Cell signaling in the context of Intrinsically disordered proteins

Life is matter that has biological processes, such as signaling and the ability to sustain itself. It is defined descriptively by the capacity for homeostasis, organisation, metabolism, growth, adaptation, response to stimuli, and reproduction. All life over time eventually reaches a state of death, and none is immortal. Many philosophical definitions of living systems have been proposed, such as self-organizing systems. Defining life is further complicated by viruses, which replicate only in host cells, and the possibility of extraterrestrial life, which is likely to be very different from terrestrial life. Life exists all over the Earth in air, water, and soil, with many ecosystems forming the biosphere. Some of these are harsh environments occupied only by extremophiles. The life in a particular ecosystem is called its biota.

Life has been studied since ancient times, with theories such as Empedocles's materialism asserting that it was composed of four eternal elements, and Aristotle's hylomorphism asserting that living things have souls and embody both form and matter. Life originated at least 3.5 billion years ago, resulting in a universal common ancestor. This evolved into all the species that exist now, by way of many extinct species, some of which have left traces as fossils. Attempts to classify living things, too, began with Aristotle. Modern classification began with Carl Linnaeus's system of binomial nomenclature in the 1740s.

Physiology (/ˌfɪziˈɒlədʒi/; from Ancient Greek φύσις (phúsis) 'nature, origin' and -λογία (-logía) 'study of') is the scientific study of functions and mechanisms in a living system. As a subdiscipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out chemical and physical functions in a living system. According to the classes of organisms, the field can be divided into medical physiology, animal physiology, plant physiology, cell physiology, and comparative physiology.

Central to physiological functioning are biophysical and biochemical processes, homeostatic control mechanisms, and communication between cells. Physiological state is the condition of normal function. In contrast, pathological state refers to abnormal conditions, including human diseases.

Slime molds or slime moulds are a variety of small or microscopic organisms in different groups. They have both single-celled and multicellular forms during their life cycle, the individual cells coming together to form fruiting bodies that produce spores. Most live in damp places such as rotting wood.

More formally, the slime molds are a polyphyletic assemblage of distantly related eukaryotic organisms in the Stramenopiles, Rhizaria, Discoba, Amoebozoa and Holomycota clades. Most are near-microscopic; those in the Myxogastria form larger plasmodial slime molds visible to the naked eye. Spores are often produced in macroscopic multicellular or multinucleate fruiting bodies formed through aggregation or fusion; aggregation is driven by chemical signals called acrasins. Slime molds contribute to the decomposition of dead vegetation; some are parasitic.

The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a semipermeable biological membrane that separates and protects the interior of a cell from the outside environment (the extracellular space). The cell membrane is a lipid bilayer, usually consisting of phospholipids and glycolipids; eukaryotes and some archaea typically have sterols (such as cholesterol in animals) interspersed between them as well, maintaining appropriate membrane fluidity at various temperatures. The membrane also contains membrane proteins, including integral proteins that span the membrane and serve as transporters, and peripheral proteins that attach to the surface of the cell membrane, acting as enzymes to facilitate interaction with the cell's environment. Glycolipids embedded in the outer lipid layer serve a similar purpose.

The cell membrane controls the movement of substances in and out of a cell, being selectively permeable to ions and organic molecules. In addition, cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity, and cell signaling and serve as the attachment surface for several extracellular structures, including the cell wall and the carbohydrate cell coat called the glycocalyx, as well as the intracellular network of protein fibers called the cytoskeleton. In the field of synthetic biology, cell membranes can be artificially reassembled.

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, and they often associate to form stable protein complexes.

In the nervous system, a synapse is a structure that allows a neuron (or nerve cell) to pass an electrical or chemical signal to another neuron or a target effector cell. Synapses can be classified as either chemical or electrical, depending on the mechanism of signal transmission between neurons. In the case of electrical synapses, neurons are coupled bidirectionally with each other through gap junctions and have a connected cytoplasmic milieu. These types of synapses are known to produce synchronous network activity in the brain, but can also result in complicated, chaotic network level dynamics. Therefore, signal directionality cannot always be defined across electrical synapses.

Chemical synapses, on the other hand, communicate through neurotransmitters released from the presynaptic neuron into the synaptic cleft. Upon release, these neurotransmitters bind to specific receptors on the postsynaptic membrane, inducing an electrical or chemical response in the target neuron. This mechanism allows for more complex modulation of neuronal activity compared to electrical synapses, contributing significantly to the plasticity and adaptable nature of neural circuits.

A hormone (from the Greek participle ὁρμῶν, "setting in motion") is a class of signaling molecules in multicellular organisms that are sent to distant organs or tissues by complex biological processes to regulate physiology and behavior. Hormones are required for the normal development of animals, plants and fungi. Due to the broad definition of a hormone (as a signaling molecule that exerts its effects far from its site of production), numerous kinds of molecules can be classified as hormones. Among the substances that can be considered hormones, are eicosanoids (e.g. prostaglandins and thromboxanes), steroids (e.g. oestrogen and brassinosteroid), amino acid derivatives (e.g. epinephrine and auxin), protein or peptides (e.g. insulin and CLE peptides), and gases (e.g. ethylene and nitric oxide).

Hormones are used to communicate between organs and tissues. In vertebrates, hormones are responsible for regulating a wide range of processes including both physiological processes and behavioral activities such as digestion, metabolism, respiration, sensory perception, sleep, excretion, lactation, stress induction, growth and development, movement, reproduction, and mood manipulation. In plants, hormones modulate almost all aspects of development, from germination to senescence.

Lipid signaling, broadly defined, refers to any biological cell signaling event involving a lipid messenger that binds a protein target, such as a receptor, kinase or phosphatase, which in turn mediate the effects of these lipids on specific cellular responses. Lipid signaling is thought to be qualitatively different from other classical signaling paradigms (such as monoamine neurotransmission) because lipids can freely diffuse through membranes (see osmosis). One consequence of this is that lipid messengers cannot be stored in vesicles prior to release and so are often biosynthesized "on demand" at their intended site of action. As such, many lipid signaling molecules cannot circulate freely in solution but, rather, exist bound to special carrier proteins in serum.

Astrocytes (from Ancient Greek ἄστρον, ástron, "star" and κύτος, kútos, "cavity", "cell"), also known collectively as astroglia, are characteristic star-shaped glial cells in the brain and spinal cord. They perform many functions, including biochemical control of endothelial cells that form the blood–brain barrier, provision of nutrients to the nervous tissue, maintenance of extracellular ion balance, regulation of cerebral blood flow, and a role in the repair and scarring process of the brain and spinal cord following infection and traumatic injuries. The proportion of astrocytes in the brain is not well defined; depending on the counting technique used, studies have found that the astrocyte proportion varies by region and ranges from 20% to around 40% of all glia. Another study reports that astrocytes are the most numerous cell type in the brain. Astrocytes are the major source of cholesterol in the central nervous system. Apolipoprotein E transports cholesterol from astrocytes to neurons and other glial cells, regulating cell signaling in the brain. Astrocytes in humans are more than twenty times larger than in rodent brains, and make contact with more than ten times the number of synapses.

Research since the mid-1990s has shown that astrocytes propagate intercellular Ca waves over long distances in response to stimulation, and, similar to neurons, release transmitters (called gliotransmitters) in a Ca-dependent manner. Data suggest that astrocytes also signal to neurons through Ca-dependent release of glutamate. Such discoveries have made astrocytes an important area of research within the field of neuroscience.

In molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; the terms are equivalent in the literature. Larger structures such as nucleic acids and proteins, and many polysaccharides are not small molecules, although their constituent monomers (ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively) are often considered small molecules. Small molecules may be used as research tools to probe biological function as well as leads in the development of new therapeutic agents. Some can inhibit a specific function of a protein or disrupt protein–protein interactions.

Pharmacology usually restricts the term "small molecule" to molecules that bind specific biological macromolecules and act as an effector, altering the activity or function of the target. Small molecules can have a variety of biological functions or applications, serving as cell signaling molecules, drugs in medicine, pesticides in farming, and in many other roles. These compounds can be natural (such as secondary metabolites) or artificial (such as antiviral drugs); they may have a beneficial effect against a disease (such as drugs) or may be detrimental (such as teratogens and carcinogens).

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from Latin ligare, which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure.

Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces. The association or docking is actually reversible through dissociation. Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition of ligand in metalorganic and inorganic chemistry, in biochemistry it is ambiguous whether the ligand generally binds at a metal site, as is the case in hemoglobin. In general, the interpretation of ligand is contextual with regard to what sort of binding has been observed.

Autocrine signaling is a form of cell signaling in which a cell secretes a hormone or chemical messenger (called the autocrine agent) that binds to autocrine receptors on that same cell, leading to changes in the cell. This can be contrasted with paracrine signaling, intracrine signaling, or classical endocrine signaling.

In cellular biology, paracrine signaling is a form of cell signaling, a type of cellular communication in which a cell produces a signal to induce changes in nearby cells, altering the behaviour of those cells. Signaling molecules known as paracrine factors diffuse over a relatively short distance (local action), as opposed to cell signaling by endocrine factors, hormones which travel considerably longer distances via the circulatory system; juxtacrine interactions; and autocrine signaling. Cells that produce paracrine factors secrete them into the immediate extracellular environment. Factors then travel to nearby cells in which the gradient of factor received determines the outcome. However, the exact distance that paracrine factors can travel is not certain.

Although paracrine signaling elicits a diverse array of responses in the induced cells, most paracrine factors utilize a relatively streamlined set of receptors and pathways. In fact, different organs in the body - even between different species - are known to utilize a similar sets of paracrine factors in differential development. The highly conserved receptors and pathways can be organized into four major families based on similar structures: fibroblast growth factor (FGF) family, Hedgehog family, Wnt family, and TGF-β superfamily. Binding of a paracrine factor to its respective receptor initiates signal transduction cascades, eliciting different responses.

Peripheral membrane proteins, or extrinsic membrane proteins, are membrane proteins that adhere only temporarily to the biological membrane with which they are associated. These proteins attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and transmembrane receptors, for example, may be defined as peripheral membrane proteins. In contrast to integral membrane proteins, peripheral membrane proteins tend to collect in the water-soluble component, or fraction, of all the proteins extracted during a protein purification procedure. Proteins with GPI anchors are an exception to this rule and can have purification properties similar to those of integral membrane proteins.

The reversible attachment of proteins to biological membranes has shown to regulate cell signaling and many other important cellular events, through a variety of mechanisms. For example, the close association between many enzymes and biological membranes may bring them into close proximity with their lipid substrate(s). Membrane binding may also promote rearrangement, dissociation, or conformational changes within many protein structural domains, resulting in an activation of their biological activity. Additionally, the positioning of many proteins are localized to either the inner or outer surfaces or leaflets of their resident membrane.This facilitates the assembly of multi-protein complexes by increasing the probability of any appropriate protein–protein interactions.

In cellular biology, membrane transport refers to the collection of mechanisms that regulate the passage of solutes such as ions and small molecules through biological membranes, which are lipid bilayers that contain proteins embedded in them. The regulation of passage through the membrane is due to selective membrane permeability – a characteristic of biological membranes which allows them to separate substances of distinct chemical nature. In other words, they can be permeable to certain substances but not to others.

The movements of most solutes through the membrane are mediated by membrane transport proteins which are specialized to varying degrees in the transport of specific molecules. As the diversity and physiology of the distinct cells is highly related to their capacities to attract different external elements, it is postulated that there is a group of specific transport proteins for each cell type and for every specific physiological stage. This differential expression is regulated through the differential transcription of the genes coding for these proteins and its translation, for instance, through genetic-molecular mechanisms, but also at the cell biology level: the production of these proteins can be activated by cellular signaling pathways, at the biochemical level, or even by being situated in cytoplasmic vesicles. The cell membrane regulates the transport of materials entering and exiting the cell.

The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components: microfilaments, intermediate filaments, and microtubules, and these are all capable of rapid growth and/or disassembly depending on the cell's requirements.

The cytoskeleton can perform many functions. Its primary function is to give the cell its shape and mechanical resistance to deformation, and through association with extracellular connective tissue and other cells it stabilizes entire tissues. The cytoskeleton can also contract, thereby deforming the cell and the cell's environment and allowing cells to migrate. Moreover, it is involved in many cell signaling pathways and in the uptake of extracellular material (endocytosis), the segregation of chromosomes during cellular division, the cytokinesis stage of cell division, as scaffolding to organize the contents of the cell in space and in intracellular transport (for example, the movement of vesicles and organelles within the cell) and can be a template for the construction of a cell wall. Furthermore, it can form specialized structures, such as flagella, cilia, lamellipodia and podosomes. The structure, function and dynamic behavior of the cytoskeleton can be very different, depending on organism and cell type. Even within one cell, the cytoskeleton can change through association with other proteins and the previous history of the network.