The Protein: Presented by Dr. Shazzad Hosain Asst. Prof. EECS, NSU
The Protein: Presented by Dr. Shazzad Hosain Asst. Prof. EECS, NSU
The Protein: Presented by Dr. Shazzad Hosain Asst. Prof. EECS, NSU
Presented By
Dr. Shazzad Hosain
Asst. Prof. EECS, NSU
Proteins
Proteins do the nitty-gritty jobs of every living cell.
Exon
Intron
DNA Transcription and Translation
mRN
A
tRN
A
mRNA
Water insoluble
Very tough physically, may
be stretchy
Functions of fibrous proteins
Contractile proteins
move cilia and flagella
Globular proteins have their chains folded into
compact, rounded shapes
POLYPEPTIDES
are formed from more
than two amino acids
bonded together
Non-polar R groups make the amino acid hydrophobic
Polar R groups make the amino acid hydrophilic
Ionic R groups make the amino acid hydrophilic
Polar vs Nonpolar Amino Acids
Hydrophilic Hydrophobic
There are 20 commonly occurring amino
acids that are found in proteins
alanine - ala - A
• leucine - leu - L
arginine - arg - R ***
• lysine - lys - K
• methionine - met - M
asparagine - asn - N • phenylalanine - phe -
aspartic acid - asp - D F
cysteine - cys - C • proline - pro - P
glutamine - gln - Q • serine - ser - S
glutamic acid - glu - E • threonine - thr - T
glycine - gly - G • tryptophan - trp - W
histidine - his - H *** • tyrosine - tyr - Y
isoleucine - ile - I • valine - val - V
For example,
mis-formed hemoglobin causes sickle cell disease
Proteins have four levels
of organization
Secondary structure results from hydrogen bonding between
the oxygen of one amino acid and the hydrogen of another
Red = oxygen
Black = Carbon
Blue = Nitrogen
Green = R
The alpha helix is a coiled secondary structure
due to a hydrogen bond every fourth amino acid
The beta pleated sheet is formed by hydrogen
bonds between parallel parts of the protein
A single polypeptide may have portions with
both types of secondary structure
Proteins have four levels
of organization
Tertiary structure depends on the interactions
among the R group side chains
Types of interactions
Hydrophobic interactions: amino acids with
nonpolar side chains cluster in the core of the
protein, out of contact with water
= charged
= hydrophobic
Types of interactions
Hydrogen bonds between polar side chains
Types of interactions
Ionic bonds between positively and negatively
charged side chains
Types of interactions
Disulfide bridge (strong covalent bonds) between
sulfur atoms in the amino acid cysteine
Link to video
Keratin is a family of fibrous structural proteins
Proteins have four levels
of organization
Quaternary structure results from
interactions among separate polypeptide
chains into a larger functional cluster
For example, hemoglobin is composed of
4 polypeptide chains
Proteins have four levels
of organization
The folding of proteins is aided by other
proteins, called chaperones
Electrostatic Interactions
Interaction of charged side chain with the
opposite charged side chain.
Hydrogen Bonds & van der Waals forces
Hydrophobic interactions
The kinetic Theory of Protein Folding
Folding proceeds through a definite series of steps or a
Pathway.
A protein does not try out all possible rotations of
conformational angles, but only enough to find the
pathway.
Energy Landscape
Protein folding models
The Framework Model
Hydrophobic collapse
Nucleation Model
The Framework Model
Local interactions are main determinants of protein
structures
native state
unfolded state Transition state
Hydrophobic Collapse
Hydrophobic core forms first.
native state
collapse
unfolded state
Hydrophobic Collapse
Formation of hydrophobic globule may hinder the
reorganization of both side chains and whole protein
Nucleation Model
Unites hydrophobic collapse and frame work model
formation of
a nucleus
unfolded state native state
Nucleation Model
Substantial expulsion of water from the burial of non
polar surfaces
Good correlation between decrease in hydrodynamic
volume and increase in secondary structure
Disease caused by Protein Mis-folding
Diseases caused by the defect in protein folding:
Kuru Disease
Creutzfedlt-Jakob Disease
Scrapie Disease in sheep
Mad cow disease
A A B
B
A
B
B
A
ribosome
A B
HO
N NH2
F3C
HN
CH3 O
N N
H
H3C
serotonin prozac
Imipramine
(a classical tricyclic antidepressant)
The mapping of the human genome should
help!
In the past, many medicines (and lead compounds) were
isolated from plant sources.
Since plants did not evolve with human beings in mind, the
fact that they posses chemicals which results in effects on
humans is incidental.
Having the genetic code for the production of an
enzyme or a receptor may enable us to over-
express that protein and determine its structure and
biological function. If it is deemed important to
the disease process, inhibitors (of enzymes), or
antagonists or agonists of the receptors can be
prepared through a process called rational drug
design.
Simultaneously, Chemistry is Improving!
This is necessary, since,
ultimately, plants and natural
sources are not likely to provide
the cures to all diseases.
In a process called
“combinatorial chemistry” large
numbers of compounds can be
prepared at one time.
The efficiency of synthetic
chemical transformations is
improving.
Selectivity is Important!
In vitro testing
Has advantages in terms of speed and requires relatively small amounts
of compound
Speed may be increased to the point where it is possible to analyze
several hundred compounds in a single day (high throughput screening)
Results may not translate to living animals
Choosing the Bioassay (cont.)
In vivo tests
More expensive
May cause suffering to animals
Results may be clouded by interference with other
biological systems
Finding the Lead
O
H2N S NH2
O
sulphanilamide
(an antibacterial with the side effect of
lowering glucose levels in the blood and also
diuretic activity)
Cl N
O
O S O
O NH
NH S S
H2N O
NH O O
tolbutamide Chlorothiazide
(a compound which has been optimized to only (a compound which has been optimized to only display diuretic
lower blood glucose levels. Useful in the treatment activity.)
of Type II diabetes.)
Use structural similarity to a natural ligand
NH2 N(CH3)2
H
HO N
H3C S
O O
N N
H H
O
N
N
N
NH
O
O S
O
N
viagra
(Sildenafil)
Structure-Activity-Relationships (SAR’s)
•Body has “goal” of removing such xenobiotics from system by excretion in the
urine
•The kidney is set up to allow polar substances to escape in the urine, so the body
tries to chemically transform the drugs into more polar structures.
Metabolism of Drugs (cont.)
Phase 1 Metabolism involves the conversion of
nonpolar bonds (eg C-H bonds) to more polar bonds
(eg C-OH bonds).
A key enzyme is the cytochrome P450 system, which
catalyzes this reaction:
Glucuronic Acid
HO O
O
P O
HO O
O P O O O
NH
glucuronosyltransferase O O
Drug
O O N enzyme HO R
HO HO O
OH HO OH
HO OH
OH
OH
R OH
Drug
Metabolism of Drugs (cont.)
Another Phase II reaction is sulfation (shown below)
NH2
N
O O N
O S O P O
O N
O-
N SO3-
R OH
O-
R O
Drug
Sulfated Drug
O OH (more easily excreted)
O P O-
O-
3'-Phosphoadenosine-5'-phosphosulfate
Phase II Metabolism
From 1956 to 1962, approximately 10,000 children were born with severe
malformities, including phocomelia, because their mothers had taken
thalidomide during pregnancy. In 1962, in reaction to the tragedy, the United
States Congress enacted laws requiring tests for safety during pregnancy before
a drug can receive approval for sale in the U.S.
N O
NH
O O
Thalidomide
He found that patients with erythema nodosum leprosum, a painful skin
condition associated with leprosy, experienced relief of their pain by
taking thalidomide.