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Part I : Introduction to
Protein Structure
Mohamed Ramadan Hassan
Manager of Research & Development Laboratory
Quality Control Department

VACSERA
Overview


What are the Importance of Protein Structure ?



The Basics of Protein Structure



Levels of Protein Structure



Classification of Protein Structure
Overview


What are the Importance of Protein Structure ?



The Basics of Protein Structure



Levels of Protein Structure



Classification of Protein Structure
What are the Importance
of Protein Structure ?
In the factory of living cells, proteins are the
workers, performing a variety of biological tasks.
 Each protein has a particular 3D structure that
brings into close proximity residues that are far
apart in the amino acid sequence.
“ Structure implies Function “
Each protein adopts a particular folding pattern that
determines its function.
 During normal cells life, most newly synthesized
proteins fold spontaneously.




Sequenc

Structure

Function
Common Characters of
Proteins


Physical Characters

Hydrophobic residues tends to be buried inside the structure.
Hydrophilic residues tends to be exposed to the solvent.



Electrostatic Characters

Hydrogen bonding between +ve and –ve Charged atoms
distantly separated, e.g.; – N and – O atoms which help to
stabilize the structure.


Structural Characters
Covalent bonding between – SH groups in 2 Cysteine residues
in two different chains or in the same chain.
Anfinsen’s Thermodynamic
Hypothesis
“ The three-dimensional structure of a native
protein in its normal physiological environment
is the one in which the Gibbs free energy of the
whole system is the lowest one; that is, that the
native conformation is determined by the
totality of interatomic interactions and hence by
the amino acid sequence, in a given
environment. “
---- Anfinsen’s Nobel Lecture, 1972
Overview


Why Protein Structure ?



The Basics of Protein Structure



Levels of Protein Structure



Classification of Protein Structure
The Basics of Protein
Structure


Proteins are linear heteropolymers.



Contains one or more polypeptide chains.



Repeat units are 20 natural amino acids.



Total Number of Amino acids from few 10s - 1000s.





Proteins enormously varied in 3D shapes ( “ folds ” )
in order to perform their biological activity.
L-amino acids are the naturally occurring configuration
in living organisms.
Common Structure of L-Amino
Acid
Cα is a chiral center : i.e.;
Has 4 chemically different
groups attached to it.

Side Chain = H , CH3 , ….

R

C

-

----

---------------------

------------------

H

------------------------------------------

N

Cα

O

----

+

-------------------------

H

------------------

Backbone
--------------------------------------------------- ------------------------------Amino

Atom lost during
Peptide bond
formation

---

-------------------------------------H
Atom lost ----Carboxylate
H
During Peptide
bond formation --------------------------

O
Aliphatic residues
Hydrocarbon side chains

Alanine

Ala or A

Valine

Val or V

Leucine

Leu or L

Only heavy atoms are usually shown ( i.e.; no hydrogens atoms ).
Also, residues lacks one oxygen atom in the carboxylate group.
Aromatic
residues
Charged
residues
These contain side chains that
are
charged
under
physiological
conditions, i.e. pH 7.0: Acidic – negative charge.

 Basic – positive charge.
Polar
residues
The odd couple

Can form cisPeptide bonds
Formation of Polypeptide
Chain
Backbone torsion
angles
Overview


Why Protein Structure ?



The Basics of Protein Structure



Levels of Protein Structure



Classification of Protein Structure
Levels of Protein
Structure
Zero Structure


Amino acid composition, i.e.; percentage of each
single amino acid which can be translated to
number of each one ( no structural information ).

Primary Structure


This is simply the order of covalent linkages along
the polypeptide chain, i.e.; the sequence itself.
MHGYRTPRSKTDYGCQILETRAS
Levels of Protein
Structure

Secondary
Structure


Local organization of protein backbone:- e.g.;
α-helix, β-strand (which assemble into β-sheet),
turn and interconnecting loop.
Secondary
Structure
The α-helix




Myoglobin is the first structure
predicted (Pauling, Corey, Branson
1951) and experimentally solved
(Kendrew et. al. 1958).
It is one of the most closely packed
arrangement of residues.



Turn: 3.6 residues.



Pitch: 5.4 Å/turn.



Rise: 1.5 Å/residue.



Dipole: start +ve and end –ve.
Secondary
Structure
Properties of the α-helix




Side chains project outwards:
proline only fits the start.
Amphipathicity if solvent exposed:
hydrophilic residues in cyan;
hydrophobic residues in magenta.
Secondary
Structure
The β-sheet




Side chains project
alternately up or down.
Backbone almost fully
extended: thus one of
the most loosely packed
arrangements of residues.
Secondary
Structure
Topologies of β-sheets
Levels of Protein
Structure
Tertiary Structure




Packing of secondary structure
elements into a compact spatial
unit.
“Fold” or domain this is the level
to which structure prediction is
currently possible.
Driving forces in protein folding





Stabilization by forming hydrogen bonds.
Exposing hydrophilic residues ( charged and polar
side chains ) and burying hydrophobic residues
( aliphatic and aromatic side chains ).
For small proteins ( usually < 75 residues ).
Formation of disulfide bridges.
Interactions with metal ions.
The disulfide bond


It equals disulfide bridges.



Mostly in extracellular proteins.





Formed by oxidation of the SH
(thiol) group of cysteine
residues.
Covalent bond between the Sγ
(or ‘SG’) atoms of two
cysteine residues.
Levels of Protein
Structure
Quaternary Structure




Assembly of homo- or
heteromeric protein chains.
Usually the functional unit
of a protein, especially for
enzymes.
Overview


Why Protein Structure ?



The Basics of Protein Structure



Levels of Protein Structure



Classification of Protein Structure
Classification of Protein
Structure
All-α (helical)

All-β (sheet)
Classification of Protein Structure
α/β (parallel β-sheet)

α+β (antiparallel β-sheet)

Most popular
class
What is meant by “Domain” Structure








A domain is a compact folding unit of protein
structure, usually associated with a function.
It is usually a “fold” - in the case of monomeric
soluble proteins.
Comprises normally only one protein chain: rare
examples involving 2 chains are known.
Domains can be shared between different
proteins.
Homologous Folds






Hemoglobin and erythrocruorin: 31%
sequence identity.
Normally at least 25% sequence
identity.
Identical or closely related functions.
Analogous Folds






Hemoglobin and phycocyanin:
9% sequence identity.
Structural architechture quite
similar.
Function not conserved.
(I) Structural Comparison Facts







Proteins adopt only a limited number of folds.
Homologous sequences show
structures: variations are mainly in
regions.

very similar
non-conserved

In the absence of sequence homology, some folds
are preferred by vastly different sequences.
There are striking regularities in the way in which
secondary structures are assembled ( Levitt &
Chothia , 1976 ).
(II) Structural Comparison Facts




The “active site” (a collection of functionally critical
residues) is remarkably conserved, even when the
protein fold is different.
Structural models (especially those based on homology)
provides insights into possible function for new proteins.
Implications for that :Protein engineering.
Ligand/Drug design.
Function assignment for genomic data.
Part I : Introduction to Protein Structure

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Over the counter (OTC)- Sale, rational use.pptx
 

Part I : Introduction to Protein Structure

  • 1. Part I : Introduction to Protein Structure Mohamed Ramadan Hassan Manager of Research & Development Laboratory Quality Control Department VACSERA
  • 2. Overview  What are the Importance of Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  • 3. Overview  What are the Importance of Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  • 4. What are the Importance of Protein Structure ? In the factory of living cells, proteins are the workers, performing a variety of biological tasks.  Each protein has a particular 3D structure that brings into close proximity residues that are far apart in the amino acid sequence. “ Structure implies Function “ Each protein adopts a particular folding pattern that determines its function.  During normal cells life, most newly synthesized proteins fold spontaneously.   Sequenc Structure Function
  • 5. Common Characters of Proteins  Physical Characters Hydrophobic residues tends to be buried inside the structure. Hydrophilic residues tends to be exposed to the solvent.  Electrostatic Characters Hydrogen bonding between +ve and –ve Charged atoms distantly separated, e.g.; – N and – O atoms which help to stabilize the structure.  Structural Characters Covalent bonding between – SH groups in 2 Cysteine residues in two different chains or in the same chain.
  • 6. Anfinsen’s Thermodynamic Hypothesis “ The three-dimensional structure of a native protein in its normal physiological environment is the one in which the Gibbs free energy of the whole system is the lowest one; that is, that the native conformation is determined by the totality of interatomic interactions and hence by the amino acid sequence, in a given environment. “ ---- Anfinsen’s Nobel Lecture, 1972
  • 7. Overview  Why Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  • 8. The Basics of Protein Structure  Proteins are linear heteropolymers.  Contains one or more polypeptide chains.  Repeat units are 20 natural amino acids.  Total Number of Amino acids from few 10s - 1000s.   Proteins enormously varied in 3D shapes ( “ folds ” ) in order to perform their biological activity. L-amino acids are the naturally occurring configuration in living organisms.
  • 9. Common Structure of L-Amino Acid Cα is a chiral center : i.e.; Has 4 chemically different groups attached to it. Side Chain = H , CH3 , …. R C - ---- --------------------- ------------------ H ------------------------------------------ N Cα O ---- + ------------------------- H ------------------ Backbone --------------------------------------------------- ------------------------------Amino Atom lost during Peptide bond formation --- -------------------------------------H Atom lost ----Carboxylate H During Peptide bond formation -------------------------- O
  • 10. Aliphatic residues Hydrocarbon side chains Alanine Ala or A Valine Val or V Leucine Leu or L Only heavy atoms are usually shown ( i.e.; no hydrogens atoms ). Also, residues lacks one oxygen atom in the carboxylate group.
  • 12. Charged residues These contain side chains that are charged under physiological conditions, i.e. pH 7.0: Acidic – negative charge.  Basic – positive charge.
  • 14. The odd couple Can form cisPeptide bonds
  • 17. Overview  Why Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  • 18. Levels of Protein Structure Zero Structure  Amino acid composition, i.e.; percentage of each single amino acid which can be translated to number of each one ( no structural information ). Primary Structure  This is simply the order of covalent linkages along the polypeptide chain, i.e.; the sequence itself. MHGYRTPRSKTDYGCQILETRAS
  • 19. Levels of Protein Structure Secondary Structure  Local organization of protein backbone:- e.g.; α-helix, β-strand (which assemble into β-sheet), turn and interconnecting loop.
  • 20. Secondary Structure The α-helix   Myoglobin is the first structure predicted (Pauling, Corey, Branson 1951) and experimentally solved (Kendrew et. al. 1958). It is one of the most closely packed arrangement of residues.  Turn: 3.6 residues.  Pitch: 5.4 Å/turn.  Rise: 1.5 Å/residue.  Dipole: start +ve and end –ve.
  • 21. Secondary Structure Properties of the α-helix   Side chains project outwards: proline only fits the start. Amphipathicity if solvent exposed: hydrophilic residues in cyan; hydrophobic residues in magenta.
  • 22. Secondary Structure The β-sheet   Side chains project alternately up or down. Backbone almost fully extended: thus one of the most loosely packed arrangements of residues.
  • 24. Levels of Protein Structure Tertiary Structure   Packing of secondary structure elements into a compact spatial unit. “Fold” or domain this is the level to which structure prediction is currently possible.
  • 25. Driving forces in protein folding    Stabilization by forming hydrogen bonds. Exposing hydrophilic residues ( charged and polar side chains ) and burying hydrophobic residues ( aliphatic and aromatic side chains ). For small proteins ( usually < 75 residues ). Formation of disulfide bridges. Interactions with metal ions.
  • 26. The disulfide bond  It equals disulfide bridges.  Mostly in extracellular proteins.   Formed by oxidation of the SH (thiol) group of cysteine residues. Covalent bond between the Sγ (or ‘SG’) atoms of two cysteine residues.
  • 27. Levels of Protein Structure Quaternary Structure   Assembly of homo- or heteromeric protein chains. Usually the functional unit of a protein, especially for enzymes.
  • 28. Overview  Why Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  • 29. Classification of Protein Structure All-α (helical) All-β (sheet)
  • 30. Classification of Protein Structure α/β (parallel β-sheet) α+β (antiparallel β-sheet) Most popular class
  • 31. What is meant by “Domain” Structure     A domain is a compact folding unit of protein structure, usually associated with a function. It is usually a “fold” - in the case of monomeric soluble proteins. Comprises normally only one protein chain: rare examples involving 2 chains are known. Domains can be shared between different proteins.
  • 32. Homologous Folds    Hemoglobin and erythrocruorin: 31% sequence identity. Normally at least 25% sequence identity. Identical or closely related functions.
  • 33. Analogous Folds    Hemoglobin and phycocyanin: 9% sequence identity. Structural architechture quite similar. Function not conserved.
  • 34. (I) Structural Comparison Facts     Proteins adopt only a limited number of folds. Homologous sequences show structures: variations are mainly in regions. very similar non-conserved In the absence of sequence homology, some folds are preferred by vastly different sequences. There are striking regularities in the way in which secondary structures are assembled ( Levitt & Chothia , 1976 ).
  • 35. (II) Structural Comparison Facts   The “active site” (a collection of functionally critical residues) is remarkably conserved, even when the protein fold is different. Structural models (especially those based on homology) provides insights into possible function for new proteins. Implications for that :Protein engineering. Ligand/Drug design. Function assignment for genomic data.