structural organizaiton of protein

1. STRUCTURAL
ORGANIZATION OF
PROTEIN
Dr Nikunj Patel
Associate Professor,
Department of Biochemistry
SMIMER,Surat

2. PROTEINS
 Derived from Greek word “Proteios” which means
“Primary”.
 Out of total dry body weight  ¾ is of protein.
 Structural & Functional role in body
 Many amino acids are linked together with peptide
bond to form polypeptide chains.
 These chains fold on itself & interact with one
another to form functional protein.

3. STRUCTURAL ORGANIZATION OF
PROTEIN
 Four levels of organization:
 Primary structure: Number & sequence of
AA
 Secondary structure: Relation b/w AAs
which are not far apart in sequence
 Tertiary structure: Relation b/w AAs
which are far apart in sequence but near
in 3D aspect.
 Quaternary structure: Relation b/w
different polypeptide chains.

4. PRIMARY STRUCTURE
 Definition: Primary structure of a protein refers to
linear structure, number & sequence of amino acids.
 Each protein has a unique sequence of amino acids.
Any change in it may lead to non-functional protein.
 Stabilization: By peptide bond.

5. PRIMARY STRUCTURE
Denote the No. and Sequence of
A.A in protein
Example:
1. Gly-Val-leu-met and Gly-met-val-leu
2. Gly-Val-leu-met and Gly-val-met

6. PEPTIDE BOND FORMATION
 It is an amide bond
between α-carboxyl group
of one AA & α-amino
group of another AA.
 Uncharged bond
 Partial double bond
 Forms backbone of protein
 Trans in nature so no
freedom of rotation.

7.  Why partial double bond?
 Distance is 1.32Å which
is b/w single bond
(1.49Å) & double bond
(1.27Å).
 No rotation is possible
around peptide bond, but
side chains are free to
rotate on either sides of
peptide bond.

8. PLANNER PEPTIDE BOND
 6 atoms lie in one plane in space
 C,CO,NH,C

9. PARTIAL DOUBLE BOND
 C-N Distance 1.49 A0
 C=N Distance 1.27 A0
But C—N distance in peptide bond is 1.32 A0

10. TRANS FORM
 In protein mostly trans form present because less
chance of classing of R-group of two aminoacids

11.  Phi and psi angle
 Angle of rotation is not possible at peptide bond
BUT possible adjacent to peptide bond
psi phi

12.  Ramachandran plot
 Try to find out possibilities of angle of rotation
 Around 75 % of various combination not possible
because of steric collision

13. NUMBERING OF AMINO ACIDS IN PROTEIN
 In a polypeptide chain, free alpha amino group is
called as Amino terminal (N-terminal) end.
 N terminal AA is written on left side & considered
as first amino acid
 Other end is called as Carboxy terminal (C-terminal)
end.
 C terminal AA is written is on right & considered
as last amino acid.

14.  It can be written as:
 Alanyl Cysteinyl Valine
 Ala-Cys-Val
 NH2-Ala-Cys-Val-COOH
 A C V

15. STRUCTURE OF INSULIN
 Originally described by Sanger in 1955. (NP 1958)
 2 polypeptide chains: A & B chains.
 A chain: Glycine chain – 21 amino acids
 B chain: Phenylalanine chain – 30 amino acids.
 2 interchain disulfide bonds: A7-B7, A20-B19.
 1 intrachain disulfide bond: A6-A11.

16. PROCESSING & PRODUCTION OF ACTIVE
INSULIN MOLECULE

17. PRIMARY STRUCTURE OF HB
 4 Polypeptide chain
 2 alpha
 2 Beta
 Alpha chain: 141 AA
 Beta Chain : 146 AA

18. PRIMARY STRUCTURE DETERMINES
BIOLOGICAL ACTIVITY OF PROTEIN
 Protein with a specific primary structure when put in
solution, it will automatically form its natural 3D
shape.
 Any mutation may interfere with final 3D shape of
the protein so active domain may not be formed
properly.
 E.g. HbA – beta chain 6th AA  Glutamic acid.
in HbS (sickle cell anemia) replaced by  Valine

19. SECONDARY STRUCTURE
 Definition:
 Folding of primary structure in to regular or ordered
structures.
 Secondary structure of protein refers to Relation
b/w AAs which are not far apart in sequence
forming regular ordered arrangement of amino
acids.
 Stabilized by Hydrogen bonds. No involvement of
‘R’ group

20. HYDROGEN BOND
 Weak bond
 attraction between partially positive
hydrogen in one molecule and an partially
negative atom(O,N) in the other.

21. HYDROGEN BOND
 Formed b/w Hydrogen donor
& Hydrogen acceptor groups.
 Hydrogen acceptor:
 -COO- of Glu, Asp
 >C=O of peptide bond
 Hydrogen donor:
 >NH of imidazole & peptide bond
 -OH of serine & threonine
 -NH2 of Lysine & Arginine
Hydrogen bond

22. VAN DER WAALS INTERACTION
 Also known as London dispersion force
 Weakest among noncovalent bonds
 Act over very short distances
 Interaction between two temporary dipole generated
because of attraction and repulsive forces between
two molecules when come closer.
 When molecules are separated/go far to each other,
bond break

28. VAN DER WAALS FORCES
 Non specific attractive forces
based on proximity of
interacting atoms due to
induced dipoles formed by
momentary fluctuations in
electron distribution in nearby
atoms.
 Very weak in nature but
collectively they act as major
stabilizing factor.
 Inversely proportional to
distance b/w two molecules.

29. ELECTROSTATIC BOND
 Also known as Ionic bond/salt bridge
 Bond between oppositely charge group
 Na+Cl-
 COO- NH3+

30. IONIC BOND
 Formed by attraction b/w
oppositely charged side
chains of AAs.
 Acidic groups (Asp, Glu)
attract basic groups (Lys, Arg,
His).

31. HYDROPHOBIC INTERACTION
 Not true bond
 Interaction of non-polar molecules with
each other
 Non polar molecule in aqueous solution lie
together not due to attraction with each
other, it is effect/forces of water molecules
over nonpolar molecules

32. HYDROPHOBIC INTERACTIONS
 Formed b/w non polar side chains of AAs.
 Repels charged/polar molecules & forms a
hydrophobic pocket/area in proteins.

33.  Two major types of secondary structure:
 Beta pleated sheet, Alpha helix

34. ALPHA HELIX
 First structure elucidated
 Most common & stable conformation
 Spiral structure where peptide bonds
form the back bone in spiral
arrangement & stabilized by hydrogen
bonds.
 3.6 residue per turn
 Generally right handed
 Distance b/w each AA is 1.5 Å
 H-bond is b/w carbonyl oxygen of AA
and amide Nitrogen of next 4th AA.
 Most common AA is methionine, then
Glutamic acid

36. HELIX DESTABILISING AA
 Long block of Glutamic Acid and Aspartic Acid
 R group repel each other
 Not form normally alpha helix at pH 7
 Long block of lysine / arginine
 Same as above
 Bulkier Side chain containing AA
 Asparagine ,serine,threonine,cysteine
 Glycine:
 Small R group form different type of helix
 More stable conformation for glycine containing poly-
peptide is B-Pleated sheet
 Proline:
 Imino group

37.  Examples:
 Hemoglobin and myoglobin
 Ferritin (around 75 %)
 Majority of all soluble protein (25% portion)
 Membrane span protein
 Less or absent Alpha Helix form:
 Collagen and elastin
 Chymotrypsin
 Cytochrome

38. BETA PLEATED SHEET
 Second type of structure elucidated
 Backbone of polypeptide is extended rather than
helical structure
 Several polypeptide chain arrange side by side or
 Single polypeptide chain may fold on itself
 All are arrange in zigzag manner to produce
pleated appearance
 Hydrogen bond between adjacent polypeptide
within sheet
 R group of adjacent AA is protrude opposite side

39. PLEATED APPEARANCE

40.  Distance b/w adjacent AA is 3.5 Å.
 Stabilized by H-bonds b/w NH &
C=O groups of neighboring
polypeptide segments.
 M.C AA in Beta sheet is valine
 Direction of sheet can be parallel
(Flavodoxin) or antiparallel (Fibroin)
or both (Carbonic anhydrase)
 Transthyretin

42. SILK FIBROIN

43. B-pleated sheet

44. ABNORMALLY ACCUMULATED B FORM
 Amyloidosis:
 Misfolded protein that have normally alpha helix
change to B pleated sheet
 Nonsoluble protein
 Deposited and form amyloid
 Damage to tissue
 May lead to cancer , Alzheimer’s disease ,or
other chronic inflammatory disease

45. LOOP AND TURN/BEND IN SECONDARY
STRUCTURE
 To connect adjacent strands in B pleated sheet
 Is small or long polypeptide chain
 Loop = long segment
 Turn = short segment

47. SUPER SECONDARY STRUCTURE/ MOTIFS
Simple Spatial relationship between various secondary
structures
1. B-α-B motif
2. B-hairpin motif
3. Greek key motif

49. SUPER SECONDARY STRUCTURES

51. DNA BINDING MOTIFS
 Leucine zipper motif
 Zinc finger motif
 Helix turn helix

53. TERTIARY STRUCTURE
 Definition: It refers to relation b/w AAs which are
far apart in sequence but near in three dimensional
(3D) aspect.
 Biologically active structure
 Stabilizing forces:
 Covalent bond: Disulfide bond
 Non covalent bonds: Hydrogen bond, van der
Waals force, hydrophobic interactions, ionic bond
(electrostatic bond or salt bridges).

54. DISULFIDE BOND
 Formed b/w –SH groups of
two cysteine residues.
 Stabilizes protein against
denaturation.

55. SIGNIFICANCE OF TERTIARY STRUCTURE
 Provide biological activity
 Denaturation leads to loss
of functional activity
 Domains: Compact
globular functional unit.
 It can provide
attachment to
molecule, can have
enzymatic activity or
can have functional
role.

58. ROSSMANN FOLD
 Domain seen in oxidoreductase enzyme for NAD /
NADP binding
 Examples:
 LDH
 MDH
 Alcohol DH
 G3PDH

60. QUATERNARY STRUCTURE
 Definition: It refers to relation b/w different
polypeptide chains of a protein.
 Certain polypeptide aggregate to form one
functional protein. Such protein can loose its
function if subunits are dissociated.
 Stabilizing forces: same as tertiary structure.

61.  Homomeric protein: Have identical subunits.
 E.g. LDH-5 (M4), CK-MM, CK-BB.
 Heteromeric protein: Have different subunits.
 E.g. HbA2 (α2β2), LDH-2 (H1M3), CK-MB.

62. STRUCTURAL ORGANIZATION OF PROTEIN

63. CLASSIFICATION OF PROTEINS
 Based on functions:
 Catalytic (Enzymes), Structural (Collagen),
contractile (Myosin, actin), Transport (Hb,
transferrin), Storage (Ferritin), Regulatory
(Hormones), Protective (Ig)
 Based on shape:
 Globular: Albumin, globulin, etc.
 Fibrous: Collagen, elastin, keratin, etc.

64.  Based on nutritional value
 Rich (complete/first class protien): contains all
essential AA in required proportion.
 E.g. Egg, Milk
 Incomplete: Lack one essential AA
 Pulses- deficient in Met, Cereals-def in Lys.
 Poor: lack many essential AA
 Zein of corn- lacks Trp, Lys.

65. CLASSIFICATION: BASED ON COMPOSITION
 Simple: contains only amino acids
 Albumin, Globulin, Protamines, Prolamines,
Lectins, etc.
 Conjugated: contains non-protein part (Prosthetic
group) also.
 Glycoprotein, Lipoprotein, Nucleoprotein,
Chromoprotein, Metalloprotein, Phosphoprotein,
etc.
 Derived: degradation product of native protein.
 Protein  Peptone  Peptide  amino acids

66. DENATURATION
 Loss of secondary, tertiary, quaternary structure of
protein when treated by denaturing agents
 Primary structure is not lost
 Leads to
 Unfolding of protein
 Decrease solubility
 Increase precipitation
 Easy to digest
 May be reversible or irreversible

67.  Denaturing agents:
 Physical:
 Heat, UV light, ionizing radiations
 Chemical:
 Acid , alkali
 Heavy metals , urea
 Alcohol, acetone
 Mechanical:
 Vigorous shaking
 grinding

68. SUMMARY: PRIMARY STRUCTURE

69. SUMMARY: SECONDARY STRUCTURE

70. SUMMARY: TERTIARY STRUCTURE

71. SUMMARY: QUATERNARY STRUCTURE

72. STRUCTURAL ORGANIZATION OF PROTEIN