Protein motif. by KK Sahu sir

Introduction:
Protein
Protein motif.
2. History:
3. A brief overview of protein structure.
4. The Structural Classification of Protein(SCOP):
All α.
All β
α/β
α+β
5.The super secondary structure.
6. Rules for formation of Protein Motifs.
7. Structural motifs.
8. Some Common Protein Motifs:
β-hairpin.
β-meander.
Alpha-alpha corner.
Helix-turn-helix motif.
β-α-β motif.
β-sandwich.
β-barrel.
Greek key.
The Jellyroll topology.
Omega loop.
Zinc finger motif.
9. Conclusion.
10. References.

1. By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. 1.Introduction:
Protein
Protein motif.
2. History:
3. A brief overview of protein structure.
4. The Structural Classification of Protein(SCOP):
All α.
All β
α/β
α+β

3. 5.The super secondary structure.
6. Rules for formation of Protein Motifs.
7. Structural motifs.
8. Some Common Protein Motifs:
β-hairpin.
β-meander.
Alpha-alpha corner.
Helix-turn-helix motif.
β-α-β motif.

4. β-sandwich.
β-barrel.
Greek key.
The Jellyroll topology.
Omega loop.
Zinc finger motif.
9. Conclusion.
10. References.

5. A. Protein:
The word “Protein” has been derived from the
Greek word “Proteios” which means pre-eminent
or first.
Proteins are organic compounds which are made
up of amino acids arranged in a particular
sequence.
Proteins occupy a central position in the
architecture and functioning of living matter.

6. B. Protein Motif:
The word motifmeans a single or repeated
image forming a design.
In case of proteins, use of the term motif
refers to a set of contiguous secondary
structuralelements, which is also referred
to as super secondary structure.
The word protein motif refers to short
segments of protein three dimensional
structures that are found in a large number
of different proteins.
A protein motif is formed by the three
dimensional arrangement of amino acids
which may not be adjacent.
Example:A helix-turn-helix motif which is
fond in many DNA binding proteins.

7. Fig: The DNA Binding Helix-turn-helix MOTIF.

8. Proteins were first described and named by
Jons Jacob Berzeliusin 1838.
However, the central role of proteins in living
organisms was not fully appreciated until
1926,when James B. Sumnershowed that
enzyme ureasewas a protein.
The first protein to be sequenced was Insulin,
by Frederick Sanger, who won the Nobel Prize
for this achievement in 1958.

9. The first protein structures to be solved were
Hemoglobin and myoglobulinby MaxPerutz
and Sir John Cowdery Kendrew, respectively
in 1958.
The three-dimensional structure of both
proteins was first determined by X-ray
diffraction analysis;Perutzand Kendrew
shared the Nobel Prize in Chemistry for these
discoveries.

10. Structure of proteins can be described
under the following heads:
Primary structure.
Secondary structure.
Super secondary structure.
Tertiary structure.
Quaternary structure.

11. The primary structure of a protein refers to
the number and sequence of amino acids ,the
constituent units of the polypeptide chain
The main mode of linkage of the amino acids
in proteins is the peptide bond which links
the α-carbonyl group of one amino acid
residue to the α-amino group of the other
rigid and planar peptide bond.
The primary structure of a protein is largely
responsible for its function.

12. The secondary structure is formed by the
spatial arrangement of protein by twisting of
the polypeptide chain.
The secondary structure focuses on regular
folding patterns of polypeptide backbone.
The most prominent are α-helix and β-
pleated sheet.

13. It is most common spiral structure of protein.
In this, the polypeptide chain is tightly wound
around an imaginary axis, drawn
longitudinally through the middle of the
helix.
The R-groups of amino acid residues
protrude outward from the central axis.

14. In this the polypeptide chains are arranged in
a zigzag manner.
The zigzag polypeptide chains can be
arranged side by side to form a structure
resembling a series of pleats.
There are two types of β-pleated sheets:
Anti-parallel and parallel β-sheets.

15. Super secondary structures also called
motifs or simply folds are particularly
stable arrangements of several elements of
secondary structure and connections
between them.

16. The three-dimentionalarrangement of
protein structure is referred to as a tertiary
structure.
Besides the hydrogen bonds, disulphide
bonds, ionic interactions and hydrophobic
interactions also contribute to the tertiary
structure of proteins.

17. Some proteins are composed up of two or
more polypeptide chains referred to as
subunits.
The spatial arrangement of these subunits is
known as quaternary structure.

18. Fig: A brief overview of protein structure.

19. Protein motifs are basis for protein structural
classification.
The SCOP provides a broad survey of all known
protein motifs (folds), detailed information about
the close relatives of any particular protein and a
framework for further research and classification.
The SCOP database borrows a scheme in which
protein structures are divided into four classes:
(a) All α
(b) All β
(c) α/β
(d) α+β

20. Protein folds
which consist
almost entirely of
α-helices are kept
in this category.
Example-
Cytokines.
A number of
cytokines consist
of four α-helices
in a bundle.
Fig: Showing all α types of protein

21. Protein folds
which consist of
almost entirely β-
sheets are put in
this category.
Example: β-
sandwiches, β-
barrels ,β-
propellers.
Fig: β-propeller

22. Protein folds in which the α and β segments
are interspersed or alternate are kept in this
category.
Many enzymes including all those involved in
glycolysis are α/β structures and most α/β
proteins are cytosolic.
Example: β-α-β structures, α/β horse shoe ,
α/β barrels

23. Alpha / beta type of protein

24. alpha/beta horseshoe

25. Protein folds in which the α&β regions are
somewhat segregated are kept in this
category.
Example: 1.Lysozyme.
2.Ubiquitin.
3.Papain.

28. Super secondary also called motifs or
simply folds are particularly stable
agreements of several elements of
secondary structure and connections
between them.
The terms (super secondary
structure/motif/folds) are also applied to
a wide range of structures.
Recognized motifs range from simple to
complex sometimes appearing in
repeating units or combinations.

29. A single large motif may comprise the entire
protein.
One well studied motif, the coiled coil of α-
keratin is also found in a number of other
proteins.
Domain :-polypeptides with more than a
few hundred amino acid residues often fold
into two or more stable, globular units
called domains.

30. In many cases, a domain from a large
protein will retain its correct 3-d structure
even when it’s separated (for example by
proteolytic cleavage) from the remainder of
the polypeptide chain.
Different domains have distinct functions
such as binding of small molecules or
interaction with other proteins.

31.  A sampling of the prominent folding rules to
provides an opportunity to introduce some
simple motifs.
 Hydrophobic interactionsmake 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 β-α-β and the α-α
corner create two layers.

32.  Where they occur together in proteins, α
helices and β sheets generally are found in
different structural layers. This is because
the backbone of a polypeptide segment in
the β conformation cannot readily
hydrogen-bond to an α helix aligned with
it.
 Polypeptide segments adjacent to each
other in the primary sequence are usually
stacked adjacentto each other in the
folded structure. Although distant segment
of a polypeptide may come together in the
tertiary structure, this is not the form.

33. Connections between elements of
secondary structure cannot cross or form
knots.
The β conformation is most stable when
the individual segments are twisted
slightly in a right-handed sense.
Two parallel β strands, for example, must
be connected by a crossover strand.
In principle, this crossover could have a
right-or left-handed conformation, but
in proteins it is almost always right-
handed

34. In a chain like biological molecule such as
protein or nucleic acid, a structural motif is
a three dimensional structural element
within the chain, which appears also in a
variety of other molecules.
In proteins, structural motifs usually consist
of just a few elements eg the helixturn
helix motifhas just 3 elements.
Protein structural motifs often include loops
of variable length and unspecified
structure.

35. β-hairpin:-
These are one of the
simplest super
secondary structures
& are wide spread in
globular protein.
In a β-hairpin two
antiparallel β-stands
are linked by a short
loop of 2-5 residues
of which one is
frequently a glycine
or proline, both of
which can assume
the usual dihedral
conformations
required for a tight
turn.

36. Consecutive anti-
parallel β-stands
when linked by
hairpins form a
super secondary
structure known as
the β-meander.

37. Short loop regions
connecting helices
which are roughly
perpendicular to
one another are
called α-α corner.

38. This motif was first observed in
prokaryotic DNA binding proteins such as
the cro-repressor from phage λ.
The Helix-turn-Helix motif is a major
structural motif capable of binding DNA.
It is composed two α-helices joined by a
short stand of amino acids.

39. The trprepressor is a DNA-binding
protein which regulates tryptophan
synthesis in E. coli

40.  The parallel β-stands are connected by
longer regions of chain which cross the β-
sheet & contain α-helical segments.
 Such motif is called β-α-β motif & is found
in most common proteins that have
parallel β-sheets.
 The β-α-β motif almost always has right
handed fold.

41. Beta alpha beta motif

42. In the
immunoglobulin
folds the strands
form two sheets
packed against
each other
forming a β-
sandwich.
Immunoglobin

43. β-barrel is a large β-sheet that twists and
coils to form a closed structurein which the
first strand is hydrogen bonded to the last.
β-strands in β-barrel are typically arranged
in an anti-parallel fashion.
Barrels are commonly found in porinsand
other proteins that span the cell
membranes and in proteins that span
the cell membranes and in proteins that
bind hydrophobic ligandsin the barrel
center.

44. Fig: Beta barrel

45. This motif is named so because of its
resemblance to Greek key meander pattern in
art.
In this topology three up and down β-strands
connected by hairpins are followed by a
longer connection to the fourth strand which
lies adjacent to the first.
Example: Plastocyanin: It has a mixed sheet
containing two parallel pairs of β-strands

46. Fig: Greek Key

47. Richardson in 1981
described Jellyroll
fold as being
formed by the
addition of an Extra
swirl to a Greek
key.
Example:
Jellyroll fold of coat
protein of satellite
Tobacco necrosis
virus.

48. Omega loopis a protein
motif which contains a loop
of any length and any
aminoacid sequence.
Its named so after its shape
which resembles the Greek
capital letter omega.
It may form a stabilizing
interaction between two
protein domains in a dimer.
For example: In the enzyme
triose phosphate isomerase
Omega loop

49. There are several
different families of
proteins containing
this particular DNA
binding motif.
The cysteine and
histidineresidues
are favoured for
Zinc binding.
Example: Zn 268is
a protein which has
three Zinc fingers.

50. Principles of biochemistryby David L.Nelson
and Michael M.Cox.
Fourth Edition-2004
Fundamentals of Biochemistryby J.L.Jain
Third Edition 2008
Biochemistryby Dr. U.Satyanarayan. Third
Edition 2006
Internet sites: www.wikipedia.com
www.kbiotech.com