Because of the danger posed by amyloid fibrils, scientists first became interested in studying them. However, recent research has shown that cells can make productive use of the same kind of structure in order to achieve their goals. Eukaryotic cells, for example, will store a range of peptide and protein hormones that they will make in specialized organelles referred to as "secretory granules." These granules pack a significant portion of their payload into dense cores that conform to a predetermined pattern. We now understand that the components of these structured cores are amyloid fibrils, which in this case have a structure that causes them to disintegrate and release soluble cargo after being secreted to the cell surface via exocytosis. This discovery was made possible by the fact that amyloid fibrils have a structure that allows them to do so. Many different types of bacteria make use of the amyloid structure, but in a very unique way. These bacteria secrete proteins that cause the production of long amyloid fibrils that extend from the surface of the cell. These amyloid fibrils contribute to the formation of biofilms by helping to bind together neighboring bacterial colonies. Because biofilms allow bacteria to survive in harsh environments, new drugs that specifically target the fibrous networks that are formed by bacterial amyloids show potential for treating human infections (including in individuals receiving antibiotic treatment).

Before relatively recently, it was thought that amyloids with functional relevance were either confined to the interior of specialized vesicles or expressed on the surface of cells. However, recent research has proven that this is not the case. However, recent research has demonstrated that a considerable number of low complexity domains can come together to generate amyloid fibers, which serve functional purposes in both the cytoplasm and the nucleus of cells. This is a very new discovery. These sections of amino acid sequence, which can span hundreds of amino acids and are often unstructured, contain only a small subset of the 20 unique amino acids. These regions can span hundreds of amino acids. Reversible amyloids are recently discovered structures that, in contrast to disease-associated amyloid, are only kept together by weaker noncovalent connections and are able to rapidly dissociate in response to signals. Reversible amyloids have been observed in a number of different organisms.

In many proteins that feature these types of domains, there is a wide array of domains that can bind to specific other protein or RNA molecules. These domains are located in the protein. As a consequence of their regulated aggregation within the cell, which can result in the formation of a hydrogel, these and other molecules have the potential to be drawn into punctate structures that are referred to as intracellular bodies, or granules. These granules can be utilized for the purpose of sequestering specific mRNAs, which are then stored within the granules until they are freed from the amyloid structure that holds them together via a process that is under careful control.

Take into consideration the FUS protein, which is an essential nuclear protein that plays an important role in the transcription, processing, and transport of certain mRNA molecules. More than eighty percent of the two hundred amino acids that make up its C-terminal domain are made up of just four of those amino acids: glycine, serine, glutamine, and tyrosine. This low complexity domain has several additional binding domains attached to it, all of which interact with RNA molecules. When present in a test tube at concentrations high enough, it is capable of producing a hydrogel that, depending on the circumstances, will either associate with other proteins of similar low complexity or with other proteins of its own kind.

The order in which amino acids are arranged within a protein molecule is what establishes its three-dimensional conformation. The unfolded state of the polypeptide chain is maintained by the noncovalent interactions that occur between its numerous constituents. The hydrophobic side chains of the amino acids have a propensity to cluster together inside the molecule, and the result of local hydrogen-bond interactions between neighboring peptide bonds is the formation of helices and sheets.

The portions of an amino acid sequence that make up a protein are referred to as domains. Many proteins are assembled from these modular building blocks. The usual length of these domains is between 40 and 350 amino acids, and their structures are globular in shape. Small proteins often only consist of a single domain, whereas large proteins typically consist of multiple domains that are joined by polypeptide chains of variable lengths, some of which may be relatively disordered. Small proteins typically have a simpler structure than large proteins. As proteins have evolved over time, their domains have been mutated and recombined with those of other proteins in order to produce an enormous variety of new proteins.

The same types of noncovalent forces that are important for controlling the folding of proteins are also responsible for keeping proteins in larger structures together. Proteins that each have binding sites on their own surface can combine to create dimers, closed rings, spherical shells, or helical polymers when they come into contact with one another. In order to construct the lengthy, unbranched amyloid fibril, a repetitive collection of sheets is used as building blocks. Because many biological assembly processes require assembly elements that are not present in the finished structure, not all structures in the cell are capable of spontaneously reassembly after being separated into their component parts and then reassembled from scratch. Even though some mixes of proteins and nucleic acids are capable of spontaneously assembling into complex structures in a test tube, this statement is still accurate.

The physical interactions that a protein molecule has with other molecules determine the biological properties that the protein molecule possesses. As a consequence of this, actin molecules link up with one another to produce actin filaments, antibodies bind to viruses or bacteria in order to mark them for elimination, the enzyme hexokinase binds glucose and ATP in order to catalyze a reaction between the two, and so on and so forth. In point of fact, every single protein is capable of binding, or adhering to, other molecules. This link, depending on the circumstances, can either be exceedingly strong and unbreakable or weak and ephemeral. Binding, on the other hand, is always characterized by a high degree of specificity due to the fact that each protein molecule can typically only bind one or a small number of molecules out of the many thousands of various types it comes into contact with. The word "ligand," which derives from the Latin word ligare, which means "to bind," refers to the substance that the protein binds to, whether it be an ion, a small molecule, or a macromolecule such as another protein. The word "ligand" originates from the Latin word ligare, which means "to bind."

For a protein to bind to a ligand preferentially and with a high affinity, it is necessary for the protein to develop a number of weak noncovalent connections, such as hydrogen bonds, electrostatic attractions, and van der Waals attractions, in addition to advantageous hydrophobic interactions. Because of the inherent weakness of each individual link, effective binding can only occur when a large number of these bonds form all at once. One can only conceive of such a binding occurring in the event that the surface contours of the ligand molecule are fully compatible with those of the protein.

The part of a protein that is known as the ligand's binding site and that interacts with a ligand often consists of a cavity in the surface of the protein that is generated by a particular arrangement of amino acids. This cavity allows the protein to interact with the ligand. These amino acids could have originated from a number of different polypeptide chains, which are then connected to one another when the protein is folded. As we will see in the following section, diverse regions of the protein surface often serve as binding sites for a variety of ligands, which in turn permits the activity of the protein to be regulated. The SH2 domain, which was discussed in the previous section, is an example of how other sections of the protein function as a handle to position the protein in the cell. Proteins that contain the SH2 domain frequently direct themselves to specific intracellular regions in response to signals.