# Proteomics/Protein - Protein Interactions

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Chapter edited and updated by: Poulami Barman and Sarah Allen

Contact pxb2979@rit.edu, sea3016@rit.edu

## Introduction

Protein interaction is crucial for every organism. Most proteins
function through interaction with other molecules, and often with other
proteins. Enzymes interact with their substrates, inhibitors interact
with enzymes, transport proteins interact with structural proteins,
hormones interact with receptors -- and that's just a few of the
interactions that happen in a cell. Some proteins are composed of more
than one polypeptide chain, and the interactions between the different
peptides are necessary for the whole protein to function. Since they are
so essential, protein-protein interactions are an important topic for
scientists to understand.

There are many characteristics of a protein-protein interaction that are
important. Obviously, it is important to know **which proteins are
interacting**. In many experiments and computational studies, the focus
is on interactions between two different proteins. However, you can have
one protein interacting with other copies of itself (oligomerization),
or three or more different proteins interacting. The
**stoichiometry** of the
interaction is also important -- that is, how many of each protein
involved are present in a given reaction. Some protein interactions are
stronger than others, because they bind together more tightly. The
strength of binding is known as **affinity**. Proteins will only bind
each other spontaneously if it is energetically favorable. **Energy**
changes during binding are another important aspect of protein
interactions. Many of the computational tools that predict interactions
are based on the energy of interactions.

In recent years there has been a strong focus on predicting protein
interactions computationally. Predicting the interactions can help
scientists predict pathways in the cell, potential drugs and
antibiotics, and protein functions. However, it has been an ongoing
challenge to decipher those interactions. Proteins are large molecules,
and binding between them often involves many atoms and a variety of
interaction types, including hydrogen
bonds, hydrophobic
interactions,
salt bridges,
and more. Proteins are also dynamic, with many of their bonds able to
stretch and rotate leading to different conformations. Therefore,
predicting protein-protein interactions requires a good knowledge of the
chemistry and physics involved in the interactions.

This chapter discusses the characteristics of protein-protein
interactions, how they are determined experimentally, and how they are
predicted computationally. It also contains a list of databases where
you can explore known and predicted protein interactions. The links
above will lead you to the various sections.

