Unit 3

# Physical interaction that determine the property of proteins

 Molecular interactions are attractive or repulsive forces between molecules and non-bonded
atoms.
 Molecular interactions are also known as non-covalent interactions or intermolecular
interactions.
 A molecule is a set of atoms that associates associate tightly with covalent bond and it does
not dissociate or lose its structure, when it interacts with its environment.
 Covalent bonds remain intact, when proteins unfold. The process of unfolding are not
chemical reactions (no covalent bonds break or form) and involve only changes in molecular
interactions.
 Therefore, molecular interactions are important in protein folding and drug design. When
proteins fold into 3D globular structures, they are called in native states.
 The proteins native state and their assemblies are stabilized by several molecular interactions
viz. electrostatic forces, Van der Waal interactions, hydrogen bonds and hydrophobic
interactions.
 In biological systems, proteins assemble with DNA, RNA, membranes and with other
proteins to perform specific function

# Short range interaction

Short range interactions are interactions that occur when two atoms or molecules are close to each
other, at distances comparable to the size of the interacting atoms. Short range interactions can be of
following nature: ionic, covalent, metallic, or dipolar origin. Ionic, covalent, metallic and hydrogen
bonds are so-called atomic forces that are important for forming strongly bonded condensed matter.
These short-range forces arise from the overlap of electron wave functions. Interactions of dipolar
nature are classified further into strong hydrogen bonds and weak Van der Waals (VdW) interactions.
They arise from dipole-dipole interactions. Both hydrogen and VdW interactions can be responsible
for cooperation and structuring in fluidic systems, but are also strong enough to build up condensed
phases. Following is a description of these short-range forces:

A. Ionic Bonds: These are simple Coulombic forces, which are a result of electron transfer. For
example, in lithium fluoride, lithium transfers its 2s electron to the fluorine 2p state. Consequently,
the shells of the atoms are filled up, but the lithium has a net positive charge and the Fluorine has a
net negative charge. These ions attract each other by Coulombic interaction which stabilizes the ionic
crystal in the rock-salt structure.

B. Covalent Bond: The standard example for a covalent bond is the hydrogen molecule. When the
wave-function overlap is considerable, the electrons of the hydrogen atoms will be indistinguishable.
The total energy will be decreased by the “exchange energy”, which causes the attractive force. The
characteristic property of covalent bonds is a concentration of the electron charge density between
two nuclei. The force is strongly directed and falls off within a few Angstroms.

C. Metallic Bonds and Interaction: The strong metallic bonds are only observed when the atoms are
condensed in a crystal. They originate from the free valence electron sea which holds together the
ionic core. A similar effect is observed when two metallic surfaces approach each other. The electron
clouds have the tendency to spread out in order to minimize the surface energy. Thus, a strong
exponentially decreasing, attractive interaction is observed.
D. Dipole Interactions:

D.1. Hydrogen Bond Interaction: Strong type of directional dipole-dipole interaction

D.2. Van der Waals Interaction: The relevance of VdW interactions goes beyond of building up matter
(e.g., Van der Waals organic crystals (Naphthalene)). Because of their “medium” range interaction
length of a few Angstroms to hundreds of Angstroms, VdW forces are significant in fluidic systems
(e.g, colloidal fluids), and for adhesion between microscopic bodies. VdW forces can be divided into
three groups: o Dipole-dipole force: Molecules having permanent dipoles will interact by dipole-
dipole interaction. o Dipole-induced dipole forces: The field of a permanent dipole induces a dipole
in a non-polar atom or molecule. o Dispersion force: Due to charge fluctuations of the atoms there is
an instantaneous displacement of the centre of positive charge against the centre of the negative
charge. Thus, at a certain moment, a dipole exists and induces a dipole in another atom. Therefore,
non-polar atoms (e.g. neon) or molecules attract each other.

# Electrostatic forces

 The electrostatic force is the force of attraction or repulsion between two charged particles.
It is also called Coulomb’s force or Coulomb’s interaction.
 For example, the force between the protons and electrons in an atom is electrostatic and is
responsible for the atom’s stability.
 Electrostatic force is one of the fundamental forces in the universe. There, are four
fundamental forces in the universe.
 They are strong nuclear force, electromagnetic force, weak nuclear force and gravitational
force.
 The electrostatic force comes under electromagnetic force. The electrostatic force exists
between two charges placed at a distance.
 The magnitude of electrostatic force depends on the magnitude of each charge and the
distance between them.
 When two positive charges or two negative charges are brought together, then the two
charges repel each other.
 The electrostatic force acting between two like charges is called electrostatic force of
repulsion.
 When two opposite charges are brought together, then two charges get attracted towards
each other.
 Then the electrostatic force acting between two opposite charges is called electrostatic force
of repulsion.
 Therefore, we can say that like charges repel and unlike charges attract. The electrostatic
force acting between two charges is greater when the magnitude of two charges is larger.
The electrostatic force is larger when the distance between the two charges is less.

The electrostatic force between two charged particles can be quantified by Coulomb’s law. It is
usually applied to point charges and gives a relationship between the electrostatic force, the
magnitude of the charges, and separation distance. According to this law, the force between the two
particles is,
 Directly proportional to the product of the magnitude of the charges
 Inversely proportional to the square of the distance between the two charges
Suppose the two charged particles are brought close to one another. There will be an attraction if the
charges are opposite, or if one is positive and the other negative. On the contrary, the charges will
repel if both of them are positive or negative. In other words, like charges repel and unlike charges
attract. Let us assume that q1 and q2 are the amounts of charges on the two particles separated by a
distance r. According to Coulomb’s law, the electrostatic force between the two charges is given by
the following equation.

F = Kq1q2/r2

Electrostatic force unit: N (Newton).

Here, k is called Coulomb’s constant. Its value is 9 x 109 N.m2.C-2. Generally, q1 and q2 can be positive
or negative. When two opposite point charges are placed close to each other, the force is attractive
and hence, its sign is negative. The magnitude is merely the value of F without the sign. According to
the above equation, F vanishes when r → ∞. Hence, at an infinitely large distance, the electrostatic
force is zero. Technically, the range of F is infinite.
The work done W by the force F on a particle is the product of the force and the displacement d.
W= F x d
The work done in displacing the particle from one position to another is independent of the path
taken. Hence, the electrostatic force is conservative.

Properties of Electrostatic force

 Like charges repel, and opposite charges attract

 Directly proportional to the product of two point-charges
 Inversely proportional to the distance of separation between the charges
 Acts along the line joining the two charges
Examples of Electrostatic force

 Rubbing of clouds generate charges. These charges will neutralize by passing through the
atmosphere until they reach the neutral ground. We perceive this as lightning.
 After combing, if we bring the comb close to a piece of paper, there is a force of attraction
between them.
# Vander wall interaction
Van der Waals forces, also known as van der Waals bonds or van der Waals interaction, are weak

intermolecular interactions observed in condensed phases like solid and liquid. They are responsible for the

bulk properties of substances, like the boiling and melting points. Van der Waals bonds are secondary

bonds in molecules where ionic and covalent bonds form the primary bonds. Van der Waals forces occur
due to the fluctuations in the charge density of particles. As a result, an atom or molecule is polarized with

positive charges at one and negative charges at the other end. The polarization gives rise to electrostatic

forces between the two atoms or molecules. These weak forces are responsible for holdings the atoms or

molecules together. Van der Waals forces disappear as the distances between the atoms or molecules

increase. Van der Waals radius is the radius of an imaginary sphere surrounding an atom. It represents the

distance of the closest approach for another atom. In other words, van der Waals radius is one half of the

distance of separation between the centre of the two approaching nuclei. It is a parameter that determines

whether the atoms or molecules will hold together in a solid or liquid.

Properties of Vander wall forces
 Additive, i.e., several intermolecular interactive forces add together to form a quantifiable force.
 Non-directional, i.e., they can attract atoms or molecules from all direction. Weaker than ionic and
covalent chemical bonds.
 Act only over a short range. The interaction is significant when molecules are positioned closer.
 Independent of temperature, except dipole-dipole interactions.

Types of Vander wall forces

1) London dispersion forces

London dispersion forces are intermolecular forces that occur between two atoms or two nonpolar
molecules due to the motion of electrons. An atom consists of a nucleus and electrons that move in orbits.
At any time, the electrons can cluster around one part of the atom. As a result, the atom becomes
negatively charged at one end and positively charged at the other end, resulting in an instantaneous dipole.
This weak and temporary dipole then influences neighboring atoms through electrostatic attraction and
repulsion, thereby inducing dipoles. The induced dipoles are feebly attracted to one another. The strength
of dispersion forces increases as the number of electrons in the atoms or nonpolar molecules increases.

2) Dipole-Dipole interaction

The dipole-dipole interactions or dipole-dipole forces arise because of the electric polarization induced
particles due to the presence of other particles. They are similar to London Dispersion forces, but they
occur in molecules that have a permanent dipole. Here, the negative end of a polar molecule attracts the
positive end of another polar molecule. This attraction between these two molecules is known as the
dipole-dipole force.

Hydrogen bonding is a particular type of dipole-dipole interaction.

Examples: Water (H2O) and hydrogen chloride (HCl)
Factors affecting Vander wall forces
1) Number of electrons held by the atoms or molecules
The strength of van der Waals forces depends primarily on the number of electrons in the atom or
molecule. So, larger atoms and molecules will have greater forces.
2) Shape of the molecule
For isoelectronic molecules, i.e., isomers with the same number of electrons, the factor that determines the
strength of the van der Waals force is the shape of the molecule and the area of surface contact. If the
isomer is branched, then the molecules are closely packed. In this case, the van der Waals forces will be
weak.
# Hydrogen bonds
A hydrogen bond is an attractive force between the hydrogen atom of one molecule bound and
more electronegative atoms of the same molecule or other molecules.
 The hydrogen bond is weaker than a covalent bond, and thus, the bond length is longer. The
hydrogen bond is denoted by a dotted line (…).
 Electronegative atoms generally involved in hydrogen bonding are fluorine, nitrogen, and
oxygen. Hydrogen bonds with sulfur, chlorine, and carbon are also observed, but these
bonds tend to be weaker.
 The hydrogen bond is a type of polar covalent bond where the pair of electrons is unequally
distributed between hydrogen and another atom resulting in small charges on both atoms.
 It has been debated that the bond has some ionic contributions due to the formation of
partially charged ions.
 Even though hydrogen bond is an electrostatic dipole-dipole interaction, the bonding is
achieved in order to achieve a stable electronic configuration in both atoms.
 Hydrogen bonding is an essential interaction as it provides different properties to the
compounds formed. Besides, as a hydrogen bond can exist between two molecules, it is
involved in the structure and function of the compounds formed.
 It is considered a weaker bond than an ionic bond and covalent bond, but it is stronger than
Van der Waal’s force.
 Hydrogen bonding exists in both organic and inorganic compounds, but the hydrogen
bonding in organic compounds occurs only when the carbon atoms are bound to a more
electronegative atom.
Hydrogen bond properties
1) Boiling and Melting point
 Hydrogen bonds affect the boiling and melting point of compounds as the greater hydrogen
bond results in increased intermolecular attraction.
 As a result, a large amount of heat energy is required to break down the forces and result in
melting or boiling.
 In a compound, intermolecular hydrogen bonding causes molecules to exist in associated
molecules.
 The association increases the size and molecular mass of the compound resulting in
increased Van der Waal’s force.
 Thus, compounds having more hydrogen bonds have a higher boiling and melting point.

2) Density and Surface tension

 Hydrogen bonding also affects other physical parameters like density, surface tension, and
even viscosity.
  The compounds have greater associations or linkages between molecules, which results in
increased density of the compounds.
 The surface tension also increased as the molecules on the surface are bound to one
another via these bonds.
3) Physical state
 Compounds with hydrogen bonds exist either in the liquid or gaseous state. Compounds
with stronger bonds exist in the liquid state whereas those with weaker hydrogen bonds
exist in the gaseous state.
 The strength of the bond depends on the electronegativity of the atom bound to hydrogen.
In H2O, hydrogen bonds are stronger due to the higher electronegativity of oxygen
whereas those in H2S are weaker as sulphur is less electronegative than oxygen.
4) Molecular association
 Compounds with hydrogen bonds form aggregates as a result of a weak association between
molecules.
 The formation of dimers and trimers in different compounds occurs due to hydrogen
bonding.
5) Solubility
 Hydrogen bonding is responsible for the solubility of different compounds as it is involved in
the hydration of anions in aqueous solutions.
 The hydration contributes to the solvent property of the compounds and helps dissolve
different ionic compounds.
Types of Hydrogen bonds
1) Intramolecular hydrogen bonds
 The intramolecular hydrogen bond is the hydrogen bond formed between the hydrogen
atoms and electronegative atoms like nitrogen, oxygen, and sulfur within the same
molecule.
 For the formation of an intramolecular hydrogen bond, hydrogen and an electronegative
atom should be present in molecules within close proximity.
 In some molecules like ethylene glycol, even though the atoms are present far apart, the
molecule geometry of the compounds enables them to indulge in hydrogen bonding.
 Intramolecular hydrogen bonding in a molecule has a pronounced effect on the molecular
structure and properties of the compounds.
 The bonding doesn’t, however, have a pronounced effect on the physical properties of the
compound overall.
2) Intermolecular hydrogen bonds
 Intermolecular hydrogen bonding is a type of hydrogen bonding that exists between two
distinct molecules either of the same compound or different compounds.
 This type of bonding can occur between any number of same or different molecules as long
as hydrogen, and electronegative atoms are present.
 Like intramolecular hydrogen bonding, intermolecular hydrogen bonding also occurs when
the two molecules are in close proximity to one another.
 Intermolecular hydrogen results in different properties of the compounds like increased
surface tension and viscosity. These changes are often drastic.
Application
 Different organic and inorganic compounds containing hydrogen bonds have different
applications in different areas.
  Hydrogen bonding is essential for the structure and function of nucleic acids like DNA and
RNA. In both RNA and DNA, the base pairing is stabilized by different numbers of hydrogen
bonds.
 Different structures of proteins are stabilized by hydrogen bonds either within the protein
molecule or with external molecules.
 Hydrogen bonding in water is responsible for different properties of water like high boiling
point, surface tension, and solvent nature.
 Hydrogen bonds have an essential role in drug discovery as most oral drugs have about 8-10
hydrogen bonds.
# Hydrophobic Interactions
 Hydrophobic interactions describe the relations between water and hydrophobes (low
water-soluble molecules).
 Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not
interact with water molecules. The mixing of fat and water is a good example of this
particular interaction.
 The common misconception is that water and fat doesn’t mix because the Van der Waals
forces that are acting upon both water and fat molecules are too weak. However, this is not
the case.
 The behaviour of a fat droplet in water has more to do with the enthalpy and entropy of the
reaction than its intermolecular forces.
 American chemist Walter Kauzmann discovered that nonpolar substances like fat molecules
tend to clump up together rather than distributing itself in a water medium, because this
allows the fat molecules to have minimal contact with water.
When a hydrophobe is dropped in an aqueous medium, hydrogen bonds between water molecules
will be broken to make room for the hydrophobe; however, water molecules do not react with
hydrophobe. This is considered an endothermic reaction, because when bonds are broken heat is
put into the system. Water molecules that are distorted by the presence of the hydrophobe will
make new hydrogen bonds and form an ice-like cage structure called a clathrate cage around the
hydrophobe. This orientation makes the system (hydrophobe) more structured with an decrease of
the total entropy of the system; therefore ΔS<0.

The change in enthalpy (ΔH) of the system can be negative, zero, or positive because the new
hydrogen bonds can partially, completely, or over compensate for the hydrogen bonds broken by
the entrance of the hydrophobe. The change in enthalpy, however, is insignificant in determining the
spontaneity of the reaction (mixing of hydrophobic molecules and water) because the change in
entropy (ΔS) is large.

According to the Gibbs Energy formula

ΔG=ΔH−TΔS ------- (1)

with a small unknown value of ΔH and a large negative value of ΔS, the value of ΔG will turn out to
be positive. A positive ΔG indicates that the mixing of the hydrophobe and water molecules is not
spontaneous.

Factors

Hydrophobic interactions are relatively stronger than other weak intermolecular forces (i.e., Van der
Waals interactions or Hydrogen bonds). The strength of Hydrophobic Interactions depends on
several factors including (in order of strength of influence):
 1. Temperature: As temperature increases, the strength of hydrophobic interactions increases
also. However, at an extreme temperature, hydrophobic interactions will denature.
2. Number of carbons on the hydrophobes: Molecules with the greatest number of carbons
will have the strongest hydrophobic interactions.
3. The shape of the hydrophobes: Aliphatic organic molecules have stronger interactions than
aromatic compounds. Branches on a carbon chain will reduce the hydrophobic effect of that
molecule and linear carbon chain can produce the largest hydrophobic interaction. This is so
because carbon branches produce steric hindrance, so it is harder for two hydrophobes to
have very close interactions with each other to minimize their contact to water.
Hydrophobic Interactions are important for the folding of proteins. This is important in keeping a
protein stable and biologically active, because it allows to the protein to decrease in surface are and
reduce the undesirable interactions with water. Besides from proteins, there are many other
biological substances that rely on hydrophobic interactions for its survival and functions, like the
phospholipid bilayer membranes in every cell of your body!
# Sedimentation analysis
Sedimentation is a natural or engineered process. In this process, solid particles are suspended in a
fluid, mostly water. These particles settle under the effect of gravity. Sedimentation is used in
various fields, such as water treatment and geology. In this process, gravity acts on particles, due to
which they sink to the bottom, and form a sediment layer. The process is affected by many factors. It
can be particle size, shape and many more. Sedimentation is important for the separation of solids
from liquids, water clarification and in various industrial and environmental processes.
Principle
Sedimentation is based on the principle that denser particles settle faster than lighter ones when
subjected to gravity. Particles are pulled downward due to the force of gravity. Factors like particle
size, shape, and fluid viscosity influence their settling speed.
Process of Sedimentation

The process of sedimentation is a natural phenomenon powered by gravity. In this process, solid
particles are suspended in a fluid, settling down over time.

 Initiation of Sedimentation

This process begins when water holds suspended particles. These particles can vary in size, density,
and composition. Gravitational force influences the sedimentation acting on the particles. The
viscosity of the fluid also influences Sedimentation.

 Forces at Play

Gravity is the primary force controlling sedimentation. The denser the particles, the faster they will
settle. Particles are pulled downward due to the force of gravity, which causes them to move
through the fluid until they encounter resistance.

 Particle Characteristics

The rate of sedimentation is affected by the size and shape of particles. Larger and denser particles
settle more rapidly than smaller and lighter ones.

 Enhancement of Sedimentation
Sedimentation can be enhanced in various applications to speed up the settling process. Coagulants
and flocculants are added to the fluid for the promotion of the aggregation of particles. These
chemicals neutralise charges on particle surfaces.

 Containers for Sedimentation

Sedimentation commonly takes place in containers known as sedimentation tanks, clarifiers, or

settling basins. These tanks come in different designs, such as rectangular, circular, or up-flow
configurations, depending on the specific needs of the application. The choice of tank design is
influenced by factors like available space, required capacity, and the characteristics of the particles
being removed.

 Separation of Phases

A layer known as sediment or sludge is formed at the bottom of the tank. The clear liquid remaining
above, known as supernatant, is separated from the settled particles. This clarified liquid can be
further processed or distributed depending on the intended use.

Functions

1) A sedimentation ranks allows suspended particles to settle out of water or wastewater as it flows
slowly through the tank, thereby providing some degree of purification.

2) A layer of accumulated solids, called sludge, forms at the bottom of the tank and is periodically
removed.

Advantage

1) Sedimentation reduces the need for chemicals used in coagulation and flocculation.

2) Sedimentation can make subsequent water treatment processes easier.

3) Sedimentation is less expensive than some other eater treatment methods.

4) Sedimentation can be used as a simple pre-treatment step before other purification methods like
filtration and disinfection.
5) Sedimentation tanks can effectively separate fine particles from water.
6) Sedimentation tanks can be modified to improve sediment removal.
Disadvantage
1) Sedimentation methods have a smaller size range and fewer size classes than other techniques,
such as laser diffraction.
2) Sedimentation analysis assumes that all particles are homogeneous in density and sphericity.
3) Sedimentation analysis can take 20-60 mins, which is longer than other methods.
4) Sedimentation can’t be used for emulsions because the material doesn’t settle.

6) Sedimentation analysis can’t be used for mixtures with different densities.

7) Sedimentation analysis depend on ambient temperatures which affect viscosity.

# Edman degradation
  Edman Degradation is a chemical method used to sequence amino acids in peptides and
proteins by selectively removing the N-terminal residue while preserving the overall
structure.
 Edman degradation stands as a pivotal milestone in the field of biochemistry, offering a
revolutionary method for sequencing amino acids in peptides and proteins. The technique
was ingeniously developed by the Swedish biochemist, Pehr Edman, in the early 1950s.
 Edman’s breakthrough brought about a deeper understanding of the molecular composition
of proteins, enabling scientists to unravel the intricate structures that govern life’s essential
processes.
 At, its core, Edman degradation is employed to label or purify proteins by selectively
removing the N-terminal residue of peptides, all while preserving the overall structure of the
protein intact.
 This chemical procedure finds its application in sequencing short peptides consisting of
approximately 50 to 60 residues. Notable examples of peptides that have undergone Edman
degradation include alpha and beta melanotropin, lysine, arginine vasopressors, and
oxytocin.
 The Edman degradation technique functions by selectively targeting the amino-terminal
residue of a peptide. Through a series of chemical reactions, the targeted residue is labelled
and then cleaved from the peptide, leaving the rest of the peptide unaffected. This stepwise
removal of amino acids allows scientists to discern the precise sequence of amino acids
within the peptide chain.
Steps:
1) Coupling: The initial step of Edman degradation involves the coupling of the peptide’s alpha-
amino group with Phenyl isothiocyanate (PITC) under basic conditions. During this reaction, a phenyl
thiocarbamoyl derivative (PTC-peptide) is formed. This coupling sets the stage for the subsequent
steps, providing a means to selectively label and detach the N-terminal amino acid from the peptide
chain while leaving the rest of the structure unharmed.
2) Cyclization: Following the coupling step, the resultant product undergoes a cyclization process,
leading to the formation of 2-anilino-thiazo-linon (ATZ amino acid). This cyclization is a critical
intermediate step that prepares the peptide for further degradation cycles. The rest of the peptide
remains intact, ready for the next round of Edman degradation.
3) Conversion: In this step, the ATZ-amino acid is converted into either PTC (phenylthiocarbamate)
or PTH (phenylthiohydantoin) amino acid, depending on the conditions employed. However, it is
essential to note that the final product of this conversion step is typically PTH amino acid since it is
more stable than the PTC counterpart. The conversion ensures that the N-terminal residue is
transformed into a stable derivative, facilitating accurate sequencing of the peptide chain.
Limitation:
1) N-Terminal Modifications: Edman degradation relies on the specific reaction of Phenyl
isothiocyanate (PITC) with the N-terminal amino group of a peptide. Therefore, if the N-terminus of
a protein has undergone chemical modifications, such as acetylation or the formation of
pyroglutamic acid, the Edman degradation process may be hindered. The modified N-terminal
residue may not effectively react with PITC, leading to inaccurate or incomplete sequencing results.
2) Non-α-Amino Acids: The Edman degradation process is designed to proceed smoothly with α-
amino acids. However, when a non-α-amino acid, such as isoaspartic acid, is encountered, the
reaction pathway is disrupted. The formation of the favored five-membered ring intermediate,
which is crucial for the cyclization step, becomes unattainable. Consequently, sequencing will be
halted, and the amino acid sequence beyond the non-α-amino acid will remain unexplored.
3) Disulfide Bridge Identification: Edman degradation is generally not well-suited for determining
the positions of disulfide bridges in proteins. The presence of disulfide bonds complicates the
sequencing process as they introduce additional constraints and challenges in the degradation
reactions. Alternative methods, such as mass spectrometry and chemical cleavage, are often
employed to address this limitation.
4) Sample Requirements: To achieve discernible results, Edman degradation typically requires
peptide amounts of at least 1 picomole. This quantity threshold can pose challenges when analyzing
low-abundance proteins or when dealing with limited sample availability.
5) Blocked N-Terminal Amino Acids: Proteins that possess blocked N-terminal amino acids cannot
be successfully sequenced using Edman degradation. If the N-terminal amino group is blocked, it will
not react with PITC, preventing the coupling step from taking place.
6) Interference from Impurities: Edman degradation relies on a series of precise chemical reactions.
However, when impurities, such as amine-containing chemicals, are present in the sample, they may
interfere with the reaction, leading to compromised results.
7) Blank Cycles: Certain amino acid residues, such as unmodified cysteine (cys) and glycosylated
residues, may give blank cycles, contributing to uncertainties or difficulties in the interpretation of
sequencing data.
Uses:
1) Amino Acid Sequencing: The primary and most significant use of Edman degradation is in the
sequencing of amino acids within peptides and proteins. By selectively cleaving and identifying the
N-terminal residue in each cycle, researchers can determine the precise order of amino acids in the
polypeptide chain. This ability to unveil the amino acid sequence plays a pivotal role in
understanding the structure and function of proteins, advancing fields like biochemistry, molecular
biology, and biotechnology.
2) Sample Simplicity: One of the notable advantages of Edman degradation is that it eliminates the
need for extensive pre-treatment of the sample protein. Unlike certain other sequencing techniques,
which require complex and time-consuming preparations, Edman degradation can be performed
directly on the sample, saving valuable time and effort.
3) Distinguishing Isobaric Amino Acids: Edman degradation can effectively distinguish between
isobaric amino acids, such as leucine and isoleucine, which have the same molecular formula but
different arrangements of atoms. This capability is crucial in resolving potential ambiguities in the
amino acid sequence, ensuring accurate and unambiguous results.
4) Identifying Uncharacterized Proteins: Edman degradation holds the unique ability to identify
proteins that may not even be present in existing databases. This advantage proves valuable in
studying newly discovered proteins or those with limited prior characterization. The ability to
analyse such proteins enables researchers to uncover novel functions and connections in various
biological processes.
5) Accuracy and Effectiveness: Edman sequencers are renowned for their accuracy and efficiency in
amino acid sequencing. The automated and controlled nature of the process ensures reliable and
reproducible results, making Edman degradation a preferred choice in many protein analysis
applications.
6) Non-Destructive Reaction: Edman degradation is a non-destructive reaction with minimal
interference on other amino acids present in the peptide or protein chain. This characteristic allows
researchers to retain the integrity of the remaining peptide, enabling further analyses or
experiments with the sequenced proteins.