural tutorial, quaternary
structure)
How to determine 3-D Structure: X-Ray
Crystallography or NMR
Nuclear Magnetic Resonance (NMR)

Molecular vibrations
lead to uncertainty in
determining structure,
e.g. a movable
“hinge” in a protein
 Protein Denaturation (loss of all but
primary structure)
• Heat
• Disulfide bond reduction
• Extremes of pH
• Acetone or alcohol (organic solvents)
• Urea and guanidine hydrochloride
• Detergents
Denaturation occurs very little, then all
at once

Suggests that
unfolding is
cooperative
process, i.e. loss
of structure in one
part destabilizes
another part
Polypeptides fold by stepwise process

Computer Simulation to predict folding intermediates (1 sec)

 Some
proteins
require
chaperone
assistance in
folding
 GroEL and GroES (bacterial protein complexes)

GroES

GroEL

GroEL “double donut” = 2 x 7 x 60 kdal subunits)

 Group Exercise
A number of natural proteins are rich in disulfide bonds, and their
mechanical properties (e.g. tensile strength, viscosity, hardness,
etc.) correlate with the degree of disulfide bonding. For example,
glutenin, a wheat protein rich in disulfide bonds, is responsible for
the cohesive and elastic character of dough made from wheat
flour. Tortise shell is tough due to the extensive disulfide bonding
in its –keratin.

•What is the molecular basis for the correlation between disulfide-

bond content and mechanical properties of the protein?
•Globular proteins that contain more disulfide bonds often must be
heated at higher temperatures for a longer period of time to
denature them. Some of these proteins, upon cooling,
spontaneously regain activity. What is the molecular basis for this
property?

Lehninger, Ch4 #5
ERRORS IN PROTEIN FOLDING
Formation of disease-causing amyloid fibrils
ERRORS IN PROTEIN FOLDING
Formation of disease-causing amyloid fibrils
ERRORS IN PROTEIN FOLDING
Formation of disease-causing amyloid fibrils
 ERRORS IN PROTEIN FOLDING--Prion Proteins

Stained section of cerebral cortex from autopsy of a patient with Creutzfeldt-Jakob disease
ERRORS IN PROTEIN FOLDING--Prion Proteins

Structure of the globular domain of human PrP in monomeric (left) and

dimeric (right) forms