Elastin, another ubiquitous protein in the extracellular matrix, is formed as a very disordered polypeptide, in stark contrast to collagen, which is synthesized as a highly organized polypeptide. This fact has been known for a long time. This state is necessary for elastin to do its function properly. An elastic meshwork is produced as a result of the covalent cross-linking of the relatively loose and unstructured polypeptide chains, and this meshwork has the ability to be pulled back and forth between different shapes. Because elastic fibers are produced as a result of this process, the skin and other tissues, such as the arteries and lungs, are able to stretch and rebound without tearing.

Proteins found in nature that have areas that are naturally disordered are quite prevalent and play important roles within the interiors of cells. As we have seen, proteins commonly contain polypeptide chain loops that extend from the center section of a protein domain to bind to other molecules. These loops extend outward from the protein domain. Some of these loops are very unstructured before they bind to a target molecule; they don't take on a specific folded shape until they bind to the target molecule, at which point they assume the shape of the folded structure. It was also found that many proteins had tails that were inherently disordered, and these tails may be found at either the left or the right end of a structured domain.

However, the full breadth of such a disorganized structure did not become clear until the genomes were sequenced. Using bioinformatic methods to analyze the sequences of amino acids that genes encode allows for the discovery of disordered regions, which may be identified by their unusually high net charge and abnormally low hydrophobicity, respectively. It is now estimated that up to 25 percent of all eukaryotic proteins have the capability to adopt structures that are largely disordered and rapidly transition between a wide range of conformations. These discoveries were combined with further evidence, which led to this conclusion. These fundamentally disordered regions typically contain sequences of amino acids that repeat themselves.

One of the primary roles that this protein plays is in the formation of highly specific binding sites for other protein molecules. These sites are able to undergo easy modification as a result of protein phosphorylation, protein dephosphorylation, or any other type of covalent change brought about by events related to cell signaling. As an illustration, we will see that the eukaryotic RNA polymerase enzyme, which is responsible for the production of mRNAs, possesses a lengthy and unstructured C-terminal tail. This tail undergoes covalent modification as the process of RNA synthesis advances, which recruits specific additional proteins to the transcription complex at various stages.

This unstructured tail interacts with a specific kind of low complexity domain when the RNA polymerase is directed to the precise DNA regions where it starts synthesis. These DNA locations are known as start sites.

In addition, an unstructured area can serve as a "tether" to hold two protein domains close to one another in order to facilitate their interaction. This helps the domains to interact with one another. This anchoring function, for example, enables substrate transport across active sites in massive multienzyme complexes. Other examples include: Thanks to a function that is analogous to that of tethering, large scaffold proteins that contain several protein-binding sites can concentrate sets of interacting proteins, thereby accelerating reactions and limiting them to a particular area inside a cell. A purpose that is directly dependent on the largely unstructured state of other proteins, such as elastin, is served by these proteins. Therefore, the presence of a large number of disordered protein chains in close proximity to one another might result in the formation of microregions within the cell that have the consistency of gel and restrict diffusion. For example, the random coil meshwork created by the multiple nucleoporins that coat the inner surface of the nuclear pore complex is required for selective nuclear transport. This is because nucleoporins coat the inner surface of the nuclear pore complex.

A great number of protein molecules are either expelled as a component of the extracellular matrix or adhered to the exterior of the plasma membrane of a cell. Both of these processes take place in the same cell. These proteins are all in direct interaction with the constituents of the extracellular environment. To assist in the preservation of the structures of these proteins, the polypeptide chains are typically stabilized by the covalent cross-linkages that are found within them.

These links can join two amino acids together to form a single protein, or they can tie several polypeptide chains together to produce a protein composed of multiple subunits. Cross-linkages in proteins most commonly take the form of covalent sulfur-sulfur bonds, despite the presence of a large number of other types. During the process by which cells get ready to export newly generated proteins, disulfide bonds, which are also known as S-S bonds, are formed.

The preferred three-dimensional structure of a protein is maintained rather than changed by the presence of disulfide bonds, which function like atomic pegs. For instance, because to the stabilizing impact that these cross-linkages have on lysozyme, which is an enzyme found in tears that is responsible for destroying the cell walls of bacteria, lysozyme is able to keep its antibacterial properties for a significantly longer period of time.

Disulfide bonds almost never form in the cytoplasm because of the high concentration of reducing agents that convert S-S bonds to cysteine-SH groups there. It should come as no surprise that proteins, which are found inside the cell in an environment that is rather benign, do not require any form of reinforcement.

The same mechanisms that allow proteins to form rings or long filaments with one another also work to create much larger structures made up of a variety of different macromolecules, such as enzyme complexes, ribosomes, viruses, and membranes. These structures can be created through the processes of self-assembly and self-organization, which are both referred to as self-organization. These gigantic objects are not produced from a single, enormous molecule that is covalently bonded throughout their entirety. Instead, they are made through a process called noncovalent assembly, which involves the joining together of many molecules that have been formed independently and that will serve as the building blocks for the finished structure.

When some protein subunits come together, they generate sheets that are flat and have patterns that look like hexagons on them. It is possible for specific membrane proteins to be arranged in lipid bilayers in this way in some instances. By making a slight modification to the geometry of each individual subunit, a hexagonal sheet can be converted into a tube or, with further modifications, into a hollow sphere. These transformations are possible because the sheet is hexagonal. Protein spheres and tubes form the surface of viruses, and inside these structures are particular molecules of RNA and DNA. Viruses are composed of protein spheres and tubes.

Proteins are more stable when they are folded into closed shapes like rings, tubes, or spheres. This is because more bonds are established between the protein subunits when these shapes are produced. Because the interactions between subunits in such a system are mutually dependent on one another and cooperative, even a relatively minor alteration that has a unique impact on each component can bring about either the formation or the disassembly of the structure.

A stunning illustration of these ideas may be seen in the protein capsids of many basic viruses. These capsids take the form of hollow spheres that are based on icosahedrons.

Capsids, the structures that enclose and protect the viral nucleic acid, typically require the employment of hundreds of identical protein subunits in order to be created. In order for the sphere to be formed, the protein contained within the capsid must engage in a variety of different sorts of interactions. However, once the virus has entered a cell, it must change this arrangement in order to release the nucleic acid and begin the process of viral reproduction. Only then can the virus spread to other cells.