In addition, it is possible to provide a more general calculation of the amount of these protein-protein interactions. Protein databases on the internet today make it possible for users to gain unrestricted access to tens of millions of protein sequences as well as tens of thousands of three-dimensional protein structures. These sequences are derived from the nucleotide sequences of genes. In the pursuit of a deeper understanding of cells, scientists have been developing novel approaches to accessing the information contained in this priceless resource. Integration of computer-based bioinformatics approaches, robots, and other technologies is currently taking place with the goal of analyzing hundreds of proteins in a single set of assays. Similar to how the term "genomics" refers to the in-depth study of DNA sequences and genes, the term "proteomics" is usually used to denote this type of research that focuses on the analysis of enormous collections of proteins. In other words, proteomics is similar to genomics.

Using a biochemical method that is founded on affinity tagging and mass spectrometry, it is possible to ascertain the direct binding relationships that exist between the various proteins that are found in a cellular structure. The tabulation and organization of the results is being done with the help of databases found on the internet. A cell biologist will find it easy, as a result, to discover which other proteins in the same cell are most likely to bind to and interact with a certain small set of proteins. In the two-dimensional network that is known as a protein interaction map, each protein is visually represented as a box or dot. Connecting the proteins that have been shown to bind to one another is a straight line that connects the proteins that have been found to bind to one another.

When trying to determine the most likely function of a protein whose function has not yet been completely elucidated, maps of protein interactions can be quite helpful. Examples include the three proteins shown in the image that do not have a simple, three-letter abbreviation. These proteins are the products of genes whose presence has thus far only been inferred based on the sequencing of the yeast genome (white letters beginning with Y). Because of their binding to Skp1, the three F-box proteins depicted in this picture are components of the ubiquitin ligase. They serve as substrate-binding arms, which allow them to recognize a wide variety of target proteins.

Because the same protein can be a component of numerous protein complexes that serve a variety of roles as a result of evolution's ability to make effective use of the genetic information contained in each organism, protein interaction networks need to be read with extreme caution. Even if protein A attaches to protein B and protein B binds to protein C, it is not necessary that proteins A and C be involved in the same process. This is because protein A binds to protein B.

When proteins from different species are compared, the ones that show similar patterns of interactions in the two maps of protein interactions are probably involved in the same biological processes. Therefore, as scientists develop more and more detailed maps of the genomes of other creatures, their ability to deduce the functions of proteins will continue to improve. These map comparisons will be an extremely useful tool for determining the functions of human proteins due to the fact that genetic engineering, mutational studies, and genetic investigations in experimental species like yeast, worms, and flies are achievable in humans but impracticable in people.

The intricate chemical characteristics of the surfaces of proteins can be used to create incredibly complex chemical devices, the operation of which is primarily dependent on these surfaces. These devices have the potential to solve some of the world's most difficult chemical problems. The folding of proteins brings together amino acid side chains in the correct positions so that surface cavities can be produced. These surface cavities act as binding sites for ligands. Through the activation of normally dormant amino acid side chains, it is possible to build and break covalent bonds in this manner.

Enzymes, which are a type of catalytic protein, significantly boost reaction speeds because they bind the high-energy transition states for the specific reaction pathways that they are responsible for. They are also capable of carrying out acid catalysis and base catalysis at the same time. Most of the time, the only thing that slows down the rates at which enzyme reactions take place is diffusion. Rates can only be increased further in one of three ways: when enzymes that work sequentially on a substrate are combined into a single multienzyme complex; when enzymes and their substrates are bound to protein scaffolds; or when enzymes and their substrates are otherwise restricted to the same region of the cell. Only in these three ways is it possible to increase rates.

A protein will experience a transformation in its three-dimensional shape whenever ligands bind to its surface. The connection between two ligand-binding sites, which is affected by the allosteric changes in protein conformation caused by one ligand, provides an important method for controlling the activities that occur within a cell. This method is known as allosteric control. For example, feedback regulation controls the manner in which certain small molecules inhibit enzymes at the beginning of a metabolic pathway, while other small molecules stimulate enzymes in the same pathway. This kind of regulation makes it possible for coordinated conformational changes to bring about a fast response to shifts in the concentrations of the ligands that control the enzymes. The enzymes that are regulated in this way often assemble into symmetric structures.

It is possible for unidirectional chemical energy expenditure to drive changes in the structure of proteins. By combining, for example, allosteric shape changes with ATP hydrolysis, proteins are able to carry out a variety of useful functions. These jobs include exerting a mechanical force or traveling huge distances in a single direction. The three-dimensional architectures of proteins have revealed how nucleoside triphosphate hydrolysis magnifies a minute local change to cause substantial alterations in other parts of the protein. These proteins are able to behave as membrane-bound pumps, motors, assembly factors, and information-transmitting input-output devices because of the way in which they do this. In order to develop highly efficient protein machines, a huge number of different protein molecules are assembled into bigger assemblies. These larger assemblies then govern the allosteric motions of the component pieces.

These apparatuses are responsible for the majority of the essential cellular functions. Proteins can undergo a wide variety of post-translational changes, some of which are reversible. Some examples of these modifications include the covalent attachment of a phosphate or an acetyl group to a specific amino acid side chain. The incorporation of these modifying groups into a protein can change its shape, as well as its capacity to interact with other proteins and its location inside a cell. As a result, the activity of the protein can be modulated. It is likely that a typical protein in a cell will have interactions with more than five different partners. Through the use of proteomics, scientists are able to analyze hundreds of proteins with just one set of tests. One notable effect is the production of in-depth protein interaction maps, the purpose of which is to attempt to explain all of the binding interactions that take place between the thousands of distinct proteins found in a cell.

However, in order to purify small groups of interacting proteins and completely investigate their chemical composition in depth, fresh biochemistry will be required. Only then will it be possible to fathom these networks. To manage this enormous level of complexity, new computational approaches are going to be required.