Mary K.

Campbell
Shawn O. Farrell
http://academic.cengage.com/chemistry/campbell

Chapter
Ch t F Four
The Three-Dimensional Structure of Proteins

Paul D. Adams • University of Arkansas

Protein Structure
• Many conformations are possible for proteins:
• Due to flexibility of amino acids linked by peptide
bonds

• At least one major conformations has biological

activity, and hence is considered the protein’s native
conformation
Levels of Protein Structure
1° structure: the sequence of amino acids in a
polypeptide chain
chain, read from the N-terminal end to
the C-terminal end
• 2
2° structure: the ordered 33-dimensional
dimensional
arrangements (conformations) in localized regions of
a polypeptide chain; refers only to interactions of the
peptide backbone
• e. g., α
α-helix
helix and β
β-pleated
pleated sheet
• 3˚ structure: 3-D arrangement of all atoms
• 4
4˚ structure: arrangement of monomer subunits with
respect to each other
1˚ Structure
• The 1˚ sequence of proteins determines its 3-D
conformation

• Changes in just one amino acid in sequence can alter

biological function, e.g. hemoglobin associated with
sickle-cell anemia

• Determination of 1˚ sequence is routine biochemistry

lab work ((See Ch. 5).
)
2˚ Structure
• 2˚ of proteins is hydrogen-bonded arrangement of
backbone of the protein
• Two bonds have free rotation:
1) Bond between α-carbon and amino nitrogen in
residue
2) Bond between the α-carbon and carboxyl carbon of
residue
• See Figure
g 4.1
α-Helix
• Coil of the helix is clockwise or right-handed
• There are 33.6
6 amino acids per turn
• Repeat distance is 5.4Å
• Each peptide bond is ss-trans
trans and planar
• C=O of each peptide bond is hydrogen bonded to the
N H of the fourth amino acid away
N-H
• C=O----H-N hydrogen bonds are parallel to helical
axis
• All R groups point outward from helix
α-Helix (Cont’d)
α-Helix (Cont’d)
• Several factors can disrupt an α-helix
• proline creates a bend because of (1) the restricted
rotation due to its cyclic structure and (2) its α-amino
group has no N-H for hydrogen bonding
• strong electrostatic repulsion caused by the proximity
of several side chains of like charge
charge, e
e.g.,
g Lys and Arg
or Glu and Asp
• steric crowding caused by the proximity of bulky side
chains, e.g., Val, Ile, Thr
β-Pleated Sheet
• Polypeptide chains lie adjacent to one another; may
be parallel or antiparallel
• R groups alternate, first above and then below plane
• Each peptide bond is s-trans and planar
• C=O and N-H groups of each peptide bond are
perpendicular to axis of the sheet
• C=O---H-N hydrogen bonds are between adjacent
sheets and perpendicular to the direction of the sheet
β-Pleated Sheet (Cont’d)
β-Pleated Sheet (Cont’d)
β-bulge- a common nonrepetive irregular 2˚ motif in
anti-parallel structure
Structures of Reverse Turns

• Glycine found in reverse turns

• Spatial
S ((steric)) reasons
yp p
• Polypeptide changes
g direction
• Proline also encountered in reverse turns. Why?
α-Helices and β-Sheets
structures: the combination of α-
• Supersecondary structures:
and β
β-sections,
sections, as for example
• βαβ
βαβ unit
unit:: two parallel strands of β-sheet connected by
a stretch of α-helix
• αα unit
unit:: two antiparallel α-helices
• β-meander:
meander: an antiparallel
p sheet formed byy a series of
tight reverse turns connecting stretches of a
polypeptide chain
• Greek key:
key: a repetitive supersecondary structure
formed when an antiparallel sheet doubles back on
itself
• β-barrel:
barrel: created when β-sheets are extensive enough
to fold back on themselves
Schematic Diagrams of Supersecondary
S uc u es
Structures
Collagen Triple Helix
• Consists of three polypeptide chains wrapped around
each other in a ropelike twist to form a triple helix
called tropocollagen; MW approx. 300,000
• 30% of amino acids in each chain are Pro and Hyp
(hydroxyproline); hydroxylysine also occurs
• Every third position is Gly
G and repeating sequences
are X-Pro-Gly and X-Hyp-Gly
• Each polypeptide chain is a helix but not an α-helix
• The three strands are held together
g by
y hydrogen
y g
bonding involving hydroxyproline and hydroxylysine
• With age,
age collagen helices become cross linked by
covalent bonds formed between Lys and His residues
Fibrous Proteins
• Fibrous proteins:: contain polypeptide chains
organized approximately parallel along a single axis.
They
• consist of long
g fibers or large
g sheets
• tend to be mechanically strong
• are insoluble in water and dilute salt solutions
• play important structural roles in nature
• Examples are
• keratin of hair and wool
• collagen of connective tissue of animals including
cartilage, bones, teeth, skin, and blood vessels
Globular Proteins
• Globular proteins: proteins which are folded to a
more or less spherical shape
• they tend to be soluble in water and salt solutions
• mostt off their
th i polar
l side
id chains
h i are on th the outside
t id andd
interact with the aqueous environment by hydrogen
bonding and ion ion-dipole
dipole interactions
• most of their nonpolar side chains are buried inside
• nearly
l allll h
have substantial
b t ti l sections
ti off α-helix
h li andd β-
β
sheet
Comparison of Shapes of Fibrous and
Globular Proteins
 3° structure

1. The 3-dimensional arrangement of atoms in the

molecule.
2 The 3-dimensional
2. 3 dimensional structure of a protein is determined
by its amino acid sequence.
3 Th
3. The ffunction
ti off a protein
t i depends
d d on itits structure.
t t
4. An isolated p
protein usually
y exists in one or a small
number of stable structural forms.
5 The most important forces stabilizing the specific
5.
structures maintained by a given protein are
noncovalent interactions.
interactions
Forces in 3˚ Structure
• Noncovalent interactions, including
• hydrogen bonding between polar side chains
chains, e
e.g.,
g
Ser and Thr
• hydrophobic interaction between nonpolar side
chains, e.g., Val and Ile
• electrostatic attraction between side chains of
opposite charge, e.g., Lys and Glu
• electrostatic repulsion between side chains of like
charge,
h e.g., L
Lys and
dA Arg, Gl
Glu and
dAAsp
• Covalent interactions:
Disulfide (-S-S-) bonds between side chains of
cysteines
Forces That Stabilize Protein Structure
3° and 4° Structure
• Tertiary (3°
(3°) structure:
structure: the arrangement in space of
all atoms in a polypeptide chain
• it is not always possible to draw a clear distinction
between 2° and 3° structure

• Q
Quaternary ( °) structure:
y (4°
(4 structure: the association of
polypeptide chains into aggregations

• Proteins are divided into two large classes based on

their three-dimensional structure
• fibrous proteins
• globular proteins
 Globular Proteins
compact and varied

Globular protein structures are compact and varied.

varied Human serum albumin (Mr
64,500) has 585 residues in a single chain. Given here are the approximate
dimensions its single polypeptide chain would have if it occurred entirely in
extended
t d d β conformation
f ti or as an α hhelix.
li
The Structure of Myoglobin
 Myoglobin
• A single polypeptide chain of 153 amino acids
• A single heme group in a hydrophobic pocket
• 8 regions of α-helix; no regions of β-sheet
• Most polar side chains are on the surface
• Nonpolar side chains are folded to the interior
• Two His side chains are in the interior,
interior involved with
interaction with the heme group
• Fe(II) of heme has 6 coordinates sites; 4 interact with N atoms
of heme, 1 with N of a His side chain, and 1 with either an O2
molecule or an N of the second His side chain
Oxygen Binding Site of Myoglobin

+Fe 2+
O2 and CO binding to the heme group of Myoglobin
 Denaturation of a Protein
•Denaturation: the loss of the structural order (2°, 3°, 4°,
), the loss of biological
or a combination of these), g activity
y
Denaturation and Refolding in Ribonuclease
• Denaturation by
• heat
• large changes in pH, which alter charges on side chains,
e.g., -COO- to -COOH or -NH3+ to -NH2
• detergents
d t t suchh as sodium
di d
dodecyl
d l sulfate
lf t (SDS) which
hi h
disrupt hydrophobic interactions
• urea or guanidine
guanidine, which disrupt hydrogen bonding
• mercaptoethanol, which reduces disulfide bonds

denaturation Refoding
 Quaternary Structure
• Quaternary (4°
(4°) structure:
structure: the association of
polypepetide monomers into multisubunit proteins
• dimers
• trimers
ti
• tetramers

• Noncovalent interactions
• electrostatics, hydrogen bonds, hydrophobic
 Structure of Hemoglobin

molecule), α2β2
- Tetramer (4 molecule)
- 1 O2/1 molecule
4 O2/1 Hb
- positive cooperativity
Oxygen Binding of Hemoglobin (Hb)
• A tetramer of two α-chains (141 amino acids each) and
two β
β-chains
chains (153 amino acids each); α2β2
• Each chain has 1 heme group; hemoglobin can bind up to
4 molecules of O2
• Binding of O2 exhibited by positive cooperativity; when
one O2 is bound,
bound it becomes easier for the next O2 to bind
• The function of hemoglobin is to transport oxygen
• The structure of oxygenated Hb is different from that of
unoxygenated Hb
• H+, CO2, Cl-, andd 2,3-bisphosphoglycerate
2 3 bi h h l t (BPG) affect
ff t
the ability of Hb to bind and transport oxygen
 hyperbolic
Sigmoidal
(
(positive
iti cooperativity)
ti it )
(cooperative binding)
Oxy- and Deoxyhemoglobin

Deoxy-Hb

oxy-Hb

Allosteric regulation
positive cooperativity
 The Bohr effect

In actively metabolizing tissue, Hb releases O2 and

binds both CO2 and H+. In the lungs, Hb releases both
CO2 and H+ and binds O2.
Oxygen binding in the presence of BPG
 Oxygen binding capacity (fetal vs mother)

Fetus: α2γ2
Mother: α2β2

Binding affinity:
β BPG BPG
β-BPG>γ-BPG
Misfolding and protein aggregation

chaperones