Dr.

Prajna Mandal
The 4 levels of protein structure

• Primary
• Secondary
• Tertiary
• Quaternary
The amino acid sequence of a protein
determines its 3D structure

The non-covalent bonds present in a protein are:

H-bonding, salt bridges, disulphide linkages and
hydrophobic interactions.

Native state of a protein – The form of the protein which

exists naturally.
Denatured state of a protein – State of the protein when the
native state is lost.
 The Amino Acid Sequence of a Protein
Determines Its Three-Dimensional Structure
Amino acids have different propensities
for forming α-helices, β-sheets, β-turns

Residues such as alanine, glutamic acid and leucine tend to

be present in α helices whereas valine and isoleucine tend to
be present in β sheets. Glycine, asparagine and proline have
a propensity for being present in turns.
Amino acid propensities
 Tertiary structure
• The overall course of the polypeptide chain of a
protein is referred to its tertiary structure.
 Supersecondary structures - Motifs
(a) The most common form of supersecondary structure is the
bab motif, in which the usually righthanded crossover
connection between two consecutive parallel strands of a b
sheet consists of an a helix.

(b) Another common supersecondary structure, the b hairpin

motif, consists of an antiparallel b sheet formed by sequential
segments of polypeptide chain that are connected by relatively
tight reverse turns.

(c) In an aa motif, two successive antiparallel a helices pack

against each other with their axes inclined soas to permit their
contacting side chains to interdigitate efficiently. Such
energetically favorable associations stabilise the coiled coil
conformation of a keratin.

(d) In the Greek key motif ; named after an ornamental design

commonly used in ancient Greece; a b hairpin is folded over
to form a four-stranded antiparallel b sheet. Of the 10 possible
ways of connecting the strands of a four-stranded antiparallel
b sheet, the two that form Greek key motifs are, by far, the
most common in proteins of known structure. Groups of
motifs combine in overlapping and nonoverlapping ways to
form the tertiary structure of a domain, which is called a fold.
 Protein Domains
• A protein domain is a part of protein
sequence and structure that can evolve,
function, and exist independently of the rest
of the protein chain. Each domain forms a
compact three-dimensional structure and
often can be independently stable and folded.
Many proteins consist of several structural
domains. One domain may appear in a variety
of evolutionarily related proteins. Domains
vary in length from between about 25 amino
acids up to 500 amino acids in length. The
shortest domains such as zinc fingers are
stabilized by metal ions or disulfide bridges.
Domains often form functional units, such as
the calcium-binding EF hand domain of
calmodulin.

Pyruvate kinase, a protein with

three domains.
 Classes of Proteins based on
Tertiary Structure
1. Fibrous Proteins
• Fibrous proteins, also called scleroproteins,
are long filamentous protein molecules.

• Fibrous proteins are only found in animals.

• Fibrous proteins form 'rod' or 'wire' -like

shapes and are usually inert structural or
storage proteins. They are generally water-
insoluble. Fibrous proteins are usually used
to construct connective tissues, tendons,
bone matrix and muscle fiber.

• Examples of fibrous proteins include

keratins, collagens and elastins.
α-Keratin Structure
 2. Globular Proteins

They comprise of a highly diverse

group of proteins in their native
state and exist as compact
spheroidal molecules. The folding
of the polypeptide chain is such
that the interior consists almost
entirely of nonpolar residues such
as leu, val. The polar charged
residues are on the surface. Some
proteins that span the biological
membranes are exceptions. This
is because they have the reverse
distribution of hydrophobic and
hydrophilic amino acids.
 Protein stability
• Factors responsible for protein stability are:
1. Electrostatic forces: Ionic interactions, dipole-
dipole interactions, van der Waals’ forces.
2. Hydrogen bonding.
3. Hydrophobic forces.
4. Disulphide bonds.
 Myoglobin – the first protein to be
seen in atomic detail

• Oxygen carrier in
muscles.
• Has a single
polypeptide chain of
153 amino acids.
 Quaternary structure
• Oligomer
• Subunits
• Homomultimer,
heteromultimer,
protomers.
 Haemoglobin
• The oxygen carrying protein in blood, consists
of two subunits of one type α and two subunits
of another type β chains.

• Sickle cell anemia. Sickle-cell disease (SCD), or

sickle-cell anæmia (or anaemia, SCA) or
drepanocytosis, is an autosomal recessive
genetic blood disorder with overdominance,
characterized by red blood cells that assume an
abnormal, rigid, sickle shape. Sickling decreases
the cells' flexibility and results in a risk of
various complications. The sickling occurs
because of a mutation in the haemoglobin gene.
Life expectancy is shortened. In 1994, in the
US, the average life expectancy of persons with
this condition was estimated to be 42 years in
males and 48 years in females, but today, thanks
to better management of the disease, patients
can live into their 50s or beyond.
 Subunit interaction
• A multisubunit protein has
interactions among its
constituent subunits via salt-
bridge, interchain disulphide
bonds, H-bonds involving
polypeptide backbone and
their side chains. Interactions Capsid of Viruses
between subunits tend to
have hydrophobicities
between those of protein
interiors and exteriors.
 The Levinthal’s Paradox

Consider a small protein with 100 residues. Cyrus Levinthal calculated that, if
each residue can assume three different conformations, the total number of
structures would be 3100, which is equal to 5 × 1047. If it takes 10-13 s to convert one
structure into another, the total search time would be 5 × 1047 × 10-13 s, which is
equal to 5 × 1034 s, or 1.6 × 1027 years. Clearly, it would take much too long for even
a small protein to fold properly by randomly trying out all possible conformations.
The enormous difference between calculated and actual folding times is called
Levinthal's paradox.

The essence of protein folding is the retention of partly correct intermediates. Local
regions, which have significant structural preference, though not necessarily stable
on their own, will tend to adopt their favored structures and, as they form, can
interact with one other, leading to increasing stabilization.
 Protein folding
• Loss of protein structure results in the loss of
function. Polypeptides fold rapidly by a
stepwise process. Several models have been
proposed to explain the process of protein
folding.
1. Hierarchical.
2. Spontaneous collapse.
3. Assisted folding.
Spontaneous Collapse
Assisted Folding
 Protein misfolding
• Protein misfolding diseases.
A prion in the Scrapie form (PrPSc) is an infectious agent composed of
protein in a misfolded form. This is the central idea of the Prion
Hypothesis, which remains debated. This would be in contrast to all other
known infectious agents (virus/bacteria/fungus/parasite) which must
contain nucleic acids (either DNA, RNA, or both). The word prion,
coined in 1982 by Stanley B. Prusiner, is derived from the words protein
and infection. Prions are responsible for the transmissible spongiform
encephalopathies in a variety of mammals, including bovine spongiform
encephalopathy (BSE, also known as "mad cow disease") in cattle and
Creutzfeldt–Jakob disease (CJD) in humans. All known prion diseases
affect the structure of the brain or other neural tissue and all are currently
untreatable and universally fatal.