Chapter 2 Protein
Section 3
Proteins,Secondary,Tertiary,and
Quaternary Structure
Outline
6.1 Forces Influencing Protein Structure
6.2 Role of the Amino Acid Sequence in
Protein Structure
6.3 Secondary Structure of Proteins
6.4 Protein Folding and Tertiary Structure
6.5 Subunit Interactions and Quaternary
Structure
6.1 The Weak Forces
What are they?
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
van der Waals(范德华力）,
hydrogen bonds（ 氢键）,
ionic bonds（ 离子键）
hydrophobic interactions
（ 疏水相互作用）
What forces determine the
structure?
Primary structure - determined by
covalent bonds
Secondary,Tertiary,Quaternary structures -
all determined by weak forces
Weak forces - H-bonds,ionic interactions,
van der Waals interactions,hydrophobic
interactions
6.2 The Role of the Sequence 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.
一级结构决定高级结构
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
6.3 Secondary Structure
Consequences of the Amide Plane
Two degrees of freedom per residue for the peptide
chain
Angle about the C(alpha)-N bond is denoted phi
Angle about the C(alpha)-C bond is denoted psi
The entire path of the peptide backbone is known
if all phi and psi angles are specified
Some values of phi and psi are more likely than
others.
The angles phi and
psi are shown here
Unfavorable orbital overlap precludes some
combinations of phi and psi
phi = 0,psi = 180 is unfavorable
phi = 180,psi = 0 is unfavorable
phi = 0,psi = 0 is unfavorable
Steric Constraints on phi & psi
G,N,Ramachandran
Steric Constraints on phi & psi
Classes of Secondary Structure
all these are local（ 局部） structures that are
stabilized by hydrogen bonds
α-helix
β-sheet
β-turns
β-bulge
coil
The Alpha Helix
First proposed by Linus Pauling and
Robert Corey in 1951
A ubiquitous component of proteins
Stabilized by H-bonds
The Alpha Helix
Know these numbers
Residues per turn,3.6
Rise per residue,0.15nm
Rise per turn,3.6 × 0.15 nm = 0.54 nm
The backbone loop that is closed by any H-
bond in an alpha helix contains 13 atoms
phi = -60°,psi = -45 ° ~ -50°
The β-Pleated Sheet
Composed of beta strands
Also first postulated by Pauling and Corey,
1951
Strands may be parallel or antiparallel
Rise per residue:
– 0.347nm for antiparallel strands
– 0.325nm for parallel strands
– Each strand of a beta sheet may be pictured
as a helix with two residues per turn
The β-Turn
(β-bend,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 beta
turns
The β-Bulge （ β-凸起）
Random coil (or coil) 无规卷曲）
Super-secondary Structure
Some proteins contain an ordered
organization of secondary structures that
form distinct functional domains or
structural motifs(图形）,
αα ββββαβ βαβ
βββ
Structural Domains结构域
structural domains:
stable,independently folding,compact
structural units within a protein that are
distinguishable from other regions
局部折叠的结构域免疫球蛋白 G (IgG)
免疫球蛋白
Tertiary Structure
The folding of a single polypeptide chain
in three-dimensional space
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
Alpha Keratin
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,Promotes association of helices!
Beta Keratin
Proteins that form extensive beta sheets
Found in silk fibers
Alternating sequence,
Gly-Ala/Ser-Gly-Ala/Ser...,
Since residues of a beta 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(咬合） with
Glys on an adjacent sheet (same for Ala/Sers)
Collagen - A Triple Helix
Principal component of connective tissue
(tendonstendon腱,cartilagecartilage软骨,bones,teeth)
basic unit is tropocollagentropocollagen 原胶原,
– three intertwined polypeptide chains (1000 residues each
– MW = 285,000
– 300 nm long,1.4 nm diameter
– unique amino acid composition
Collagen
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 res,
Globular Proteins
Some design principles
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
Molecular Chaperones分子伴侣
Chaperone proteins were first identified
as "heat-shock proteins" (hsp60 and
hsp70)
Protein Modules
An important insight into protein structure
Many proteins are constructed as a composite
of two or more "modules" or domains
Each of these is a recognizable domain that
can also be found in other proteins
Sometimes modules are used repeatedly in the
same protein
There is a genetic basis for the use of modules
in nature
How Do Proteins Know How to Fold
Anfinsen’s experiment
How Do Proteins Know How to Fold
If the sequence holds the secrets of folding,
can we figure it out?
Many protein chemists have tried to
predict structure based on sequence
6.5 Quaternary Structure
quaternary structure,which refers to the
spatialal 空间 relationship of the
polypeptides,or subunits,within the
protein,
symmetry 对称
What are the structural and functional
advantages driving quaternary association?
Know these!
Stability,reduction of surface to volume
ratio
Genetic economy and efficiency
Bringing catalytic sites together
Cooperativity
Denaturation变性作用
denaturation,
– Partial or complete unfolding of the specific
native conformation of a polypeptide chain,
protein,
denatured protein,
– A protein that has lost its native
conformation by exposure to a destabilizing
agent such as heat or detergent,
Denaturation
Renaturation
主要标志 function丧失实质 advanced structure破坏引起的因素理化因素,加热,UV,X-射线；
强酸,（碱）、重金属、三氯乙酸、
浓乙醇等可逆性变性蛋白质的特性凝固作用
PI或去电荷加热或加酒精加热或加酒精加热或变性脱水调到 PI点加热带电荷的蛋白质稀酸中带电荷的蛋白质稀碱中带电荷的蛋白质凝固凝固
Section 3
Proteins,Secondary,Tertiary,and
Quaternary Structure
Outline
6.1 Forces Influencing Protein Structure
6.2 Role of the Amino Acid Sequence in
Protein Structure
6.3 Secondary Structure of Proteins
6.4 Protein Folding and Tertiary Structure
6.5 Subunit Interactions and Quaternary
Structure
6.1 The Weak Forces
What are they?
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
van der Waals(范德华力）,
hydrogen bonds（ 氢键）,
ionic bonds（ 离子键）
hydrophobic interactions
（ 疏水相互作用）
What forces determine the
structure?
Primary structure - determined by
covalent bonds
Secondary,Tertiary,Quaternary structures -
all determined by weak forces
Weak forces - H-bonds,ionic interactions,
van der Waals interactions,hydrophobic
interactions
6.2 The Role of the Sequence 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.
一级结构决定高级结构
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
6.3 Secondary Structure
Consequences of the Amide Plane
Two degrees of freedom per residue for the peptide
chain
Angle about the C(alpha)-N bond is denoted phi
Angle about the C(alpha)-C bond is denoted psi
The entire path of the peptide backbone is known
if all phi and psi angles are specified
Some values of phi and psi are more likely than
others.
The angles phi and
psi are shown here
Unfavorable orbital overlap precludes some
combinations of phi and psi
phi = 0,psi = 180 is unfavorable
phi = 180,psi = 0 is unfavorable
phi = 0,psi = 0 is unfavorable
Steric Constraints on phi & psi
G,N,Ramachandran
Steric Constraints on phi & psi
Classes of Secondary Structure
all these are local（ 局部） structures that are
stabilized by hydrogen bonds
α-helix
β-sheet
β-turns
β-bulge
coil
The Alpha Helix
First proposed by Linus Pauling and
Robert Corey in 1951
A ubiquitous component of proteins
Stabilized by H-bonds
The Alpha Helix
Know these numbers
Residues per turn,3.6
Rise per residue,0.15nm
Rise per turn,3.6 × 0.15 nm = 0.54 nm
The backbone loop that is closed by any H-
bond in an alpha helix contains 13 atoms
phi = -60°,psi = -45 ° ~ -50°
The β-Pleated Sheet
Composed of beta strands
Also first postulated by Pauling and Corey,
1951
Strands may be parallel or antiparallel
Rise per residue:
– 0.347nm for antiparallel strands
– 0.325nm for parallel strands
– Each strand of a beta sheet may be pictured
as a helix with two residues per turn
The β-Turn
(β-bend,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 beta
turns
The β-Bulge （ β-凸起）
Random coil (or coil) 无规卷曲）
Super-secondary Structure
Some proteins contain an ordered
organization of secondary structures that
form distinct functional domains or
structural motifs(图形）,
αα ββββαβ βαβ
βββ
Structural Domains结构域
structural domains:
stable,independently folding,compact
structural units within a protein that are
distinguishable from other regions
局部折叠的结构域免疫球蛋白 G (IgG)
免疫球蛋白
Tertiary Structure
The folding of a single polypeptide chain
in three-dimensional space
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
Alpha Keratin
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,Promotes association of helices!
Beta Keratin
Proteins that form extensive beta sheets
Found in silk fibers
Alternating sequence,
Gly-Ala/Ser-Gly-Ala/Ser...,
Since residues of a beta 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(咬合） with
Glys on an adjacent sheet (same for Ala/Sers)
Collagen - A Triple Helix
Principal component of connective tissue
(tendonstendon腱,cartilagecartilage软骨,bones,teeth)
basic unit is tropocollagentropocollagen 原胶原,
– three intertwined polypeptide chains (1000 residues each
– MW = 285,000
– 300 nm long,1.4 nm diameter
– unique amino acid composition
Collagen
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 res,
Globular Proteins
Some design principles
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
Molecular Chaperones分子伴侣
Chaperone proteins were first identified
as "heat-shock proteins" (hsp60 and
hsp70)
Protein Modules
An important insight into protein structure
Many proteins are constructed as a composite
of two or more "modules" or domains
Each of these is a recognizable domain that
can also be found in other proteins
Sometimes modules are used repeatedly in the
same protein
There is a genetic basis for the use of modules
in nature
How Do Proteins Know How to Fold
Anfinsen’s experiment
How Do Proteins Know How to Fold
If the sequence holds the secrets of folding,
can we figure it out?
Many protein chemists have tried to
predict structure based on sequence
6.5 Quaternary Structure
quaternary structure,which refers to the
spatialal 空间 relationship of the
polypeptides,or subunits,within the
protein,
symmetry 对称
What are the structural and functional
advantages driving quaternary association?
Know these!
Stability,reduction of surface to volume
ratio
Genetic economy and efficiency
Bringing catalytic sites together
Cooperativity
Denaturation变性作用
denaturation,
– Partial or complete unfolding of the specific
native conformation of a polypeptide chain,
protein,
denatured protein,
– A protein that has lost its native
conformation by exposure to a destabilizing
agent such as heat or detergent,
Denaturation
Renaturation
主要标志 function丧失实质 advanced structure破坏引起的因素理化因素,加热,UV,X-射线；
强酸,（碱）、重金属、三氯乙酸、
浓乙醇等可逆性变性蛋白质的特性凝固作用
PI或去电荷加热或加酒精加热或加酒精加热或变性脱水调到 PI点加热带电荷的蛋白质稀酸中带电荷的蛋白质稀碱中带电荷的蛋白质凝固凝固
