The document discusses protein-protein interactions (PPIs), which refer to physical contacts between two or more proteins that are important for biological processes. It covers several types of PPIs based on composition and duration, as well as techniques like X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy that are used to study PPI structures. Methods to investigate PPIs include yeast two-hybrid screening and co-immunoprecipitation. The document also discusses applications of PPI research like drug development and functional annotation of unknown proteins.

1. Topic: Protein-Protein Interactions
Presented by:-
Sunil kentura
Enrollment no:-
201306100210079

2. Introduction
• Proteins facilitates most biological processes in a cell, including
gene expression, cell growth, proliferation, nutrient uptake,
morphology, motility, intercellular communication and apoptosis.
• Protein–protein interactions (PPIs) refer to physical contacts
established between two or more proteins as a result of biochemical
events.
• These interactions are very important in our lives as any disorder in
them can lead to fatal diseases such as Alzheimer’s and Creutzfeld-
Jacob Disease.
• The most well known example of Protein-Protein Interaction is
between Actin and Myosin while regulating Muscular contraction in
our body.
• The protein –protein interaction have commonly been termed
the ‘INTERACTOME’ by scientists.

3. Types of Protein-Protein Interactions
On the basis of their Composition
 Homo-Oligomers: Complexes having one type of protein subunits.
E.g. : PPIs in Muscle Contraction
 Hetero-Oligomers: Complexes having multiple types protein subunits.
E.g. : PPI between Cytochrome Oxidase and TRPC3 (Transient receptor
potential cation channels

4. On the basis of their Duration of Interaction
• Stable Interactions: These comprises of interactions that last for a
long duration. These Interactions carry out Functional or Structural
roles.
E.g.: Haemoglobin structure
• Transient Interactions : Interactions that last a short period of
time.
E.g.: Muscle Contraction

6. Techniques Used to study structure of Protein Complexes
There are three major techniques used to study the structure of Protein
Complexes.
1. X-Ray Crystallography
2. Protein NMR Spectroscopy
3. Cryo microscopy

7. X –Ray Crystallography
• Devised by Sir John Cowdery Kendrew, which is the oldest of
the three methods used for examining Protein structures.
• He solved the structure of Myoglobin in Whale.
• This technique uses beams of X-rays that are diffracted by
crystals on a film and thus, producing the image of the proteins
on the film which reveals a 3-Dimensional view of the protein.

8. X-Ray Crystallography
output

9. Protein NMR Spectroscopy
• It is a field of structural biology in which NMR spectroscopy is used to
obtain information about the structure and dynamics of proteins, and
also nucleic acids, and their complexes which was pioneered by Richard
R. Ernst and Kurt Wüthrich who were awarded the Nobel for their
contributions in 2002.
• The sample is prepared, measurements are made, interpretive
approaches are applied, and a structure is calculated and validated.

10. • The blue arrows represent
the orientation of the N – H
bond of selected peptide
bonds.
• Protein structure is
calculated by determining
orientation of the bond and
influence of Magnetic
Field.

11. Cryo Electron Microscopy
• This is a form of transmission electron microscopy (EM) where the
sample is studied at cryogenic temperatures (generally liquid
nitrogen temperatures).
• This technique was devised by a group of scientists led by Frank Joachim
in EMBL i.e. European Molecular Biology Laboratory.
• The advantage is that the specimen does not need to be stained unlike the
other two methods.

12. Methods to Investigate PPIs
• There are many methods to investigate Protein-Protein Interactions namely
o-immuno-precipitation, protein microarrays, analytical
ultracentrifugation, light scattering, fluorescence spectroscopy, Resonance-
energy transfer systems, Surface Plasmon resonance, protein-fragment
complementation assay, and Calorimetry etc…
• The two most prominent methods used for investigating PPIs are:
1. Yeast two-hybrid screening
2. Co- Immunoprecipitation

13. Yeast two-hybrid screening Technique
 It was first proven using Saccharomyces cerevisiae as biological model by
Fields and Song.
 Yeast cells are transfected with two plasmids: Prey and Bait
 Bait comprises of protein of interest with DNA binding domain factor like
GaI4.
 Prey has cDNA portion that can active the above domain.
 Thus, transcription does not take place until both of them bind.

15. CO-IMMUNOPRECIPITATION (coIP)
 The most common co-complex method is co-immunoprecipitation (co-IP) .
 Co-immunoprecipitation (co-IP) is a popular technique for protein interaction
discovery. Co-IP is conducted in essentially the same manner as
an immunoprecipitation (IP) of a single protein, except that the target protein
precipitated by the antibody, also called the "bait", is used to co-precipitate a
binding partner/protein complex, or "prey", from a lysate.

17. Applications of PPIs
 Many PPIs are being used as therapeutic targets as they exhibit properties such
as allosteric sites.
 Maraviroc, a drug that inhibits CCR5 gp 120 interaction and is a prominent
anti HIV drug.
 Recently , a group of scientists were able to develop 30 peptides using
protein–protein interaction studies to inhibit telomerase recruitment towards
telomeres.
 PPIs have been used to identify the functions of unknown proteins.
 It is based on the assumption that uncharacterized proteins have similar
functions as their interacting proteins
 YbeB, a protein of unknown function was found to interact with ribosomal
proteins and later shown to be involved in translation.

18. REFERENCES
 De Las Rivas J, Fontanillo C (June 2010). "Protein-protein interactions essentials:
key concepts to building and analyzing interactome networks". PLoS
Computational Biology. 6 (6): e1000807
 Jaiswal A, Lakshmi PT (9 September 2014). "Molecular inhibition of telomerase
recruitment using designer peptides: an in silico approach". Journal of
Biomolecular Structure & Dynamics. 33 (7): 1442–59.
 Prieto C, De Las Rivas J (July 2006). "APID: Agile Protein Interaction
DataAnalyzer". Nucleic Acids Research.
 Casado-Vela J, Fuentes M, Franco-Zorrilla JM (2014). "Screening of protein-
protein and protein-DNA interactions using microarrays: applications in
biomedicine". Advances in Protein Chemistry and Structural Biology. 95: 231–81.