DEFINITION:

Discipline that deals with studying the

INTERACTOME i.e. the interactions (and their
consequences) between & among molecules
within a cell, generally proteins.
More…
It is an example of "top-down" systems
biology. Large sets of genome-wide data are
collected, & correlations between different
molecules are inferred. From the data new
hypotheses are formulated, & tested by new
experiments, & generalizations are made for
comparable molecules.
Contd…
The field of interactomics is rapidly expanding
and developing. While no biological
interactomes have been fully characterized,
over 90% of proteins in Saccharomyces
cerevisiae have been screened & their
interactions characterized, making it the first
interactome to be nearly fully specified.
SIGNIFICANCE:
Most biomolecules interact with other
molecules. These interfaces (►Interfaceome)
are highly conserved throughout evolution to
avoid undesirable interactions that lead to fatal
disorders in cells (►Misinteraction Disease
theory).
De novo METHODS:
►Yeast two-hybrid system
► Tandem Affinity Purification
► Co-immunoprecipitation
► Fluorescent Resonance Energy Transfer
(FRET)
► Surface Plasmon Resonance (SPR)
► X-ray tomography, Optical fluorescence
microscopy, etc.
Yeast Two-hybrid system:
X Y

Protein X expressed as a fusion Protein Y expressed as a fusion

with DNA-binding domain with Transcriptional Activator

RNA
X Y Pol

Interaction results in activation of the gene

Tandem Affinity Purification :
Immunoglobulin/ Calmodulin
Affinity Column

Protein A CBP Protein X NH2

Protein Y
Co-immunoprecipitation :
Interaction between two proteins is indicated if the
immunoprecipitation of one protein results in the co-
precipitation of the other.
Fluorescent Resonance Energy
Transfer (FRET):
Interaction between two proteins is indicated where
energy is transferred from an excited donor
fluorophore to a nearby acceptor fluorophore. FRET
occurs only when the two fluorophores are up to 10
nm apart.
Surface Plasmon Resonance :
Interaction between protein X (immobilized on metal
surface) and protein Y (free in solution) is
demonstrated by a change in the refractive index of
the surface layer. SPR has been used for detecting
interactions on protein chips.
In silico METHODS:
►Protein Structural Interactome Map
(PSIMAP) Algorithm

►Accessible Surface Area (ASA) Method

►Voronoi Diagram

►Domain Fusion (Rosetta stone)

PSIMAP Algorithm :
The Protein Structural Interactome Map, is a
database of all the structurally observed interactions
among protein domains of known three-dimensional
structures in the PDB. It can be constructed using any
reliable protein domain definition, where domains are
defined as evolutionarily conserved structural and
functional protein units.

Contd…
PSIMAP Algorithm :
Most commonly used domain definitions used include
SCOP(Structural classification of Proteins), Pfam
(Protein families), CATH, FSSP, etc.
PSIMAP provides an overview of all the observed
domain-domain interactions at the protein family or
superfamily level. Domains from a multi-domain PDB
entry are empirically denoted as interacting with each
other if at least 5 residue pairs are within a 5
Angstrom distance.
Accessible Surface Area Method :
The ASA method detects protein regions that are
buried to be excluded from a solvent when forming a
multimer or a complex. If more than two subunits
interact or aggregate with each other, they lose some
area that could be accessible by a solvent in the state
of free subunit or domain.

Contd…
Accessible Surface Area Method :
Relative accessibilities are calculated for each amino
acid in the protein by expressing the summed residue
accessible surface as a percentage of that observed
in an ALA-X-ALA tri-peptide. Surface residues are
defined as those residues that have a relative ASA of
more than 5%. Interior residues are defined as those
residues that have a relative ASA of less than 5%.
Voronoi Diagram:
The Voronoi diagram, known as Dirichlet tessellation,
has been widely used in the fields of science and
engineering. The Voronoi diagram was first
introduced as an application to the study of protein
structure by Richards et al.

Contd…
Light blue circles (atoms) are
contained in domain A and
green atoms are in domain B.
Dotted lines denote Voronoi
edges and a solid line
represents the interface-faces
between two domains. Any
polygon which is adjacent to at
least one interface-face is
called interface-cell. If a cell is
an interface-cell, then we call
the atom in the cell an
interface-atom. Interface-
atoms are slightly darker than
non-interface atoms.
Domain Fusion:
Genome 1 Gene X Gene Y ?

Use Gene X as query to

screen Genome 2

Genome 2 Gene X Gene Y

Probable functional
association

Genome 1 Gene X Gene Y

UTILITY:
Rational drug design & discovery include a
step for identifying interaction sites of lead
compound to the target molecules using
computers. Identifying & classifying protein
interaction interfaces on a large scale can help
researchers identify drug targets more
efficiently.
 Non-clinical
development &
Lead Identification Clinical Trials
Lead Optimization

Hit Identification

Target Validation
Target Identification
The Drug Discovery Process
SHORTCOMINGS:
• Noisy results
• Technique determines which interactions are
found
• Interactomes may vary between tissues and
developmental stages