ANNOUNCEMENTS!
Lecture 7 & 8:
PROTEIN ARCHITECTURE IV:
Tertiary and Quaternary Structure
OLD HOMEWORKS AND EXAM QUESTIONS POSTED
ON WEBSITE UNDER OTHER MATERIAL:
“PRACTICE QUESTIONS”
Margaret Daugherty
Fall 2003
By request: Lecture 7 class powerpoints
on web as
Lecture 7: Class Powerpoints
BIOC 205
Tertiary Structures
Fibrous
proteins:
Filamentous; play
a major
structural role in
cells & tissues
insoluble in H 2O
Globular
proteins:
Membrane
Proteins:
compact structures;
different folds for
different functions
Hydrophobes inside,
hydrophiles outside
found associated
with various
membrane systems
“inside out”
insoluble in H 20
soluble in detergents
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Secondary Structures and
Properties of Fibrous Proteins
Examples of
occurrence
Structure
Characteristics
α-Helix, Cross-linked
by disulfide bonds
Tough, insoluble
protective structures of
varying hardness and
flexibility
α – Keratin of hair,
feathers and nails
β-Conformation
Soft, flexible filaments
Silk fibroin
Collagen triple helix
High tensile strength,
without stretch
Collagen of tendons,
bone matrix
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GLOBULAR PROTEIN
Globular proteins: some features
• Folding of 2˚ structural elements;
1). Compact, relatively spherical molecules;may contain domains
amino acids distant in the 1 o sequence fold closely
• Side chain
polarity;
2). Soluble in cytosol or in lipid phase of membranes
hence - amino acid composition is important for location!
location
varies
with
– Non-polar are inside
• (A, V, L, I, M & F);
3). Primary agents of biological action in cell;
enzymes,regulatory, transport,storage, motor, structural,
defense, exotic.
– Charged on the surface
• (D, E, K, R, H);
– Uncharged polar mostly surface,
but interior as well
4). Globular does not imply structural monotony or simplicity;
diversity of forms
all α; all β; α/β mixture; heterologous components
• (S, T, N, Q, Y & W);
– Nearly all H-bond donors have an
H-bond acceptor;
– Interior of a structure
TIGHTLY packed;
5). Tertiary structure allows globular proteins to
bind other molecules selectively and transiently
is
• 3˚ structures are frequently built of
domains.
What does 1o sequence tell us?
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Myoglobin:What does looking at 3o structure tell us?
Linear sequence of AAs linked by
peptide bonds
secondary structure
1
31
61
91
M
S
R
L
R
S
T
A
L
Q
S
P
A
E
Y
Y
F
A
L
N
C
S
E
L
V
K
C
K
L
C
I
P
L
S
R
V
C
S
A
V
A
F
I
A
G
R
L
E
S
H
A
F
L
N
N
Y
G
M
E
G
L
K
A
S
C
K
D
K
L
I
A
D
A
L
V
D
F
P
T
P
P
V
I
Q
K
E
D
T
E
G
G
H
T
P
G
Y
V
H
L
Y
R
V
V
A
W
S
F
V
C
C
E
A
T
V
A
V
protein surfaces
V
K
G
V
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side chain distribution
space filling
Functional sites of proteins are accessible to , but not on the surface
CORES OF PROTEINS: α-HELICES AND β-SHEETS
Citrate synthase
As an added note: compare the space filling model on the previous page
with the surface representation models - you can get a better idea of
how the amino acid side chains tightly fill in the surface clefts.
Ribonuclease A
Remember hydrophobes partition to
inside of molecule; they have polar N-H
and C=O groups; formation of helices and
sheets neutralize these groups!
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GLOBULAR PROTEINS AND α-HELICES:
return of the helical wheel!
GLOBULAR PROTEINS AND α-HELICES:
return of the helical wheel!
INTERIOR HELIX: HYDROPHOBIC
SURFACE HELIX: AMPHIPATHIC
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β-sheets: an example of IFABP
GLOBULAR PROTEINS AND α-HELICES:
return of the helical wheel!
Looking in cavity
from bottom
left of the 3
front sheets
Hydrophobic = green
Charged = red
SOLVENT-EXPOSED HELIX: POLAR/CHARGED
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POLYPEPTIDE CHAINS HAVE A RIGHT-HANDED TWIST
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pdb file: 1AEL
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SINGLE “LAYER” STRUCTURES ARE NOT STABLE
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Importance of layers
SINGLE “LAYER” STRUCTURES ARE NOT STABLE
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GLOBULAR PROTEIN STRUCTURE: other considerations
Umbrella of ’3o structure'
1). Proteins are tightly packed; packing
densities are ~.77; remaining space is very
small cavities - usually not enough for H20
molecules; need them for flexibility?
2). Proteins have natively random
structure; Some parts of a protein
(motifs)
domains
structure are not regular. These are often
incorrectly referred to as disordered or
random coil regions
3). Proteins have flexible segments;
they can be truly disordered; or they
can be ordered but the segment is so
flexible that it doesn’t crystallize
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http://www.cryst.bbk.ac.uk/PPS2/course/section9/9_term.html
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Proteins Are Dynamic:
X-ray vs NMR Structures
Myoglobin - dynamics in a storage protein
A chain of insulin
Static structure
Solution structure
“family” of structures
Mobility in loops, surfaces, near N & C-termini
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MOTIONS COVER A RANGE OF TIME: seconds to femtoseconds
MULTIMERIC PROTEINS
• Quaternary structure
describes how two or
more polypeptide chains
associate to form a
native protein structure
(but some proteins
consist of a single type
of polypeptide chain).
Hemoglobin
BIOC 205
Hb tetramer: 2 “alpha chains” and 2 “beta chains”
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CLOSED QUATERNARY STRUCTURES
OPEN QUATERNARY STRUCTURE
The association stiochiometry is finite
Liver alcohol dehydrogenase
2 identical subunits
Tubulin: αβ dimer
Hemoglobin (α2β2)
non-identical chains
Microtubule
Dynamic structure
Continual polymerization/depolymerization
HIV-1 particle
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OPEN QUATERNARY STRUCTURE
Tobacco mosaic virus
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STABILIZATION OF QUATERNARY STRUCTURE
Quaternary Structure are Stable!
Coat protein
40 kD
Kd = 10-8 to 10-16 M
or
50 to 100 kJ/mol in stability!
Chemical interactions offset loss of entropy
(-)
Recall S = klnW
RNA genome in red
surrounded by helical array of subunits
300 nm x 18 nm
2134 copies of coat protein!
2 molecules ---> one
Loss in translational degrees of
freedom
Amino acid side chains are more
restricted at interface
alcohol dehydrogenase
(+)
Hydrophobic interactions
Electrostatic interactions
Van der Waals interactions
Hydrogen bonds
Ionic interactions
Sometimes disulfide bonds
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WHY HAVE QUATERNARY STRUCTURE:
ADVANTAGES OF HAVING ASSOCIATING SUBUNITS
Reduction in surface to volume ratio: we
will see that hydrophobic interactions in
the protein core have a greater impact
on protein stability than surface
hydrogen bonding with water
WHY HAVE QUATERNARY STRUCTURE:
ADVANTAGES OF HAVING ASSOCIATING SUBUNITS
Genetic Economy and Efficiency: less DNA is used to code for a protein;
less chance for error; limit appears to be about 100 kD; proteins with molecular
weights > 100 kD usually are multi-subunit.
Tomato bushy stunt virus
4800 nt RNA
180 identical coat proteins
2
Satellite tobacco mosaic virus
1059 nt RNA
60 identical coat proteins
Subunit association can shield hydrophobic
groups from water
Adenovirus
DNA: 36000 bases
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WHY HAVE QUATERNARY STRUCTURE:
ADVANTAGES OF HAVING ASSOCIATING SUBUNITS
Creating catalytic sites: each subunit contributes a component of the active site
QUATERNARY
STRUCTURES
CAN BE
SIMPLE OR
COMPLEX
HIV protease: dimeric; each contributes an asp residue
Bringing catalytic sites together: important for proteins with multiple
catalytic functions - more efficient in terms of “handing off” substrates from
one site to another for subsequent chemistry.
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REVIEW
1). Tertiary structure describes the three-dimensional structure of a polypeptide
chain.
2). The 3 major classes of 3o structure are fibrous proteins, globular proteins, and
membrane proteins.
3). Fibrous proteins are hydrophobic proteins that give strength and flexibility.
4). Coiled-coils are stabilized by hydrophobic interactions.
5). Globular proteins constitute the majority of proteins , consist of α-helices and
β-sheet and have a hydrophobic core.
6). Polypeptide chains have a right-handed twist.
7). Globular proteins have layers.
8). Globular proteins are densely packed
9). Globular proteins can have flexible regions.
10). Proteins display motions (returning to the idea that life is dynamic!)
11). Quaternary structures describe the association between polypeptide chains.
12). Quaternary associations can be “open” or “closed”
13). Quaternary structures are stable (an interplay between entropy and chemical
interactions) and confer certain advantages to an organism.
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