This document provides an overview of protein structure, including levels of structure and classification. It discusses the importance of protein structure in determining function. The primary levels of structure are defined as primary (amino acid sequence), secondary (local folding patterns like alpha helices and beta sheets), tertiary (packing of secondary structures), and quaternary (assembly of protein chains). Protein structures can be classified based on their secondary structure composition as all-alpha, all-beta, alpha/beta, or alpha+beta. Domains are compact folding units associated with function.

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.

11. Aromatic
residues

12. Charged
residues
These contain side chains that
are
charged
under
physiological
conditions, i.e. pH 7.0: Acidic – negative charge.
 Basic – positive charge.

13. Polar
residues

14. The odd couple
Can form cisPeptide bonds

15. Formation of Polypeptide
Chain

16. Backbone torsion
angles

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.

23. Secondary
Structure
Topologies of β-sheets

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.