PART TWO
• Long biochemically important proteins have certain folding patterns
involving combinations of the different types of secondary structure
patterns called super secondary structures. i.e these super
secondary structures involve -helices and -sheets
• The most common super secondary structure pattern is the
sheet-turn-sheet pattern, of which large b-sheet array within a
protein can be formed.
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Among the frequently found folding patterns are
the helix-turn-helix pattern
the helix turn sheet pattern
helix-turn-helix β & β unit,
the leucine zipper
the zinc finger
Other types of helices or loops and turns can occur that differ
from one protein to another (random coils).
-TURN
It’s the secondary level of protein
organization which permit the change of
direction of the peptide chain to get a
folded structure
They are known as well as reverse turns, hairpin
bends or W loops
SECONDARY-STRUCTURE
FORMING AMINO ACIDS
-helix
-pleated sheet
-turn
Glutamate
Tyrosine
Aspartate
Methionine
Valine
Serine
Alanine
Isoleucine
Glycine
Proline produces distortion of the structure
Supersecondary structures
Tertiary structure
• The tertiary structure of a protein refers to its overall three-dimensional
conformation.
• Tertiary structure is the overall arrangement of secondary structure
elements- the specific overall shape of a protein.
• The "tertiary structure" of a protein refers to the protein's overall
topology in space.
• When you look at an actual polypeptide chain, the final shape is made up of
secondary features, and some apparently random conformations. This
overall structure is referred to as the tertiary structure.
• This tertiary structure that finally determines the function of the protein,
results from further folding of the protein leading to a unique three
dimensional structure.
• Tertiary structure is determined and stabilized by noncovalent
interactions or chemical bonds and forces, including weak bonds
(Hydrogen bonds, Ionic bonds, Van der Waals bonds, and Hydrophobic
attractions).
• The tertiary structure of a protein involves attractions and repulsions
between the side chain groups of the amino acids in the polypeptide chain.
• As interactions occur between different parts of the peptide chain, segments
of the chain twist and bend until the protein acquires a specific threedimensional shape. Such interactions are produced between amino acid
residues that may be located at a considerable distance from each other in
the primary sequence of the polypeptide chain.
• Note that hydrophobic interactions and non-polar side chains tend toward
the center of the protein, while polar and charged side-chains tend toward
the outside where they can interact with water.
• To repeat: Hydrophobic amino acid residues tend to collect in the interior of
globular proteins, where they exclude water, while hydrophilic residues are
usually found on the surface, where they interact with water.
• The types of interactions between amino acid residues that produce the
three-dimensional shape of a protein include hydrophobic interactions,
electrostatic interactions, and hydrogen bonds, all of which are noncovalent.
Covalent disulfide bonds also occur.
• REMEMBER!
• Tertiary Structure of Globular Proteins is the folding of domains and final
arrangement of domains in protein such that compact, hydrophobic side
chains are buried in interior of the molecule, with maximum hydrogen
bonding of hydrophilic groups within the molecule.
Tertiary Structure
• Specific overall shape of a protein
• Cross links between R groups of amino acids
in chain
disulfide
–S–S–
+
ionic
–COO–
H3N–
H bonds
C=O
HO–
hydrophobic
–CH3 H3C–
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Cross-Links in Tertiary Structures
The tertiary structure of a protein is stabilized by interactions between the R groups
of the amino acids in one region of the polypeptide chain with R groups of amino
acids in other regions of the protein.
1. Hydrophobic interactions are interactions between two nonpolar R groups.
For example, hydrophobic interactions would occur between the aromatic group in
phenylalanine and the alky group of valine or leucine. Within the compact shape of a
globular protein, the amino acids with nonpolar side chains push as far away from
the aqueous environment as possible, which forms a hydrophobic center at the
interior of the protein molecule.
2. Hydrophilic interactions are attractions between the external aqueous
environment and amino acids that have polar or ionized side chains. The polar
side chains pull toward the outer surface of globular proteins to hydrogen bond with
water. The presence of the hydrophilic side chains on the exterior surface makes
globular proteins soluble in water.
3. Salt bridges are ionic bonds between side groups of basic and acidic amino
acids, which have positive and negative charges. For example, at a pH of 7.4, the
side chain of lysine has a positive charge, and the side chain of glutamic acid has a
negative charge. The attraction of the oppositely charged side chains forms a strong
bond called a salt bridge. If the pH changes, the basic and acidic side chains lose
their ionic charges and cannot form salt bridges, which causes a change in the shape
of the protein.
4. Hydrogen bonds form between polar amino acids. For example, a hydrogen
bond can occur between the — OH of serine and the — NH of glutamine.
5. Disulfide bonds (— S — S —) are covalent bonds that form between the
— SH groups of cysteines in the polypeptide chain. In some proteins, there are
several disulfide bonds between the R groups of cysteine in the polypep tide chain.
Interactions between amino acid R groups fold a protein into a specific
three-dimensional shape called its tertiary structure.
Myoglobin is a globular protein with a heme pocket in its tertiary
structure that binds oxygen to be carried to the tissues.
Globular and Fibrous Proteins
Globular proteins
“spherical” shape
Insulin
Hemoglobin
Enzymes
Antibodies
Fibrous proteins
long, thin fibers
Hair
Wool
Skin
Nails
Globular and Fibrous Proteins
• A group of proteins known as globular proteins have
compact, spherical shapes because their secondary
structures of the polypeptide chain fold over on top of each
other. It is the globular proteins that carry out the work of
the cells: functions such as synthesis, transport, and
metabolism.
• Myoglobin is a globular protein that stores oxygen in skeletal
muscle. High concentrations of myoglobin have been found in
the muscles of sea mammals, such as seals and whales, that
stay under the water for long periods. Myoglobin contains 153
amino acids in a single polypeptide chain with about threefourths of the chain in the a-helix secondary I structure.
• The polypeptide chain, including its helical regions, forms a
compact tertiary structure by folding upon itself. Within the
tertiary structure, a pocket of amino acids and a heme group
binds and stores oxygen (02).
• The fibrous proteins are proteins that consist of
long, thin, fiber-like shapes. They are typically
involved in the structure of cells and tissues. Two
types of fibrous protein are the a- and β-keratins.
• The a-keratins are the proteins that make up hair,
wool, skin, and nails. In hair, three a-helixes coil
together like a braid to form a fibril. Within the fibril, the
a-helices are held together by disulfide (— S S —)
linkages between the R groups of the many cysteine
amino acids in hair. Several fibrils bind together to
form a strand of hair.
• The β-keratins are the type of proteins found in the
feathers of birds and scales of reptiles. In β-keratins,
the proteins consist of large amounts of β-pleated
sheet structure.
The tertiary structure of a protein refers to its
overall three-dimensional conformation.
• It is produced by interactions between amino acid residues that
may be located at a considerable distance from each other in
the primary sequence of the polypeptide chain.
• Hydrophobic amino acid residues ten to collect in the interior of
globular proteins, where they exclude water, while hydrophilic
residues are usually found on the surface, where they interact
with water.
• The types of interactions between amino acid residues that
produce the three-dimensional shape of a protein include
hydrophobic interactions, electrostatic interactions, and
hydrogen bonds, all of which are noncovalent. Covalent
disulfide bonds also occur.
Tertiary Structure of Globular Proteins
Tertiary structure – folding of domains and final arrangement of
domains in protein
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Compact, hydrophobic side chains buried in interior
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Maximum hydrogen bonding of hydrophilic groups within
molecule
Figure 2.10, tertiary structure of Trypsin
Learning Check P2
Select the type of tertiary interaction as
(1) disulfide
(2) ionic
(3) H bonds
(4) hydrophobic
A.
B.
C.
D.
Leucine and valine
Two cysteines
Aspartic acid and lysine
Serine and threonine
Solution P2
Select the type of tertiary interaction as
(1) disulfide
(2) ionic
(3) H bonds
(4) hydrophobic
A.
B.
C.
D.
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1
2
3
Leucine and valine
Two cysteines
Aspartic acid and lysine
Serine and threonine
Quaternary Structure
• The quaternary structure of a protein refers to the spatial
arrangement of subunits in a protein that consists of more
than one polypeptide chain.
• Only proteins with two or more chains have quaternary
structures. A good example is hemoglobin, the globular
protein molecule that carries oxygen in blood.
• The quaternary structure of hemoglobin consists of four
polypeptide chains or subunits, two alpha chains and two
beta chains. Each chain contains a heme group that binds
an oxygen molecule.
• The subunits are held together in the quaternary structure
by the same types of noncovalent interactions that join
various segments of a single chain to form and stabilize
the tertiary structure, such as hydrogen bonds and salt
bridges between side groups, disulfide links, and
hydrophobic attractions.
• Quaternary structure
• Many biological proteins are constructed of multiple polypeptide chains.
Often a single "protein" consists of more than one polypeptide chain. Each
polypeptide chain is called a "subunit." The way these chains fit together or
associate with one another is referred to as the "quaternary structure."
• The quarternary structure of the protein refers to the way multiple
subunits of a protein interact. This is the arrangement of the individual
subunits of a protein with multiple polypeptide subunits (i.e.
hemoglobin has 2 alpha and 2 beta subunits). Only proteins with multiple
polypeptide subunits have quaternary structure. The local arrangement
of the different chains to each other is very crucial for the function of the
protein.
• Note the following about the subunits that constitute a protein.
• a. "dimers" consist of two subunits ; a protein can be a "homodimer" (the
two subunits are identical, and often arranged symmetrically), or a
"heterodimer" (subunits are different).
• b. multimers, consist of many subunits
• REMEMBER: The quarternary structure of the protein refers to the way
multiple subunits of a protein interact. This is the arrangement of the
individual subunits of a protein with multiple polypeptide subunits (i.e.
hemoglobin has 2 alpha and 2 beta subunits). Only proteins with multiple
polypeptide subunits have quaternary structure.
The quaternary structure of hemoglobin consists of four polypeptide
subunits, each containing a heme group that binds an oxygen molecule.
• The primary structure of a protein consists of
the amino acid sequence along the chain.
• Secondary structure involves -helices, sheets, and other types of folding patterns.
• Tertiary structure (the three-dimensional
conformation of a protein) involves
electrostatic and hydrophobic interactions
and hydrogen and disulfide bonds.
• Quaternary structure refers to the interaction
of one or more subunits to form a protein.
Hierarchy of structures in proteins
LEVELS OF ORGANIZATION
OF PROTEIN STRUCTURE
Quaternary level
Tertiary level
Primary level
Secondary level
Interactions between amino acid
residues in a polypeptide chain.
• Let us now briefly discuss the bonding found in the primary, secondary,
tertiary and quaternary structures of proteins in more detail. There are
several important, non-covalent, interactions between amino acid side
chains:
• Electrostatic interactions
• van der Waals interactions
• Hydrogen bonds
• Hydrophobic interactions
• Very stable interactions known as salt bridges can occur when two
oppositely charged side chains are in close proximity. A protein chain will
also have one free alpha-amino group and one free alpha-carboxyl group
which can participate in electrostatic interactions.
• van der Waals interactions result from the presence of transient changes in
the electron distribution around an atom. These changes result in
complementary changes in the electron distribution around an adjacent
atom. The net result of this process is the formation of an attractive force.
This force only occurs if atoms are in close proximity, and the magnitude of
the force decreases with sixth power of the separation distance. At very
close contact, however, repulsion between electron clouds counteracts the
attractive force. The distance at which this occurs is known as the van der
Waals radius.
• Hydrogen bonds are not intrinsically very strong, but as there are so many
hydrogen bond donors and acceptors in proteins they are very significant
overall, and very important in both the structure and interactions in proteins.
• In a protein molecule hydrogen bonds form concerted hydrogen bond
networks involving many side chains.
• This is facilitated by the fact that some atoms such as oxygen can act as
both hydrogen bond donors and acceptors:
• Hydrogen bonds result from the partial sharing of a hydrogen atom between
two electronegative atoms. The hydrogen atom that is shared has it's
electron delocalised onto the atom to which it is covalently bonded, resulting
in it posessing a partial positive charge.
• This charge separation allows an electrostatic interaction between the
hydrogen and another, electronegative, atom. In proteins the important
electronegative atoms are oxygen and nitrogen as both donors and
acceptors.
• These atoms are found on the polypeptide backbone and on side chains of
amino acids such as the acidic and basic amino acids e.g. the hydroxyl
amino acids serine and threonine.
• (NB THE STATEMENT the hydroxyl amino acids serine and threonine GO
BACK AND CHECK THE STRUCTURES AND SEE WHY THIS SHOULD
BE SO.
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Hydrophobic interactions occur between non-polar molecules in the presence of a
polar solvent such as water. In the context of protein structures, several amino acid
side chains are, to varying degreees, hydrophobic.
The most hydrophobic of the amino acid side chains are those of alanine, valine,
leucine and isoleucine.(VAIL) These amino acids side chains are bulky alkyl chains
with different molecular geometries.
It is a general rule (with, of course, many exceptions) that these residues are found
in the interior of protein molecules where they form a hydrophobic core containing
very little water.
It is believed that the different molecular geometries of the side chains are important
in facilitating close packing of the alkyl chains inside the protein.
Another group of hydrophobic resdiues are the aromatic amino acids tyrosine
tryptophan and phenylalanine. These amino acids are the residues responsible for
the uv absorbance of proteins and also participate in hydrophobic interactions.
There is one more amino acid that can participate in hydrophobic interactions,
although it is more polar than the others. This is one of the sulphur-containing amino
acids, methionine. NOTE THIS STATEMENT METHIONINE CAN PARTICIPATE IN
HYDROPHOBIC REACTIONS ALTHOUGH IT IS POLAR. Can you see why from
the structure?
So far, we have only discussed non-covalent interactions between side chains. There
is, however, one very important covalent interaction that represents a stabilising
influence in protein molecules, the disulphide bond.
The side chain of the amino acid cysteine contains a highly reactive thiol group. Two
such thiol groups can react to form a disulphide bond.
These bonds are always formed after protein biosynthesis and contribute to the
stability of the folded state by linking together distant parts of the polypeptide chain.
•END