1.

1 Proteins:
Motifs, Structural &
Functional domains, Quaternary
Structure and Protein families
Dr. Kinjalka Ghosh
MBBS, MD Biochemistry.
Assistant Professor, Dept. of Biochemistry,
Seth G.S.M.C & KEM Hospital, Mumbai

11/5/16

Structural Motif
In proteins, a structural motif describes the connectivity
between secondary structural elements.
An individual motif usually consists of only a few
elements, e.g., the 'helix-turn-helix' motif which has just
three.

11/5/16

Structural Motif
While the spatial sequence of elements may be identical
in all instances of a motif, they may be encoded in any
order within the underlying gene.
In addition to secondary structural elements, protein
structural motifs often include loops of variable length
and unspecified structure.

11/5/16

SUPER SECONDARY STRUCTURES (MOTIFS)

Certain groupings of secondary structural elements are called motifs.

beta-alpha-beta motif

-meander motif

Greek key motif

Beta barrel

Structural Motif
Beta hairpin:
Extremely common.
Two antiparallel beta strands connected by a tight turn of a
few amino acids between them.

11/5/16

Structural Motif
Greek key:
4 beta strands folded over into a sandwich shape.
The Greek key motif consists of four adjacent antiparallel
strands and their linking loops.
It consists of three antiparallel strands connected by hairpins,
while the fourth is adjacent to the first and linked to the third
by a longer loop.
This type of structure forms easily during the protein folding
process.
Eg: Plastocyanin
11/5/16

Structural Motif
Omega loop:
A loop in which the residues that make up the beginning and end of
the loop are very close together.
It is named after its shape, which resembles the upper-case Greek
letter Omega ().
omega loops can help stabilize interactions between protein and
ligand
A heritable coagulation disorder is caused by a single-site mutation
in an omega loop of protein C
Identified as playing a role in the folding of some proteins, including
HIV-1 reverse transcriptase; cytochrome c; and nucleases.
11/5/16

Structural Motif
Helix-loop-helix:

Consists of alpha helices bound by a looping stretch of amino acids.

Seen in transcription factors.
The motif is characterized by two -helices connected by a loop.
In general, transcription factors including this domain are dimeric,
each with one helix containing basic amino acid residues that
facilitate DNA binding.
In general, one helix is smaller, and, due to the flexibility of the
loop, allows dimerization by folding and packing against another
helix.
The larger helix typically contains the DNA-binding regions
11/5/16

Structural Motif
Zinc finger:
Two beta strands with an alpha helix end folded over to bind a
zinc ion. Important in DNA binding proteins.
Small protein motifs that contain multiple finger-like
protrusions that make tandem contacts with their target
molecule

11/5/16

Structural Motif
Helix-turn-helix:
Two helices joined by a short strand of amino acids and
found in many proteins that regulate gene expression.
The helix-turn-helix motif is a DNA-binding motif.
The recognition and binding to DNA by helix-turn-helix
proteins is done by the two helices, one occupying the Nterminal end of the motif, the other at the C-terminus.

11/5/16

10

Structural Motif
Nest:
Extremely common. Just three consecutive amino acid
residues form an anion-binding concavity.
The main chain NH groups bind the anions while the side
chain atoms are often not involved.
Proline residues lack NH groups so are rare in nests.
About one in 12 of amino acid residues in proteins, on
average, belongs to a nest.

11/5/16

11

Structural Motif
Nest:
The conformation of a nest is such that one of more of the NH
groups of the first, second and third amino acid residues are
liable to be hydrogen bonded to a negatively charged, or
partially negatively charged, atom, often an oxygen atom.
These main chain atoms form a concavity called a nest into
which an anionic atom fits.
The antibiotic peptide vancomycin which binds a key
carboxylate group needed during bacterial cell wall synthesis

11/5/16

12

Structural Motif
Niche:
Extremely common.
Just three consecutive amino acid residues form a
cation-binding feature.
Eg:
thrombin, Na+;
annexin, Ca++;
pyruvate dehydrogenase, K+.

11/5/16

13

11/5/16

14

Tertiary structure
The overall three-dimensional arrangement of all atoms in a
protein is referred to as the proteins tertiary structure.
Whereas the term secondary structure refers to the spatial
arrangement of amino acid residues that are adjacent in the
primary structure.
Tertiary structure includes longer-range aspects of amino
acid sequence.
Amino acids that are far apart in the polypeptide sequence
and that reside in different types of secondary structure may
interact within the completely folded structure of a protein.
11/5/16

15

TERTIARY STRUCTURE
Tertiary structure is the three-dimensional
conformation of a polypeptide.
The common features of protein tertiary structure
reveal much about the biological functions of the
proteins and their evolutionary origins.
The function of a protein depends on its tertiary
structure. If this is disrupted, it loses its activity.

INTERACTIONS STABILIZING 30 STRUCTURE

This final shape is determined by a
variety of bonding interactions
between the "side chains" on the
amino acids.
Hydrogen bonds
Ionic Bonds
Disulphide Bridges
Hydrophobic Interactions:

DOMAINS
Polypeptide chains containing more than ,200 residues usually fold into two or more
globular clusters known as domains.
Fundamental functional and 3 dimensional structure of proteins.
Domains often have a specific function such as the binding of a small molecule.
Many domains are structurally independent units that have the characteristics of small
globular proteins.

The two-domain protein glyceraldehyde3-phosphate dehydrogenase.

NAD+

Domains
A protein domain is a conserved part of a given protein sequence and (tertiary)
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 different proteins.
Molecular evolution uses domains as building blocks and these may be recombined in
different arrangements to create proteins with different functions.
11/5/16

19

Domains
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.
Because they are independently stable, domains can be "swapped" by genetic
engineering between one protein and another to make chimeric proteins.

11/5/16

20

QUATERNARY STRUCTURE
The biological function of some
molecules is determined by multiple polypeptide chains
multimeric proteins.
Arrangement of polypeptide sub unit is called
quaternary structure.
Sub units are held together by non covalent
interactions.
Eg: Hemoglobin has the subunit composition a2b2

Quaternary structure of hemoglobin.

Quaternary structure
The protein consists of more than one polypeptide.
The different polypeptide chains bind together to form a
whole molecule.
Eg insulin is made up of two polypeptide chains whilst
haemoglobin is made up of four.

11/5/16

22

Haemoglobin is
made up of 4
different
polypeptide
chains.

Keratin is a secondary
structure protein. it has a
spiral shape and is held in
position by hydrogen bonds.

Globular proteins.
Globular proteins have the following characteristics:
Irregular amino acid sequence
Sequence is highly specific and never varies between 2
examples of the same protein.
Polypeptides fold into a spherical shape.
Relatively unstable structure.
Metabolic functions.
Egs enzymes, hormones and haemoglobin.

Enzymes.

Structure and function of globular

proteins.
The shape of a globular protein is very delicate and vital
to its function.
An enzyme has a precise tertiary structure that provides
it with its active site. Any change in the shape of the
active site will stop the enzyme from working.
High temperatures make the molecules vibrate and this
causes the weak hydrogen bonds to break and as a
result the shape changes. The enzyme is denatured and
will not work.

Fibrous Proteins
Secondary Structures and Properties of Fibrous Proteins

11/5/16

27

Denaturation of proteins.
The three dimensional shape of proteins is maintained
by hydrogen bonds and ionic bonds which are fairly
weak.
Any agent such as heat, acids or alkalis will break these
bonds and cause a change in shape.
With a change in shape the protein can no longer carry
out its function.

Folding
Folding of polypeptides is subject to an array of physical
and chemical constraints. A sampling of the prominent
folding rules that have emerged provides an opportunity
to introduce some simple motifs.
1. Hydrophobic interactions make a large contribution to the
stability of protein structures. Burial of hydrophobic amino
acid R groups so as to exclude water requires at least two
layers of secondary structure.
. Two simple motifs, the -- loop and the - corner (Fig. a),
create two layers.
11/5/16

29

Folding
2. Where they occur together in proteins, helices and sheets
generally are found in different structural layers.
This is because the backbone of a polypeptide segment in the
conformation cannot readily hydrogen-bond to an helix
aligned with it.

11/5/16

30

Family
Proteins with significant primary sequence similarity, and/or with
demonstrably similar structure and function, are said to be in the same
protein family.
A strong evolutionary relationship is usually evident within a protein
family.
For example, the globin family has many different proteins with both structural
and sequence similarity to myoglobin
Two or more families with little primary sequence similarity sometimes make
use of the same major structural motif and have functional similarities; these
families are grouped as superfamilies

11/5/16

31

Thank You!
11/5/16

32