Proteins Part 2, Proteins secondary, tertiary, and quaternary structure.ppt

Protein structure, stability

1. Reginald H. Garrett
Charles M. Grisham
www.cengage.com/chemistry/garrett
Reginald Garrett & Charles Grisham • University of Virginia
Chapter 6
Proteins: Secondary, Tertiary, and
Quaternary Structure

2. Chapter 6
“Growing in size and complexity
Living things, masses of atoms, DNA, protein
Dancing a pattern ever more intricate
Out of the cradle onto the dry land
Here it is standing
Atoms with consciousness
Matter with curiosity.
Stands at the sea
Wonders at wondering
A universe of atoms
An atom in the universe.”
Richard P. Feynman
Like the Greek sea god Proteus,
who could assume different forms,
proteins act through changes in
conformation.

3. Essential Question
•How do the forces of chemical bonding
determine the formation, stability, and myriad
functions of proteins?

4. Outline
•What noncovalent interactions stabilize protein
structure?
•What role does the amino acid sequence play in
protein structure?
•What are the elements of secondary structure in
proteins, and how are they formed?
•How do polypeptides fold into three-dimensional
protein structures?
•How do protein subunits interact at the
quaternary level of protein structure?

5. Protein Structure and Function Are Tightly Linked
The three-dimensional structures of proteins and
their biological functions are linked by several
overarching principles:
•Function depends on structure
•Structure depends on sequence and on weak,
noncovalent forces
•The number of protein folding patterns is large but
finite
•Structures of globular proteins are marginally stable
•Marginal stability facilitates motion
•Motion enables function

6. 6.1 What Noncovalent Interactions Stabilize
the Higher Levels of Protein Structures?
What are these “weak forces”?
What are the relevant numbers?
•van der Waals: 0.4 - 4 kJ/mol
•hydrogen bonds: 12-30 kJ/mol
•ionic bonds: 20 kJ/mol
•hydrophobic interactions: <40 kJ/mol

7. 6.1 What Noncovalent Interactions Stabilize
the Higher Levels of Protein Structure?
•Secondary, tertiary, and quaternary structure of
proteins is formed and stabilized by weak forces
•Hydrogen bonds are formed wherever possible
•Hydrophobic interactions drive protein folding
•Ionic interactions usually occur on the protein
surface
•van der Waals interactions are ubiquitous

8. Electrostatic Interactions in Proteins
Figure 6.1 An electrostatic interaction between a
positively charged lysine amino group and a
negatively charged glutamate carboxyl group.

9. Electrostatic Interactions in Proteins
Figure 6.1 An electrostatic interaction
between lysine and glutamate side
chains in IRAK-4, an enzyme that
phosphorylates other proteins. The
positively charged amino group (left)
forms an ionic interaction with the
negatively charged glutamate (right).

10. 6.2 What Role Does the Amino Acid
Sequence Play in Protein Structure?
All of the information necessary for folding the
peptide chain into its "native” structure is contained
in the primary amino acid structure of the peptide.

11. How do proteins recognize and interpret the
folding information?
•Certain loci along the chain may act as
nucleation points
•Protein chain must avoid local energy minima
•Chaperones may help

12. 6.3 What Are the Elements of Secondary Structure
in Proteins, and How Are They Formed?
•The atoms of the peptide bond lie in a plane
•All protein structure is based on the amide plane
•The resonance stabilization energy of the planar
structure is 88 kJ/mol
•A twist about the C-N bond involves a twist
energy of 88 kJ/mol times the square of the twist
angle.
•Rotation can occur about either of the bonds
linking the alpha carbon to the other atoms of
the peptide backbone

13. 6.3 What Are the Elements of Secondary Structure
in Proteins, and How Are They Formed?
Figure 6.2 The amide or peptide
bond planes are joined by the
tetrahedral bonds of the α-
carbon.
The rotation parameters are φ
and ψ. The conformations
shown corresponds to φ= 180°
and ψ= 180°.

14. Consequences of the Amide Plane
Two degrees of freedom per residue for the
peptide chain
Angle about the C
α
-N bond is denoted φ (phi)
Angle about the C
α-C bond is denoted ψ (psi)
The entire path of the peptide backbone is
known if all φ and ψ angles are specified
Some values of φ and ψ are more likely than
others.

15. Some Values of φ and ψ Are Not Allowed
Figure 6.3 Many of the possible conformations about an
α-carbon between two peptide planes are forbidden
because of steric crowding.

16. Steric Constraints on φ & ψ
Unfavorable orbital overlap/steric crowding
precludes some combinations of φ and ψ
φ = 0°, ψ = 180° is unfavorable
φ = 180°, ψ = 0° is unfavorable
φ = 0°, ψ = 0° is unfavorable

17. Steric Constraints on φ & ψ
•G. N. Ramachandran was the first to
demonstrate the convenience of plotting
phi, psi combinations from known protein
structures
•The sterically favorable combinations are
the basis for preferred secondary
structures

18. Steric Constraints on φ & ψ
Figure 6.4 A Ramachandran
diagram showing the sterically
reasonable values of the angles
φ & ψ. The shaded regions
indicate favorable values of
these angles. Dots in purple
indicate actual angles measured
for 1000 residues (excluding
glycine, for which a wider range
of angles is permitted) in eight
proteins.

19. Classes of Secondary Structure
Secondary structures are local structures
that are stabilized by hydrogen bonds
•Alpha helices
•Other helices
•Beta sheet (composed of "beta strands")
•Tight turns (aka beta turns or beta bends)
•Beta bulge

20. Hydrogen Bonds in Proteins
Figure 6.5 Schematic
drawing of a hydrogen
bond between a
backbone C=O and a
backbone N-H.

21. Hydrogen Bonds in Proteins
Figure 6.5 A hydrogen
bond between a a
backbone C=O and a
backbone N-H in an
acetylcholine binding
protein of a snail,
Lymnaea stagnalis.

22. The α-Helix
•First proposed by Linus Pauling and Robert
Corey in 1951 (Read the box about Pauling on
page 143)
•Identified in keratin by Max Perutz
•A ubiquitous component of proteins
•Stabilized by H bonds

23. The α-Helix
Figure 6.6 Four different representations of the α-helix.

24. The α-Helix
Numbers to Know
•Residues per turn: 3.6
•Rise per residue: 1.5 Angstroms (0.15 nm)
•Rise per turn (pitch): 3.6  1.5Å = 5.4
Angstroms
•The backbone loop that is closed by any H-
bond in an alpha helix contains 13 atoms
•
φ = −60 degrees, ψ = −45 degrees
•The non-integral number of residues per turn
was a surprise to crystallographers

25. The α-Helix in Proteins
Figure 6.7 Two proteins that contain substantial amounts of α-helix.

26. The α-Helix Has a Substantial Net Dipole
Moment
Figure 6.8 The arrangement of N-H and
C=O groups (each with an individual
dipole moment) along the helix axis
creates a large net dipole moment for
the helix. The numbers indicate
fractional charges on respective atoms.

27. Exposed N-H and C=O groups at the ends
of an α-helix can be “capped”.
Figure 6.9 Four N-H groups at the N-
terminal end of an α-helix and four C=O
groups at the C-terminal end lack
partners for H-bond formation. The
formation of H bonds with other nearby
donor and acceptor groups is referred to
as helix capping. Capping may also
involve appropriate hydrophobic
interactions that accommodate nonpolar
side chains at the ends of helical
segments.

28. Amino acids can be classified as helix-
formers or helix breakers

29. The β-Pleated Sheet
•The β-pleated sheet is composed of β-strands
•Also first postulated by Pauling and Corey,
1951
•Strands in a β-sheet may be parallel or
antiparallel
•Rise per residue:
•3.47 Angstroms for antiparallel strands
•3.25 Angstroms for parallel strands
•Each strand of a β-sheet may be pictured as
a helix with two residues per turn

30. The β-Pleated Sheet
Figure 6.10a. A “pleated sheet” of paper with an antiparallel
β-sheet drawn on it.

31. The β-Pleated Sheet
Figure 6.10b. H bonds
in parallel and
antiparallel β-sheets

32. Helix-Sheet Composites in Spider Silk
Figure 6.11 Spider web silks are composites of α-helices and β-sheets.
The radial strands of webs must be strong and rigid and have a higher
percentage of β-sheets. The circumferential strands (termed capture
silk) must be flexible and contain a higher percentage of α-helices.

33. The β-Turn
(aka β-bend, or tight turn)
•Allows the peptide chain to reverse direction
•Carbonyl C of one residue is H-bonded to the
amide proton of a residue three residues away
•Proline and glycine are prevalent in β-turns
•There are two principal forms of β-turns

34. The β-Turn
Figure 6.12 The structures of two kinds of β-turns (also
called tight turns or β-bends). Four residues are required
to form a β-turn. Left: Type I; right: Type II.

35. 6.4 How Do Polypeptides Fold into Three-
Dimensional Protein Structures?
Several important principles:
•Secondary structures form wherever possible (due to
formation of large numbers of H bonds)
•Helices and sheets often pack close together
•Peptide segments between secondary structures tend
to be short and direct
•Proteins fold so as to form the most stable structures.
Stability arises from:
•Formation of large numbers of intramolecular
hydrogen bonds
•Reduction in the surface area accessible to solvent
that occurs upon folding

36. 6.4 How Do Polypeptides Fold into Three-
Dimensional Protein Structures?
•Two factors lie at the heart of these principles:
•Proteins are typically a mixture of
hydrophilic and hydrophobic amino acids
•The hydrophobic groups tend to cluster
together in the folded interior of the protein

37. Fibrous Proteins
•Much or most of the polypeptide chain is
organized approximately parallel to a single axis
•Fibrous proteins are often mechanically strong
•Fibrous proteins are usually insoluble
•Usually play a structural role in nature
•Three types of fibrous protein are discussed here:
•α-Keratin
•β-Keratin
•Collagen

38. α-Keratin
•A fibrous protein found in hair, fingernails,
claws, horns and beaks
•Sequence consists of 311-314 residue
alpha helical rod segments capped with
non-helical N- and C-termini
•Primary structure of helical rods consists
of 7-residue repeats: (a-b-c-d-e-f-g)
n,
where a and d are nonpolar.
•This structure promotes association of
helices to form coiled coils

39. α-Keratin
Figure 6.13 The structure of α-keratin.

40. The Coiled Coil – An Important Structural
Motif in Proteins
The coiled coil is a
bundle of α-helices
wound into a
superhelix.The left-
handed twist of the
structure reduces
the number of
resides per turn to
3.5, so that the
positions of the side
chains repeat every
7 residues.

41. Fibroin and β-Keratin: β-Sheet Proteins
Proteins that form extensive beta sheets
•Found in silk fibers and bird feathers
•Alternating sequence:
Gly-Ala/Ser-Gly-Ala/Ser....
•Since residues of a β-sheet extend alternately
above and below the plane of the sheet, this
places all glycines on one side and all alanines
and serines on other side!
•This allows Glys on one sheet to mesh with Glys
on an adjacent sheet (same for Ala/Sers)

42. Fibroin and β-Keratin: β-Sheet Proteins
Figure 6.14 Silk fibroin consists of a stacked array of β-sheets.

43. Collagen – A Triple Helix
Principal component of connective tissue (tendons,
cartilage, bones, teeth)
•Basic unit is tropocollagen:
•Three intertwined polypeptide chains (1000
residues each)
•MW = 285,000
•300 nm long, 1.4 nm diameter
•Unique amino acid composition, including
hydroxylysine and hydroxyproline
•Hydroxyproline is formed by the vitamin C-
dependent prolyl hydroxylase reaction.

44. Collagen – A Triple Helix
Figure 6.15
Hydroxylation
of proline
residues is
catalyzed by
prolyl
hydroxylase.

45. Collagen – A Triple Helix
The secrets of its a.a. composition...
•Nearly one residue out of three is Gly
•Proline content is unusually high
•Unusual amino acids found:
•4-hydroxyproline
•3-hydroxyproline
•5-hydroxylysine
•Pro and HyPro together make 30% of
residues

46. A case of structure following composition

•The unusual amino acid composition of
collagen is unsuited for alpha helices or beta
sheets
•It is ideally suited for the collagen triple helix:
three intertwined helical strands
•Much more extended than alpha helix, with a
rise per residue of 2.9 Angstroms
•3.3 residues per turn
•Long stretches of Gly-Pro-Pro/HyP
The Collagen Triple Helix

47. Collagen – A Triple Helix
Figure 6.16 Poly(Gly-Pro-Pro), a
collagen-like right-handed triple
helix composed of three left-
handed helical chains.

48. Staggered arrays of tropocollagens
•Banding pattern in electron micrographs with
68 nm repeat
•Since tropocollagens are 300 nm long, there
must be 40 nm gaps between adjacent
tropocollagens (5  68 = 340 nm)
•40 nm gaps are called "hole regions" - they
contain carbohydrate and are thought to be
nucleation sites for bone formation
Collagen Fibers

49. Collagen – A Triple Helix
Figure 6.17 In the
electron microscope,
collagen fibers exhibit
alternating light and
dark bands. The dark
bands correspond to
the 40-nm gaps
between pairs of
aligned collagen triple
helices.

50. •Every third residue faces the crowded center of
the helix - only Gly fits here
•Pro and HyP suit the constraints of φ and ψ
•Interchain H bonds involving HyP stabilize helix
•Fibrils are further strengthened by intrachain
lysine-lysine and interchain hydroxypyridinium
crosslinks
Structural basis of the collagen
triple helix

51. The hole regions of collagen fibrils may be the
sites of nucleation for bone mineralization
A disaccharide of
galactose and glucose is
covalently linked to the
5-hydroxyl group of
hydroxylysines in
collagen by the
combined action of
galactosyltransferase
and glucosyltransferase.

52. Globular Proteins Mediate Cellular Function
•Globular proteins are more numerous than fibrous
proteins
•The diversity of protein structures in nature reflects
the remarkable variety of functions they perform
•Functional diversity derives in turn from:
•The large number of folded structures that
polypeptides can adopt
•The varied chemistry of the side chains of the 20
common amino acids

53. Some design principles
•Helices and sheets make up the core of most
globular proteins
•Most polar residues face the outside of the
protein and interact with solvent
•Most hydrophobic residues face the interior of
the protein and interact with each other
•Packing of residues is close
•However, ratio of vdW volume to total volume
is only 0.72 to 0.77, so empty space exists
•The empty space is in the form of small cavities
Globular Proteins

54. Why does the protein core consist primarily
of α–helices and β–sheets?
•The protein core is predominantly hydrophobic
•The highly polar N-H and C=O moieties of the
peptide backbone must be neutralized in the
hydrophobic core
•The extensively H-bonded nature of α-helices and β-
sheets is ideal for this purpose

55. Protein core versus protein surface
•The helices and sheets in the core of a globular
protein are typically constant and conserved in
sequence and structure
•The protein surface is different in several ways
•Much of the surface is composed of loops and tight
turns that connect the helices and sheets of the core
•Thus the surface is a complex landscape of different
structural elements
•These surface elements can interact with small
molecules or with other proteins
•They are the basis for enzyme-substrate
interactions, cell signaling, and immune responses

56. “Random coils” are not random
•The segments of a protein that are not helices or
sheets are traditionally referred to as “random coil”,
although this term is misleading:
•Most of these segments are neither coiled or random
•They are usually organized and stable, but don’t
conform to any frequently recurring pattern
•Random coil segments are strongly influenced by
side-chain interactions with the rest of the protein

57. Globular Proteins
Figure 6.19 The structure of ribonuclease, showing elements of
helix, sheet and random coil.

58. Protein surfaces are complex
Figure 6.20 The
surfaces of proteins are
complementary to the
molecules they bind.

59. Waters on the Protein Surface Stabilize
the Structure
•The surface structure of a globular protein includes
water molecules
•The polar backbone and side chain groups on the
protein surface make H bonds with solvent water
•α-Helices on a protein surface are usually
amphiphilic, with polar and charged residues facing
the solvent and nonpolar residues facing the interior
•A helical wheel presentation can reveal the
amphiphilic nature of an α-helix
•Some α-helices are hydrophobic and buried in the
protein interior
•Some helices are polar and entirely solvent-exposed

60. Waters on the Protein Surface Stabilize
the Structure
Figure 6.21 The
surfaces of proteins
are ideally suited to
form multiple H bonds
with water molecules.

61. α-Helices May be Polar, Nonpolar or
Amphiphilic
Figure 6.22 The so-called
helical wheel presentation can
reveal the polar or nonpolar
character of α-helices.

62. Packing Considerations in Globular Proteins
•Secondary structures pack closely to one another and
also intercalate with extended polypeptide chains
•The sum of the van der Waals volumes of a protein’s
amino acids divided by the total volume occupied by
the protein is typically 0.72 to 0.77
•These “packing densities” are similar to those of a
collection of solid spheres
•Thus, approximately 25% of the total volume of a
protein is not occupied by protein atoms
•Most of this volume is in the form of small cavities
•Such cavities provide flexibility for proteins and
facilitate conformation changes and protein dynamics

63. Protein domains are nature’s modular
strategy for protein design
•Proteins composed of about 250 amino acids or less
often have a simple, compact globular shape
•Larger globular proteins are typically made up of two
or more recognizable and distinct structures, termed
domains or modules – compact, folded protein
structures that are usually stable by themselves in
aqueous solution
•Domains may consist of a single continuous portion
of the protein sequence (see Figure 6.23)
•In some proteins, the domain sequence is
interrupted by a sequence belonging to another part
of the protein (Figure 6.24)

64. Most domains consist of a single continuous
portion of the protein sequence
Figure 6.23 Ton-EBP
is a DNA-binding
protein consisting of
two distinct domains.

65. A large domain consisting of two sequences
interrupted by the sequence of another domain
Figure 6.24 Malonyl CoA:ACP
transacylase is a metabolic enzyme
consisting of two domains. The large
(blue) domain includes residues 1-132
and 198-316. The small (gold) domain
consists of residues 133-197.

66. Many proteins are composed of several
distinct domains
•Multidomain proteins typically are the sum of the
functional properties and behaviors of their
constituent domains
•Proteins consisting of multiple domains probably
evolved by the fusion of genes that once coded for
separate proteins
•About 90% of domains in proteins have been
duplicated in other proteins
•Many proteins even contain multiple copies of the
same domain
•Some of these often-duplicated domains are shown
in Figure 6.25

67. Many proteins are composed of several
distinct domains
Figure 6.25 Several protein modules used in the
construction of complex multimodule proteins.

68. Many proteins are composed of several
distinct domains
Figure 6.26 A sampling of
proteins that consist of
mosaics of individual protein
modules.

69. Protein Sectors
•Evolutionary units of three-dimensional structure
•Many protein structures can be decomposed into
quasi-independent groups of correlated amino acids
termed protein sectors
•Such sectors are physically connected in the tertiary
structure and each has a distinct role
•Each protein sector constitutes an independent
mode of sequence divergence in the protein family
•The existence and behavior of protein sectors
reflects the evolutionary histories of proteins

70. Protein Sectors
Trypsin (rat): Red shading indicates a contiguous
network of amino acids that determine substrate
specificity

71. Protein Sectors
Trypsin (rat): Blue shading indicates a contiguous
network of amino acids in the core of the protein

72. Protein Sectors
Trypsin (rat): Green shading indicates a
contiguous network of amino acids that define the
catalytic core of the serine proteases.

73. Classification Schemes for the Protein
Universe Are Based on Domains
•Several comprehensive projects have organized the
available information on protein domains into defined
hierarchies or levels of protein structure.
•The Structural Classification of Proteins (SCOP)
database recognizes five overarching classes
•SCOP is based on levels that embody the
evolutionary and structural relationships among
known proteins
•CATH (standing for Class, Architecture, Topology,
Homologous superfamily) is another system
•CATH differs from SCOP in combining manual
analysis with quantitative algorithmic analysis

74. Classification Schemes for the Protein
Universe Are Based on Domains
•Common features of SCOP and CATH:
•Class is determined from overall composition of
secondary structure elements in a domain
•Fold describes the number, arrangement, and
connections of these secondary structure elements
•Superfamily includes domains of similar folds and
usually similar functions
•Family usually includes domains with closely related
amino acid sequences

75. Classification Schemes for the Protein
Universe Are Based on Domains
Figure 6.27 SCOP and CATH are
hierarchical classification systems
for the known proteins. Proteins
are classified in SCOP by a
manual process, whereas CATH
combines manual and automated
procedures. Numbers indicate the
population of each category.

76. Structure and Function are Not Always
Linked
•Because structure depends on sequence, and
because function depends on structure, it is tempting
to imagine that all proteins of similar structure should
share a common function, but this is not always true
•Some proteins of similar domain structure have
different functions
•Some proteins of similar function possess very
different structures
•See examples in Figure 6.28

77. Structure and Function are Not Always
Linked
Figure 6.28 (a)
Some proteins share
similar structural
features but carry out
different functions.
(b) Proteins with
different structures
can carry out similar
functions.

78. Denaturation Leads to Loss of Protein
Structure and Function
•The cellular environment is suited to maintaining the
weak forces that preserve protein structure and
function
•External stresses – heat, chemical treatment, etc. –
can disrupt these forces in a process termed
denaturation – the loss of structure and function
•The cooking of an egg is an everyday example
•Ovalbumin, the principal protein in egg white,
remains in its native structure up to a characteristic
melting temperature, T
m
•Above this temperature, the structure unfolds and
function is lost

79. Denaturation Leads to Loss of Protein
Structure and Function
Figure 6.29 The proteins of egg white are denatured during
cooking. More than half of the protein in egg white is
ovalbumin.

80. Denaturation Leads to Loss of Protein
Structure and Function
Protein 6.30 Proteins
can be denatured by
heat, with
commensurate loss
of function.

81. Denaturation Leads to Loss of Protein
Structure and Function
Figure 6.31 Proteins can be
denatured (unfolded) by high
concentrations of guanidine-
HCl or urea. The
denaturation of chymotrypsin
is plotted here.

82. Anfinsen’s Classic Experiment Proved that
Sequence Determines Structure
Figure 6.32 Ribonuclease
can be unfolded by
treatment with urea.
β-Mercaptoethanol (MCE)
cleaves disulfide bonds.
Anfinsen showed that
ribonuclease structure
(and function) could be
restored under appropriate
conditions.

83. Is There a Single Mechanism for Protein
Folding?
•How a protein achieves its stable, folded state is a
complex question
•Levinthal’s paradox demonstrates that proteins
cannot fold by sampling all possible conformations
•This implies that proteins actually fold via specific
“folding pathways”
•What factors play a role in protein folding processes?

84. Postulated Themes of Protein Folding
•Secondary structures – helices, sheets, and turns –
probably form first
•Nonpolar residues may aggregate or coalesce in a
process termed a hydrophobic collapse
•Subsequent steps probably involve formation of
long-range interactions between secondary
structures or involving other hydrophobic interactions
•The folding process may involve one or more
intermediate states, including transition states and
what have become known as molten globules

85. Folding of Globular Proteins
The Forces That Drive Folding

•Peptide chain must satisfy the constraints
inherent in its own structure
•Peptide chain must fold so as to "bury" the
hydrophobic side chains, minimizing their
contact with water
•Peptide chains, composed of L-amino
acids, have a tendency to undergo a "right-
handed twist"

86. Simulations of Protein Folding
Figure 6.33 Computer simulations of folding and unfolding
of proteins can reveal possible folding pathways.

87. The Protein Folding Energy Landscape
Figure 6.34 A model for the
steps involved in the folding
of globular proteins.
Ken Dill has suggested that the
folding process can be pictured
as a funnel of free energies.
The rim at the top represents
the many unfolded states.
Polypeptides ‘fall down the wall
of the funnel’ to ever fewer
possibilities and lower energies
as they fold.

88. What is the Thermodynamic Driving Force
for Folding of Globular Proteins?
•Separate the enthalpy and entropy terms for the
peptide chain and the solvent
•Further distinguish polar and nonpolar groups
•The largest favorable contribution to folding
is the entropy term for the interaction of
nonpolar residues with the solvent
•This is a very important point – nonpolar residues
force order on the solvent in the unfolded state.
Folding buries the nonpolar residues inside the
protein structure, producing a large entropy
increase for the liberated solvent molecules.

89. Marginal Stability of the Tertiary Structure
Makes Proteins Flexible
•A typical folded protein is only marginally stable
•It is logical to think that stability is important to
function, so why are proteins often only marginally
stable?
•The answer appears to lie in flexibility and motion
•It is becoming increasingly clear that flexibility and
motion are important to protein function

90. Motion is Important for Globular Proteins
•Protein are dynamic structures – they oscillate and
fluctuate continuously about their average or
equilibrium structures
•This flexibility is essential for protein functions,
including:
•Ligand binding
•Enzyme catalysis
•Enzyme regulation

91. Motion is Important for Globular Proteins
Figure 6.35 Proteins
are dynamic structures.
The marginal stability
of a tertiary structure
leads to flexibility and
motion in the protein.

92. Motion is Important for Globular Proteins

93. Motion is Important for Globular Proteins
Figure 6.36 The cis and trans configurations of proline residues
in peptide chains are almost equally stable. Proline cis-trans
isomerizations, often occurring over relatively long time scales,
can alter protein structure significantly.

94. The Folding Tendencies and Patterns of
Globular Proteins
•Globular proteins adopt the most stable tertiary
structures possible
•To do this, the peptide chain must
•satisfy the constraints inherent in their structure
•fold so as to bury hydrophobic side chains
•Polypeptide chains have a tendency to twist slightly
in a right-handed direction.
•This tendency is manifested in the formation of right-
handed twists in β-sheets and right-handed
crossovers in parallel β-sheets

95. The Folding Tendencies and Patterns of
Globular Proteins
Figure 6.37 (a) The natural right-handed twist of polypeptide
chains, and (b) the types of connections between β-strands.

96. Metamorphic Proteins
•A consequence of dynamism and marginal stability
•Many proteins exist as an ensemble of structures
•With more or less similar energies and stabilities
•One or a few mutations can dramatically change a
protein’s structure

97. Metamorphic Proteins
Leu45Tyr mutation
changes structure of
Streptococcus protein
G as shown

98. Metamorphic Proteins
Lys21Pro mutation results in an equilibrium
between two structures. A subsequent Gly11Val
mutation completes the transition.

99. Layer Structures in Globular Proteins
•The need to bury hydrophobic residues inside the
protein, protecting them from solvent water, leads to
formation of “layers” of structure in the protein
•Globular proteins can be pictured as consisting of
layers of backbone, with hydrophobic core regions
between and on either side of them
•More than half the known globular proteins have two
layers of backbone, with one hydrophobic core
•One-third of proteins are composed of three layers,
with two hydrophobic cores
•There are a few four-layer structures and one five-
layer structure

100. Layer Structures in Globular Proteins
Figure 6.38 Examples of protein
domains with different numbers of layers
of backbone structure. Hydrophobic
residues (shown in yellow) are buried
between the backbone layers.

101. Most Globular Proteins Belong to One of
Four Structural Classes
•Proteins can be classified according to the type and
arrangement of secondary structure
•There are four classes:
•All α proteins, in which α helices predominate
•All β proteins, in which β sheets predominate
•α/β proteins, in which helices and sheets are
intermingled
•α+β proteins, which contain separate α-helical
and β-sheet domains

102. Most Globular Proteins Belong to One of
Four Structural Classes
Figure 6.39 Four major
classes of protein structure
(as defined in the SCOP
database).

103. Molecular Chaperones Are Proteins That
Help Other Proteins to Fold
Why are chaperones needed if the
information for folding is inherent in the
sequence?
•to protect nascent proteins from the
concentrated protein matrix in the cell
and perhaps to accelerate slow steps
•Chaperone proteins were first identified as
"heat-shock proteins" (Hsp60 and Hsp70)

104. Some Proteins Are Intrinsically Unstructured
•Many proteins exist and function normally in a
partially unfolded state
•These intrinsically unstructured proteins (IUPs)
do not possess uniform structural properties but are
still essential for cellular function
•These proteins are characterized by a nearly
complete lack of structure and high flexibility
•IUPs adopt well-defined structures in complexes with
their target proteins
•IUPs are characterized by an abundance of polar
residues and a lack of hydrophobic residues

105. Some Proteins Are Intrinsically Unstructured
Figure 6.40 Intrinsically unstructured proteins (IUPs) contact
their target proteins over a large surface area.

106. Some Proteins Are Intrinsically Unstructured
Figure 6.40 Intrinsically
unstructured proteins (IUPs)
contact their target proteins
over a large surface area.

107. α
1-Antitrypsin – A Tale of Molecular
Mousetraps and a Folding Disease
•α
1-Antitrypsin normally blocks elastase in the lungs
•It functions as a molecular mousetrap, binding
elastase, then dragging the bound elastase to the
other side of the antitrypsin
•At this new site, elastase is inactivated and degraded
•Defects in α
1
-antitrypsin can result in lung and liver
damage
•Genetic variants are often inactive
•In smokers, oxidation of a crucial Met in the flexible
loop also inactivates α
1-antitrypsin, leading to
emphysema

108. α
1-Antitrypsin – A Tale of Molecular
Mousetraps and a Folding Disease
Elastase is
inactivated by
binding to α
1
-
antitrypsin

109. Diseases of Protein Folding
•A number of human diseases are linked to
abnormalities of protein folding
•Protein misfolding may cause disease by a variety of
mechanisms
•Misfolding may result is loss of function and the
onset of disease
•The table on the next slide summarizes some known
protein folding disease

110. Diseases of Protein Folding

111. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
What are the forces driving quaternary
association?
•
Typical K
d for two subunits: 10
−8
to 10
−16
M!
•These values correspond to energies of 50-100
kJ/mol at 37° C
•Entropy loss due to association - unfavorable
•Entropy gain due to burying of hydrophobic
groups - very favorable!

112. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
Figure 6.41 The quaternary structure of liver alcohol
dehydrogenase.

113. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
The subunit compositions of several proteins. Proteins with two
or four subunits predominate in nature, and many cases of
higher numbers exist.

114. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
Figure 6.42
Isologous and
heterologous
associations
between protein
subunits.

115. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
Figure 6.43 Many proteins form
tetramers by means of two sets of
isologous interactions. The
tetramer of transthyretin is formed
by isologous interactions between
the large β-sheets of two
transthyretin dimers.

116. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
Figure 6.44 Multimeric
proteins are symmetric
arrangements of asymmetric
objects. A variety of
symmetries is displayed in
these multimeric structures.

117. 6.5 How Do Protein Subunits Interact at the
Quaternary Level of Structure?
Figure 6.45
Schematic drawing of
an immunoglobulin
molecule, showing the
intermolecular and
intramolecular
disulfide bonds.

118. Open Quaternary Structures Can Polymerize
Figure 6.46 The
structure of a typical
microtubule, showing the
arrangement of the α-
and β-monomers of the
tubulin dimer.

119. What Are the Structural and Functional
Advantages Driving Quaternary Association?
Things to Know
•Stability: reduction of surface to volume ratio
•Genetic economy and efficiency
•Bringing catalytic sites together
•Cooperativity