A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction). Cofactors can be considered "helper molecules" that assist in biochemical transformations. The rates at which these happen are characterized in an area of study called enzyme kinetics. Cofactors typically differ from ligands in that they often derive their function by remaining bound.
Cofactors can be classified into two types: inorganic ions and complex organic molecules called coenzymes.<ref>Template:Cite journal</ref> Coenzymes are mostly derived from vitamins and other organic essential nutrients in small amounts. (Some scientists limit the use of the term "cofactor" for inorganic substances; both types are included here.<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref><ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>)
Coenzymes are further divided into two types. The first is called a "prosthetic group", which consists of a coenzyme that is tightly (or even covalently and, therefore, permanently) bound to a protein.<ref>Template:Cite book</ref> The second type of coenzymes are called "cosubstrates", and are transiently bound to the protein. Cosubstrates may be released from a protein at some point, and then rebind later. Both prosthetic groups and cosubstrates have the same function, which is to facilitate the reaction of enzymes and proteins. An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is called a holoenzyme.<ref name="Metzler">Template:Cite book</ref>Template:Page needed
The International Union of Pure and Applied Chemistry (IUPAC) defines "coenzyme" a little differently, namely as a low-molecular-weight, non-protein organic compound that is loosely attached, participating in enzymatic reactions as a dissociable carrier of chemical groups or electrons; a prosthetic group is defined as a tightly bound, nonpolypeptide unit in a protein that is regenerated in each enzymatic turnover.<ref>Template:Cite book</ref>
Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase<ref>Template:Cite book</ref> at the junction of glycolysis and the citric acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide (FAD), cosubstrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg2+).<ref>Template:Cite news</ref>
Organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers.<ref name=Denessiouk/>
ClassificationEdit
Cofactors can be divided into two major groups: organic cofactors, such as flavin or heme; and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+ and iron–sulfur clusters.
Organic cofactors are sometimes further divided into coenzymes and prosthetic groups. The term coenzyme refers specifically to enzymes and, as such, to the functional properties of a protein. On the other hand, "prosthetic group" emphasizes the nature of the binding of a cofactor to a protein (tight or covalent) and, thus, refers to a structural property. Different sources give slightly different definitions of coenzymes, cofactors, and prosthetic groups. Some consider tightly bound organic molecules as prosthetic groups and not as coenzymes, while others define all non-protein organic molecules needed for enzyme activity as coenzymes, and classify those that are tightly bound as coenzyme prosthetic groups. These terms are often used loosely.
A 1980 letter in Trends in Biochemistry Sciences noted the confusion in the literature and the essentially arbitrary distinction made between prosthetic groups and coenzymes group and proposed the following scheme. Here, cofactors were defined as an additional substance apart from protein and substrate that is required for enzyme activity and a prosthetic group as a substance that undergoes its whole catalytic cycle attached to a single enzyme molecule. However, the author could not arrive at a single all-encompassing definition of a "coenzyme" and proposed that this term be dropped from use in the literature.<ref>Template:Cite journal</ref>
Inorganic cofactorsEdit
Metal ionsEdit
Template:Further Metal ions are common cofactors.<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}Template:Dead link</ref> The study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors. In humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum.<ref>Template:Cite journal</ref> Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref> Iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor.<ref>Template:Cite journal</ref> Calcium is another special case, in that it is required as a component of the human diet, and it is needed for the full activity of many enzymes, such as nitric oxide synthase, protein phosphatases, and adenylate kinase, but calcium activates these enzymes in allosteric regulation, often binding to these enzymes in a complex with calmodulin.<ref>Template:Cite journal</ref> Calcium is, therefore, a cell signaling ion, and not usually considered a cofactor of the enzymes it regulates.<ref>Template:Cite journal</ref>
Other organisms require additional metals as enzyme cofactors, such as vanadium in the nitrogenase of the nitrogen-fixing bacteria of the genus Azotobacter,<ref>Template:Cite journal</ref> tungsten in the aldehyde ferredoxin oxidoreductase of the thermophilic archaean Pyrococcus furiosus,<ref>Template:Cite journal</ref> and even cadmium in the carbonic anhydrase from the marine diatom Thalassiosira weissflogii.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref>
In many cases, the cofactor includes both an inorganic and organic component. One diverse set of examples is the heme proteins, which consist of a porphyrin ring coordinated to iron.<ref>Template:Cite journal</ref>
Iron–sulfur clustersEdit
Iron–sulfur clusters are complexes of iron and sulfur atoms held within proteins by cysteinyl residues. They play both structural and functional roles, including electron transfer, redox sensing, and as structural modules.<ref>Template:Cite journal</ref>
OrganicEdit
Organic cofactors are small organic molecules (typically a molecular mass less than 1000 Da) that can be either loosely or tightly bound to the enzyme and directly participate in the reaction.<ref name=Metzler/><ref>Template:Cite book</ref><ref>Template:Cite book</ref><ref>Template:Cite book</ref> In the latter case, when it is difficult to remove without denaturing the enzyme, it can be called a prosthetic group. There is no sharp division between loosely and tightly bound cofactors.<ref name=Metzler/> Many such as NAD+ can be tightly bound in some enzymes, while it is loosely bound in others.<ref name=Metzler/> Another example is thiamine pyrophosphate (TPP), which is tightly bound in transketolase or pyruvate decarboxylase, while it is less tightly bound in pyruvate dehydrogenase.<ref>Template:Cite journal</ref> Other coenzymes, flavin adenine dinucleotide (FAD), biotin, and lipoamide, for instance, are tightly bound.<ref name="2017-Hanukoglu-JME">Template:Cite journal</ref> Tightly bound cofactors are, in general, regenerated during the same reaction cycle, while loosely bound cofactors can be regenerated in a subsequent reaction catalyzed by a different enzyme. In the latter case, the cofactor can also be considered a substrate or cosubstrate.
Vitamins can serve as precursors to many organic cofactors (e.g., vitamins B1, B2, B6, B12, niacin, folic acid) or as coenzymes themselves (e.g., vitamin C). However, vitamins do have other functions in the body.<ref>Template:Cite journal</ref> Many organic cofactors also contain a nucleotide, such as the electron carriers NAD and FAD, and coenzyme A, which carries acyl groups. Most of these cofactors are found in a huge variety of species, and some are universal to all forms of life. An exception to this wide distribution is a group of unique cofactors that evolved in methanogens, which are restricted to this group of archaea.<ref>Template:Cite journal</ref>
Vitamins and derivativesEdit
Non-vitaminsEdit
Cofactors as metabolic intermediatesEdit
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups.<ref>Template:Cite journal</ref> This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.<ref>Template:Cite journal</ref> These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes.
Each class of group-transfer reaction is carried out by a particular cofactor, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. An example of this are the dehydrogenases that use nicotinamide adenine dinucleotide (NAD+) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NAD+ to NADH. This reduced cofactor is then a substrate for any of the reductases in the cell that require electrons to reduce their substrates.<ref name="Pollak">Template:Cite journal</ref>
Therefore, these cofactors are continuously recycled as part of metabolism. As an example, the total quantity of ATP in the human body is about 0.1 mole. This ATP is constantly being broken down into ADP, and then converted back into ATP. Thus, at any given time, the total amount of ATP + ADP remains fairly constant. The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. In typical situations, humans use up their body weight of ATP over the course of the day.<ref name="Di Carlo">Template:Cite journal</ref> This means that each ATP molecule is recycled 1000 to 1500 times daily.
EvolutionEdit
Template:Further Organic cofactors, such as ATP and NADH, are present in all known forms of life and form a core part of metabolism. Such universal conservation indicates that these molecules evolved very early in the development of living things.<ref>Template:Cite journal</ref> At least some of the current set of cofactors may, therefore, have been present in the last universal ancestor, which lived about 4 billion years ago.<ref>Template:Cite book</ref><ref>Template:Cite journal</ref>
Organic cofactors may have been present even earlier in the history of life on Earth.<ref>Template:Cite journal</ref> The nucleotide adenosine is a cofactor for many basic metabolic enzymes such as transferases. It may be a remnant of the RNA world.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref> Adenosine-based cofactors may have acted as adaptors that allowed enzymes and ribozymes to bind new cofactors through small modifications in existing adenosine-binding domains, which had originally evolved to bind a different cofactor.<ref name="Denessiouk">Template:Cite journal</ref> This process of adapting a pre-evolved structure for a novel use is known as exaptation.
Prebiotic origin of coenzymes. Like amino acids and nucleotides, certain vitamins and thus coenzymes can be created under early earth conditions. For instance, vitamin B3 can be synthesized with electric discharges applied to ethylene and ammonia.<ref>Template:Cite journal</ref> Similarly, pantetheine (a vitamin B5 derivative), a precursor of coenzyme A and thioester-dependent synthesis, can be formed spontaneously under evaporative conditions.<ref>Template:Cite journal</ref> Other coenzymes may have existed early on Earth, such as pterins (a derivative of vitamin B9), flavins (FAD, flavin mononucleotide = FMN), and riboflavin (vitamin B2).<ref>Template:Cite journal</ref>
Changes in coenzymes. A computational method, IPRO, recently predicted mutations that experimentally switched the cofactor specificity of Candida boidinii xylose reductase from NADPH to NADH.<ref>Template:Cite journal</ref>
Evolution of enzymes without coenzymes. If enzymes require a co-enzyme, how does the coenzyme evolve? The most likely scenario is that enzymes can function initially without their coenzymes and later recruit the coenzyme, even if the catalyzed reaction may not be as efficient or as fast. Examples are Alcohol Dehydrogenase (coenzyme: NAD⁺),<ref>Template:Cite book</ref> Lactate Dehydrogenase (NAD⁺),<ref>Template:Cite book</ref> Glutathione Reductase (NADPH).<ref>Template:Citation</ref>
HistoryEdit
Template:Further The first organic cofactor to be discovered was NAD+, which was identified by Arthur Harden and William Young 1906.<ref>Template:Cite journal</ref> They noticed that adding boiled and filtered yeast extract greatly accelerated alcoholic fermentation in unboiled yeast extracts. They called the unidentified factor responsible for this effect a coferment. Through a long and difficult purification from yeast extracts, this heat-stable factor was identified as a nucleotide sugar phosphate by Hans von Euler-Chelpin.<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> Other cofactors were identified throughout the early 20th century, with ATP being isolated in 1929 by Karl Lohmann,<ref>Template:Cite journal</ref> and coenzyme A being discovered in 1945 by Fritz Albert Lipmann.<ref>Template:Cite journal</ref>
The functions of these molecules were at first mysterious, but, in 1936, Otto Heinrich Warburg identified the function of NAD+ in hydride transfer.<ref>Template:Cite journal</ref> This discovery was followed in the early 1940s by the work of Herman Kalckar, who established the link between the oxidation of sugars and the generation of ATP.<ref>Template:Cite journal</ref> This confirmed the central role of ATP in energy transfer that had been proposed by Fritz Albert Lipmann in 1941.<ref>Template:Cite book</ref> Later, in 1949, Morris Friedkin and Albert L. Lehninger proved that NAD+ linked metabolic pathways such as the citric acid cycle and the synthesis of ATP.<ref>Template:Cite journal</ref>
Protein-derived cofactorsEdit
In a number of enzymes, the moiety that acts as a cofactor is formed by post-translational modification of a part of the protein sequence. This often replaces the need for an external binding factor, such as a metal ion, for protein function. Potential modifications could be oxidation of aromatic residues, binding between residues, cleavage or ring-forming.<ref name="Davidson 5283–5292">Template:Cite journal</ref> These alterations are distinct from other post-translation protein modifications, such as phosphorylation, methylation, or glycosylation in that the amino acids typically acquire new functions. This increases the functionality of the protein; unmodified amino acids are typically limited to acid-base reactions, and the alteration of resides can give the protein electrophilic sites or the ability to stabilize free radicals.<ref name="Davidson 5283–5292" /> Examples of cofactor production include tryptophan tryptophylquinone (TTQ), derived from two tryptophan side chains,<ref>Template:Cite journal</ref> and 4-methylidene-imidazole-5-one (MIO), derived from an Ala-Ser-Gly motif.<ref>Template:Cite journal</ref> Characterization of protein-derived cofactors is conducted using X-ray crystallography and mass spectroscopy; structural data is necessary because sequencing does not readily identify the altered sites.
Non-enzymatic cofactorsEdit
The term is used in other areas of biology to refer more broadly to non-protein (or even protein) molecules that either activate, inhibit, or are required for the protein to function. For example, ligands such as hormones that bind to and activate receptor proteins are termed cofactors or coactivators, whereas molecules that inhibit receptor proteins are termed corepressors. One such example is the G protein-coupled receptor family of receptors, which are frequently found in sensory neurons. Ligand binding to the receptors activates the G protein, which then activates an enzyme to activate the effector.<ref>Template:Cite book</ref> In order to avoid confusion, it has been suggested that such proteins that have ligand-binding mediated activation or repression be referred to as coregulators.<ref>Template:Cite journal</ref>
See alsoEdit
- Enzyme catalysis
- Inorganic chemistry
- Organometallic chemistry
- Bioorganometallic chemistry
- Cofactor engineering
- Vitamin
ReferencesEdit
Further readingEdit
External linksEdit
- Cofactors lecture Template:Webarchive (Powerpoint file)
- Template:MeshName
- The CoFactor Database
Template:Enzymes Template:Enzyme cofactors Template:Authority control