The three Dimensional

structure of proteins:
Structure of Proteins

 Proteins are the polymers of L-α-amino acids.

 The structure of proteins is rather complex which can be divided into 4 levels of organization
 Structure of protein

Consist of Amino acid

monomers
Primary structure
3-D structure that
reflects its function
• Compact
Secondary
Majority of protein are: • Complex
• Highly convoluted
structure

There are three levels of

structural organization Tertiary structure
1. Primary structure :
The linear sequence of amino acids forming the backbone of proteins (polypeptides).
2. Secondary structure :
The spatial arrangement of protein by twisting of the polypeptide chain.
3. Tertiary structure :
The three dimensional structure of a functional protein.
4. Quaternary structure :
Some of the proteins are composed of two or more polypeptide chains referred to as
subunits. The spatial arrangement of these subunits is known as quaternary structure.
 Primary structure of a protein:

The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain.

The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis.

The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature
of the free group on each extremity.

Counting of residues always starts at the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond.

The primary structure of a protein is determined by the gene corresponding to the protein.

A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation.

No of amino acids = few to several 100

Change in single amino acid results in dramatic change of properties.

Peptide bond

 The amino acids are held together in a protein by covalent peptide bonds or
linkages.
 These bonds are rather strong and serve as the cementing material between the
individual amino acids (considered as bricks).
 Formation of a peptide bond: When the amino group of an amino acid combines
with the carboxyl group of another amino acid, a peptide bond is formed
 Note that a dipeptide will have two amino acids and one peptide (not two) bond.
 Peptides containing more than 10 amino acids (decapeptide) are referred to as
polypeptides.
Example of Normal Hemoglobin and Hemoglobin S
 Examples of Primary Structure:

 Given table is showing the no of amino acid residues in some of

the primary structure of proteins:
Primary proteins No. of Amino Acids Primary proteins No. of Amino Acids
Insulin 51 Human alpha MSH 13
Ribonuclease 124 Beta MSH of human
22
Proteins of tobacco origin
158
mosaic virus Angiotensin I 10
Alpha chain of Hb 141 Angiotensin II 8
Beta chain of Hb 146 Angiotensin III 7
Oxcytocin 8 Glucagon 29
Vasopressin 8 Calcitonin 32
ACTH 39 TRH 3
Which protein sequence was first identified?

Insulin of a beef origin

Sanger in 1953

Nobel prize in chemistry

Human insulin

Consist of 2 chains

A chain also called alpha chain- 21 A.A

B chain also called beta chain- 30 A.A

S-S bridge or Di-sulphide bridge

Insulin of pork & whale are same but differ in 1 amino acid with human

Beef and sheep insulin differ from human by 3-4 A.A

Determination of
Primary Structure of
polypeptide
Sanger method
Edman’s method
DNA sequence method
Sanger's reagent

 Sanger used 1-fluoro 2, 4-dinitrobenzene (FDNB) to determine insulin structure.

 FDNB specifically binds with N-terminal amino acid to form a dinitrophenyl (DNP)
derivative of peptide.
 This on hydrolysis yields DNP-amino acid (N-terminal) and free amino acids from
the rest of the peptide chain.
 DNP-amino acid can be identified by chromatography.
 Sanger's reagent has limited use since the peptide chain is hydrolysed to amino
acids.
Sanger Method:

2,4 Dinitro Hydrolysis

Thiol flourobenzene
Edman's reagent

 Phenyl isothiocyanate is the Edman's reagent. It reacts with the N-terminal

amino acid of peptide to form a phenyl thiocarbamyl derivative.
 On treatment with mild acid, phenyl thiohydantoin (PTH)–amino acid, a cyclic
compound is liberated.
 This can be identified by chromatography
 Edman's reagent has an advantage since a peptide can be sequentially degraded
liberating N-terminal amino acids one after another which can be identified.
 This is due to the fact that the peptide as a whole is not hydrolysed but only
releases PTH amino acid.
 Edman’s Method

Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide.

In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide
bonds between other amino acid residues.
DNA sequence Method:

DNA sequencing may be used to determine the

sequence of individual genes, larger genetic regions like
full chromosomes, or entire genomes of any organism.

DNA sequencing is also the most efficient way to

indirectly sequence RNA or proteins.
 Secondary Structure of Protein:

Secondary structure refers to highly regular local sub-structures on the actual polypeptide backbone chain.

Two main types of secondary structure, the α-helix and the β-strand or β-sheets, were suggested in 1951 by Linus Pauling.

These secondary structures are defined by patterns of hydrogen bonds between the main-chain peptide groups.

They have a regular geometry.

Both the α-helix and the β-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone.

Some parts of the protein are ordered but do not form any regular structures.

They should not be confused with random coil, an unfolded polypeptide chain lacking any fixed three-dimensional structure. Several
sequential secondary structures may form a "super-secondary unit".
α-helix

 1. The α-helix is a tightly packed coiled structure with amino acid side chains
extending outward from the central axis.
 2. The α-helix is stabilized by extensive hydrogen bonding. It is formed between H
atom attached to peptide N, and O atom attached to peptide C.
 The hydrogen bonds are individually weak but collectively, they are strong
enough to stabilize the helix.
 3. All the peptide bonds, except the first and last in a polypeptide chain,
participate in hydrogen bonding.
α-helix

 4. Each turn of α-helix contains 3.6 amino acids and travels a distance of 0.54
nm. The spacing of each amino acid is 0.15 nm.
 5. α-Helix is a stable conformation formed spontaneously with the lowest energy.
 6. The right handed α-helix is more stable than left handed helix (a right handed
helix turns in the direction that the fingers of right hand curl when its thumb
points in the direction the helix rises).
 7. Certain amino acids (particularly proline) disrupt the α-helix. Large number of
acidic (Asp, Glu) or basic (Lys, Arg, His) amino acids also interfere with αhelix
structure.
α-helix
β-Pleated sheet

 This is the second type of structure (hence β after α) proposed by Pauling and
Corey.
 β-Pleated sheets (or simply β-sheets) are composed of two or more segments of
fully extended peptide chains
 In the β-sheets, the hydrogen bonds are formed between the neighbouring
segments of polypeptide chain(s).
β-Pleated sheet
Tertiary Structure of a Protein:

Overall 3 dimension of shape and conformation

Example:
• Myoglobin
• If its chain could be extended
• Its length will be 20 times more than its width
• X-ray diffraction
• Myoglobin is like football
• It means that it is folded and refolded many times.
• Globular

Domain- perform specific chemical and physical properties

Also act as binding site for the substrate or ligand

Tertiary Structure
of protein
Tertiary structure of protein

 The three-dimensional arrangement of protein structure is referred to as tertiary structure.

 It is a compact structure with hydrophobic side chains held interior while the hydrophilic
groups are on the surface of the protein molecule.
 This type of arrangement ensures stability of the molecule.
 Bonds of tertiary structure Besides the hydrogen bonds, disulfide bonds (–S–S), ionic
interactions (electrostatic bonds), hydrophobic interactions and van der Waals forces also
contribute to the tertiary structure of proteins.
 Domains The term domain is used to represent the basic units of protein structure
(tertiary) and function. A polypeptide with 200 amino acids normally consists of two or
more domains.
Factors effecting the tertiary structure of proteins:

Attraction between
Di-sulphide covalent negatively charged
Hydrogen bonding
linkage COOH and positively
charged NH2 group

Vander wall’s forces Ester linkages

X-ray diffraction analysis:

Kendrew first presented

this method for
myoglobin protein
 Quaternary Structure of protein:

Quaternary structure is the three-dimensional structure consisting of the aggregation of two or more individual polypeptide chains
(subunits) that operate as a single functional unit .

The resulting multimer is stabilized by the same non-covalent interactions namely hydrogen bonds, hydrophobic interactions & ionic
bonds.

There are many possible quaternary structure organisations.

Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers.

Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, a tetramer if it contains four
subunits, and a pentamer if it contains five subunits.

The subunits are frequently related to one another by symmetry operations, such as a 2-fold axis in a dimer.

Multimers made up of identical subunits are referred to with a prefix of "homo-" and those made up of different subunits are referred to
with a prefix of "hetero-", for example, a heterotetramer, such as the two alpha and two beta chains of hemoglobin.
Examples of protein structure

 Structure of human insulin: Insulin consists of two polypeptide chains, A and B

 The A chain has glycine at the N-terminal end and asparagine at the C-terminal
end.
 The B chain has phenylalanine and alanine at the N-and C-terminal ends,
respectively.
 Originally, insulin is synthesized as a single polypeptide preproinsulin which
undergoes proteolytic processing to give proinsulin and finally insulin.
Structure of human insulin:
Structure of Hemoglobin
Functions of Proteins: (Summary)

Essential part of protoplasm- form life

Nucleoproteins- carrier of genetic information

• Replication
• Transcription
• Translation

Chaperones proteins- control correct intracellular folding and assembly of polypeptides

Enzymes- biological catalysts

Integral part of all viruses- important for pathogenesis

Hemoglobin- carry oxygen

Functions of Proteins: (Summary)

Act as hormones
• Reproduction
• Growth
• Metabolism

Present in plasma- colloidal properties+ maintain osmotic pressure

Blood coagulation

Antibodies- immune system

Transporting proteins- plasma membrane

Make complexes with carbohydrates

Make complexes with lipids

Functions of Proteins: (Summary)

Protein domain

Ligand binding

Protein ligand complexes

Sources of proteins:
• Animals
• Plants

Macromolecules

MW = few thousands to several millions

Classification of proteins

 Proteins are classified in several ways.

 Three major types of classifying proteins based on their function, chemical
nature and solubility properties and nutritional importance
 A Functional classification of proteins Based on the functions they perform,
proteins are classified into the following groups (with examples)
A Functional classification of proteins

 1. Structural proteins : Keratin of hair and nails, collagen of bone.

 2. Enzymes or catalytic proteins : Hexokinase, pepsin.
 3. Transport proteins : Hemoglobin, serum albumin.
 4. Hormonal proteins : Insulin, growth hormone.
 5. Contractile proteins : Actin, myosin.
 6. Storage proteins : Ovalbumin, glutelin.
 7. Genetic proteins : Nucleoproteins.
 8. Defense proteins : Snake venoms, Immunoglobulins.
 9. Receptor proteins for hormones, viruses.
B Protein classification based on chemical nature and
solubility

 This is a more comprehensive and popular classification of proteins.

 It is based on the amino acid composition, structure, shape and solubility
properties.
 Proteins are broadly classified into 3 major groups
 1. Simple proteins : They are composed of only amino acid residues.
 2. Conjugated proteins : Besides the amino acids, these proteins contain a
nonprotein moiety known as prosthetic group or conjugating group.
 3. Derived proteins : These are the denatured or degraded products of simple
and conjugated proteins. The above three classes are further subdivided into
different groups
Summary of classification of proteins