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Structural Organization
Of Proteins
By
N.Santhosh Kumar
Asst.Professor
Department of Biochemistry
SIMS & RH
• It refers to the sequence of amino acids
• Protein have unique a.a’ sequences specified by
gene.
• Stabilized by Peptide bonds (covalent bonds)
PRIMARY STRUCTURE
• Strong, high energy covalent bonds &
also part of primary structure of
protein
• Formed b/w the sulphydryl (-SH)
groups of side chain of cysteine in
the same or in different PP chains.
• Help to stabilize against denaturation
and provides additional stability
• Example: Insulin
Disulphide (-S-S-) Bond
Disulphide bond
Clinical imp of primary structure
Knowledge of the sequence of protein :
essential to elucidating its mechanism of action
A.a sequences determine the 3-dimensional
structure of proteins
Provides the link b/w the genetic message in DNA
Many genetic diseases are caused by minor
changes in amino acid sequence of proteins
Ex: Sickle cell anemia and cystic fibrosis
Secondary Structure of proteins
The PP chain is folded, twisted, turned and coiled to form various
types of 2o structures(α-helix, β- pleated sheet, β-turns)
• Spiral structure of proteins
• Stabilized by H- bonds b/w the -NH
and -CO gps of the same chains
• All the peptide bonds, except the 1st
and last in a chain participated in H-
bond
• Has a rigid arrangement of PP-chain.
• Tightly packed coiled structure with
a.a side chains, extending outward
from the central axis.
H- bonds
a-Helix
• Right handed a-Helix is more stable
 Proline & OH-proline, disrupt the helix,
and produce turns or kinks
 Provides mechanical support to the
secondary structure
Ex: α-keratin of hair & fibrion of skin
0.54 nm
0.15nm
β-Pleated sheets
H-bonds
Polypeptide chains forming the β - pleated sheets may be running
in same direction or in opposite directions
Composed of 2 or more segments of
fully extended peptide chains
produces zigzag structure resembling
a series of pleats
The surfaces of β-sheet appear like pleated
Carbonic anhydrase (both) Ex: Silk Fibroin
Ex: Flavodoxin
Examples:
- Ribonucease contains β- pleated sheet
- α helix, β-pleated sheets found in both fibrous &
globular proteins
β-Loop / β-Turn
Promotes the formation of antiparallel
β- sheets at protein surfaces
Gives a protein globularity rather than
linearity
Allows the peptide chain to reverse
direction- get a folded structure
The polypeptide chain of 4 successive
amino acid residues involved to turn
sharply to form a β-loop / β-turn.
Tertiary Structure
Three –dimensional folded compact & biologically
active conformation of a protein
Relatively independent region of
protein and functional unit
Provide specific catalytic or binding
sites in enzymes / regulatory
proteins
2o structure of peptide chain is further folded and twisted itself
forming completely folded structure of protein -domains
Phenylalanine hydroxylase enzyme : contains 3 domains,
regulatory, catalytic and protein-protein interaction domains.
Motif
• Super structure of proteins & enzyme with dissimilar functions.
• Loops of variable length & unspecified structure
Beta hairpin motif
2 antiparallel β-stands connected by a
tight turns with a.a’s
Common to all protein
Zinc finger
2 β-stands with an α-helices end folded over
to bind zinc ion
DNA binding proteins
Helix turn-helix
2 α-helices joined by a short stands of a.a’s
Gene expression of regulatory protein
Helix-loop-helix
Consists of α-helices bounded by a looping
stretch of a.a’s
Transcriptional factors
• The folding occurs due to formation of:
• Disulphide (-S-S-) Bond
• Hydrogen bonds
• Hydrophobic bonds
• Electrostatic bonds
• Van der waals forces
• It reflects the overall shape of the molecule
Eg: lysozyme, triose phosphate isomerase
oxygen storage protein -myoglobin
Hydrophobic Bonds
Occurs between the non-polar side chains of amino acids
(Val, Leu, Ile, Met, Phe)
However, this is only a physical attraction and no chemical
bonds are formed
When two hydrophobic molecules come together,
surrounding water molecules are minimal
Electrostatic / Ionic bond / Salt bridge
Occurs between two oppositely
charged polar side groups of
amino acids(e.g. Lys, Arg, His &
acidic amino acids)
Van der waals interaction
This forces are extremely week
Between two hydrophobic regions of amino acids
residues
• Consists of two or more PP chains (Subunits) that may be
structurally identified or totally unrelated
• PP chains will aggregate to form one functional protein.
• The sub-units are joined to each other by covalent bonds or by
non-covalent cross links.
• Examples of proteins having
quaternary structure are
– Creatinine Kinase (dimer)
– Lactate Dehydrogenase
(tetramer)
– Haemoglobin (tetramer)
– Immunoglobulin's (tetramer)
Next class
CA&P- 06: Structure -Functional
Relationship of proteins
C-A&P 05  Structural organization of proteins

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C-A&P 05 Structural organization of proteins

  • 1. Structural Organization Of Proteins By N.Santhosh Kumar Asst.Professor Department of Biochemistry SIMS & RH
  • 2. • It refers to the sequence of amino acids • Protein have unique a.a’ sequences specified by gene. • Stabilized by Peptide bonds (covalent bonds) PRIMARY STRUCTURE
  • 3. • Strong, high energy covalent bonds & also part of primary structure of protein • Formed b/w the sulphydryl (-SH) groups of side chain of cysteine in the same or in different PP chains. • Help to stabilize against denaturation and provides additional stability • Example: Insulin Disulphide (-S-S-) Bond Disulphide bond
  • 4. Clinical imp of primary structure Knowledge of the sequence of protein : essential to elucidating its mechanism of action A.a sequences determine the 3-dimensional structure of proteins Provides the link b/w the genetic message in DNA Many genetic diseases are caused by minor changes in amino acid sequence of proteins Ex: Sickle cell anemia and cystic fibrosis
  • 5. Secondary Structure of proteins The PP chain is folded, twisted, turned and coiled to form various types of 2o structures(α-helix, β- pleated sheet, β-turns)
  • 6. • Spiral structure of proteins • Stabilized by H- bonds b/w the -NH and -CO gps of the same chains • All the peptide bonds, except the 1st and last in a chain participated in H- bond • Has a rigid arrangement of PP-chain. • Tightly packed coiled structure with a.a side chains, extending outward from the central axis. H- bonds a-Helix
  • 7. • Right handed a-Helix is more stable  Proline & OH-proline, disrupt the helix, and produce turns or kinks  Provides mechanical support to the secondary structure Ex: α-keratin of hair & fibrion of skin 0.54 nm 0.15nm
  • 8. β-Pleated sheets H-bonds Polypeptide chains forming the β - pleated sheets may be running in same direction or in opposite directions Composed of 2 or more segments of fully extended peptide chains produces zigzag structure resembling a series of pleats
  • 9. The surfaces of β-sheet appear like pleated Carbonic anhydrase (both) Ex: Silk Fibroin Ex: Flavodoxin
  • 10. Examples: - Ribonucease contains β- pleated sheet - α helix, β-pleated sheets found in both fibrous & globular proteins
  • 11. β-Loop / β-Turn Promotes the formation of antiparallel β- sheets at protein surfaces Gives a protein globularity rather than linearity Allows the peptide chain to reverse direction- get a folded structure The polypeptide chain of 4 successive amino acid residues involved to turn sharply to form a β-loop / β-turn.
  • 12. Tertiary Structure Three –dimensional folded compact & biologically active conformation of a protein
  • 13. Relatively independent region of protein and functional unit Provide specific catalytic or binding sites in enzymes / regulatory proteins 2o structure of peptide chain is further folded and twisted itself forming completely folded structure of protein -domains Phenylalanine hydroxylase enzyme : contains 3 domains, regulatory, catalytic and protein-protein interaction domains.
  • 14. Motif • Super structure of proteins & enzyme with dissimilar functions. • Loops of variable length & unspecified structure Beta hairpin motif 2 antiparallel β-stands connected by a tight turns with a.a’s Common to all protein
  • 15. Zinc finger 2 β-stands with an α-helices end folded over to bind zinc ion DNA binding proteins Helix turn-helix 2 α-helices joined by a short stands of a.a’s Gene expression of regulatory protein Helix-loop-helix Consists of α-helices bounded by a looping stretch of a.a’s Transcriptional factors
  • 16. • The folding occurs due to formation of: • Disulphide (-S-S-) Bond • Hydrogen bonds • Hydrophobic bonds • Electrostatic bonds • Van der waals forces • It reflects the overall shape of the molecule Eg: lysozyme, triose phosphate isomerase oxygen storage protein -myoglobin
  • 17. Hydrophobic Bonds Occurs between the non-polar side chains of amino acids (Val, Leu, Ile, Met, Phe) However, this is only a physical attraction and no chemical bonds are formed When two hydrophobic molecules come together, surrounding water molecules are minimal
  • 18. Electrostatic / Ionic bond / Salt bridge Occurs between two oppositely charged polar side groups of amino acids(e.g. Lys, Arg, His & acidic amino acids)
  • 19. Van der waals interaction This forces are extremely week Between two hydrophobic regions of amino acids residues
  • 20.
  • 21. • Consists of two or more PP chains (Subunits) that may be structurally identified or totally unrelated • PP chains will aggregate to form one functional protein. • The sub-units are joined to each other by covalent bonds or by non-covalent cross links.
  • 22. • Examples of proteins having quaternary structure are – Creatinine Kinase (dimer) – Lactate Dehydrogenase (tetramer) – Haemoglobin (tetramer) – Immunoglobulin's (tetramer)
  • 23. Next class CA&P- 06: Structure -Functional Relationship of proteins