Ras-related protein Rab-7a is a protein that in humans is encoded by the RAB7A gene. Ras-related protein Rab-7a is involved in endocytosis, a process that brings substances into a cell; the process of endocytosis works by folding the cell membrane around a substance outside of the cell and forms a vesicle. The vesicle is brought into the cell and cleaved from the cell membrane. RAB7A plays an important role in the movement of vesicles into the cell as well as with vesicle trafficking. Various mutations of RAB7A are associated with Hereditary sensory neuropathy type 1C known as Charcot-Marie-Tooth syndrome type 2B. Members of the RAB family of RAS-related GTP-binding proteins are important regulators of vesicular transport and are located in specific intracellular compartments. RAB7 has shown to be important in the late endocytic pathway. In addition, it has been shown to have a fundamental role in the cellular vacuolation induced by the cytotoxin VacA of Helicobacter pylori. RAB7A functions as a key regulator in endo-lysosomal trafficking, governs early-to-late endosomal maturation, microtubule minus-end as well as plus-end directed endosomal migration and positions, endosome-lysosome transport through different protein-protein interaction cascades.
RAB7A is involved in regulation of some specialized endosomal membrane trafficking, such as maturation of melanosomes through modulation of SOX10 and the oncogene MYC. Mutations in the lysosomal pathway result in tumor progression in melanoma cells. RAB7 is expressed; the RAB7A gene is located on chromosome 3 in humans on the long q arm from base pair 128,726,135 to 128,814,797. The location was found using mapping, first done by Davies et al. in 1997 to map the RAB7A gene to chromosome 3 using PCR analysis. In 1995 it had been mapped to chromosome 9 in mice by al.. Using fluorescence in situ hybridization, Kashuba et al. were able to map the RAB7A gene to 3q21 in 1997. RAB7a was cloned by screening a human placenta cDNA library with a rat Rab7 cDNA to show that the RAB7a cDNA encodes a 207-amino acid protein whose sequence is 99% identical to those of mouse and dog Rab7a and 61% identical to that of yeast Rab7a. Using Northern Blot Analysis, Vitelli et al. found that RAB7a was expressed as 1.7- and 2.5-kb transcripts in all cell lines examined but that there was a large difference in the total amount of RAB7a mRNA among the cell lines.
It is linked that RAB7a levels and function were independent of melanocyte lineage-specific transcription factors but recent research has shown that SOX10 and MYC are the major regulators. Rab7a is regulated by SOX10 and MYC in a lineage-specific wiring. Studies show that RAB7a can be up regulated through MITF-independent manners like changing levels of SOX10 or MYC to affect tumor proliferation in melanoma. In studies using antisense RNA, downregulation of RAB7 gene expression in HeLa cells using antisense RNA induces severe cell vacuolation that resembles the phenotype seen in fibroblasts from patients with Chédiak–Higashi syndrome. In the presence of growth factor, growth factor inhibition of mammalian Rab7 had no effect on nutrient transporter expression in mouse pro-B-lymphocytic cells. In growth factor-deprived cells, blocking Rab7 function prevented the clearance of glucose and amino acid transporter proteins from the cell surface; when Rab7 was inhibited, growth factor-deprived cells maintained their mitochondrial membrane potential and displayed prolonged, growth factor-independent, nutrient-dependent cell survival.
The authors concluded that RAB7 functions as a proapoptotic protein by limiting cell-autonomous nutrient uptake. RAB7A has been shown to interact with RILP and CHM. RILP has been shown to have a key role in the control of transport to degradative compartments along with Rab7 and may link Rab7 function to the cytoskeleton. RILP plays the role of a downstream effector for Rab7 and together both of these proteins act to regulate late endocytic traffic. Other key interactions include RAC1, NTRK1/TRKA, C9orf72, CHM, RILP, as well as PSMA7, RNF115 and FYCO1. Interacts with the PIK3C3/VPS34-PIK3R4 complex; the GTP-bound form interacts with OSBPL1A and CLN3. Rab7A was shown to interact with the Retromer Complex, most through the Vps35 subunit. RAB7 is a small GTPase, it is found. The RAB7A gene belongs to the RAB family of genes, a member of the RAS oncogene family; these genes in the RAB family provides the instructions that are necessary for making proteins for vesicle trafficking. These proteins are GTPases and act like switch, turned on and off by GTP and GDP molecules.
Melanoma cells retain a developmental memory that reflects a unique wiring of vesicles trafficking pathways. Rab7 is seen to control the proliferative and invasive potential of these aggressive tumors upon identification of melanoma enriched endolysosomal gene cluster. Lysosomal-associated degradation, a universal feature of eukaryotic cells, can be hijacked in a tumor-type- and stage –dependent manner. Finding that RAB7 is controlled by SOX10 and MYC in a MITF-independent manner has important basic and translational implications. Sox10 is not inhibited by mechanisms that downregulate MITF, some of which in
Dominance in genetics is a relationship between alleles of one gene, in which the effect on phenotype of one allele masks the contribution of a second allele at the same locus. The first allele is dominant and the second allele is recessive. For genes on an autosome, the alleles and their associated traits are autosomal dominant or autosomal recessive. Dominance is a key concept in Mendelian inheritance and classical genetics; the dominant allele codes for a functional protein whereas the recessive allele does not. A classic example of dominance is the inheritance of seed shape in peas. Peas associated with allele r. In this case, three combinations of alleles are possible: RR, Rr, rr; the RR individuals have round peas and the rr individuals have wrinkled peas. In Rr individuals the R allele masks the presence of the r allele, so these individuals have round peas. Thus, allele R is dominant to allele r, allele r is recessive to allele R; this use of upper case letters for dominant alleles and lower case ones for recessive alleles is a followed convention.
More where a gene exists in two allelic versions, three combinations of alleles are possible: AA, Aa, aa. If AA and aa individuals show different forms of some trait, Aa individuals show the same phenotype as AA individuals allele A is said to dominate, be dominant to or show dominance to allele a, a is said to be recessive to A. Dominance is not inherent to either its phenotype, it is a relationship between two alleles of their associated phenotypes. An allele may be dominant for a particular aspect of phenotype but not for other aspects influenced by the same gene. Dominance differs from epistasis, a relationship in which an allele of one gene affects the expression of another allele at a different gene; the concept of dominance was introduced by Gregor Johann Mendel. Though Mendel, "The Father of Genetics", first used the term in the 1860s, it was not known until the early twentieth century. Mendel observed that, for a variety of traits of garden peas having to do with the appearance of seeds, seed pods, plants, there were two discrete phenotypes, such as round versus wrinkled seeds, yellow versus green seeds, red versus white flowers or tall versus short plants.
When bred separately, the plants always produced generation after generation. However, when lines with different phenotypes were crossed and only one of the parental phenotypes showed up in the offspring. However, when these hybrid plants were crossed, the offspring plants showed the two original phenotypes, in a characteristic 3:1 ratio, the more common phenotype being that of the parental hybrid plants. Mendel reasoned that each parent in the first cross was a homozygote for different alleles, that each contributed one allele to the offspring, with the result that all of these hybrids were heterozygotes, that one of the two alleles in the hybrid cross dominated expression of the other: A masked a; the final cross between two heterozygotes would produce AA, Aa, aa offspring in a 1:2:1 genotype ratio with the first two classes showing the phenotype, the last showing the phenotype, thereby producing the 3:1 phenotype ratio. Mendel did not use the terms gene, phenotype, genotype and heterozygote, all of which were introduced later.
He did introduce the notation of capital and lowercase letters for dominant and recessive alleles still in use today. Most animals and some plants have paired chromosomes, are described as diploid, they have two versions of each chromosome, one contributed by the mother's ovum, the other by the father's sperm, known as gametes, described as haploid, created through meiosis. These gametes fuse during fertilization during sexual reproduction, into a new single cell zygote, which divides multiple times, resulting in a new organism with the same number of pairs of chromosomes in each cell as its parents; each chromosome of a matching pair is structurally similar to the other, has a similar DNA sequence. The DNA in each chromosome functions as a series of discrete genes that influence various traits. Thus, each gene has a corresponding homologue, which may exist in different versions called alleles; the alleles at the same locus on the two homologous chromosomes may be different. The blood type of a human is determined by a gene that creates an A, B, AB or O blood type and is located in the long arm of chromosome nine.
There are three different alleles that could be present at this locus, but only two can be present in any individual, one inherited from their mother and one from their father. If two alleles of a given gene are identical, the organism is called a homozygote and is said to be homozygous with respect to that gene; the genetic makeup of an organism, either at a single locus or over all its genes collectively, is called its genotype. The genotype of an organism directly and indirectly affects its molecular and other traits, which individually or collectively are called its phenotype. At heterozygous gene loci, the two alleles interact to produce the phenotype. In complete dominance, the effect of one allele in a heterozygous genotype masks the effect of the other; the allele that mas
Guanine nucleotide exchange factor
Guanine nucleotide exchange factors are proteins or protein domains that activate monomeric GTPases by stimulating the release of guanosine diphosphate to allow binding of guanosine triphosphate. A variety of unrelated structural domains have been shown to exhibit guanine nucleotide exchange activity; some GEFs can activate multiple GTPases. Guanine nucleotide exchange factors are proteins or protein domains involved in the activation of small GTPases. Small GTPases act as molecular switches in intracellular signaling pathways and have many downstream targets; the most well-known GTPases comprise the Ras superfamily and are involved in essential cell processes such as cell differentiation and proliferation, cytoskeletal organization, vesicle trafficking, nuclear transport. GTPases are active when bound to GTP and inactive when bound to GDP, allowing their activity to be regulated by GEFs and the opposing GTPase activating proteins. GDP dissociates from inactive GTPases slowly; the binding of GEFs to their GTPase substrates catalyzes the dissociation of GDP, allowing a GTP molecule to bind in its place.
GEFs function to promote the dissociation of GDP. After GDP has disassociated from the GTPase, GTP binds in its place, as the cytosolic ratio of GTP is much higher than GDP at 10:1; the binding of GTP to the GTPase results in the release of the GEF, which can activate a new GTPase. Thus, GEFs both destabilize the GTPase interaction with GDP and stabilize the nucleotide-free GTPase until a GTP molecule binds to it. GAPs act antagonistically to inactivate GTPases by increasing their intrinsic rate of GTP hydrolysis. GDP remains bound to the inactive GTPase until a GEF stimulates its release; the localization of GEFs can determine. For example, the Ran GEF, RCC1, is present in the nucleus while the Ran GAP is present in the cytosol, modulating nuclear import and export of proteins. RCC1 converts RanGDP to RanGTP in the nucleus; when the Ran GAP catalyzes conversion of RanGTP to RanGDP in the cytosol, the protein cargo is released. The mechanism of GTPase activation varies among different GEFs. However, there are some similarities in how different GEFs alter the conformation of the G protein nucleotide-binding site.
GTPases contain two loops called switch 1 and switch 2 that are situated on either side of the bound nucleotide. These regions and the phosphate-binding loop of the GTPase interact with the phosphates of the nucleotide and a coordinating magnesium ion to maintain high affinity binding of the nucleotide. GEF binding induces conformational changes in the P loop and switch regions of the GTPase while the rest of the structure is unchanged; the binding of the GEF sterically hinders the magnesium-binding site and interferes with the phosphate-binding region, while the base-binding region remains accessible. When the GEF binds the GTPase, the phosphate groups are released first and the GEF is displaced upon binding of the entering GTP molecule. Though this general scheme is common among GEFs, the specific interactions between the regions of the GTPase and GEF vary among individual proteins; some GEFs are specific to a single GTPase. While different subfamilies of Ras superfamily GTPases have a conserved GTP binding domain, this is not the case for GEFs.
Different families of GEFs correspond to different Ras subfamilies. The functional domains of these GEF families are not structurally related and do not share sequence homology; these GEF domains appear to be evolutionarily unrelated despite similar function and substrates. The CDC25 homology domain called the RasGEF domain, is the catalytic domain of many Ras GEFs, which activate Ras GTPases; the CDC25 domain comprises 500 amino acids and was first identified in the CDC25 protein in budding yeast Saccharomyces cerevisiae. Dbl-like RhoGEFs were present at the origin of eukaryotes and evolved as adaptive cell signaling mediators. Dbl-like RhoGEFs are characterized by the presence of a Dbl Homology domain, responsible for GEF catalytic activity for Rho GTPases; the human genome encodes 71 members, distributed into 20 subfamilies. All 71 members were present in early Vertebrates, most of the 20 families were present in early Metazoans. Many of the mammalian Dbl family proteins are tissue-specific and their number in Metazoa varies in proportion of cell signaling complexity.
Pleckstrin homology domains are associated in tandem with DH domains in 64 of the 71 Dbl family members. The PH domain is located adjacent to the C terminus of the DH domain. Together, these two domains constitute the minimum structural unit necessary for the activity of most Dbl family proteins; the PH domain is involved in intracellular targeting of the DH domain. It is thought to modulate membrane binding through interactions with phospholipids, but its function has been shown to vary in different proteins; this PH domain is present in other proteins beyond RhoGEFs. The DHR2 domain is the catalytic domain of the DOCK family of Rho GEFs. Like DH domain, DHR2 was present at the origin of eukaryotes; the DOCK family is a separate subset of GEFs from the Dbl family and bears no structural or sequence relation to the DH domain. There are 11 identified DOCK family members divided into subfamilies based on their activation of Rac and Cdc42. DOCK family members are involved in cell migration and phagocytosis.
The DHR2 domain is 400 amino acids. These proteins contain a second conserved domain, DHR1, 250 amino acids; the DHR1 doma
Heredity is the passing on of traits from parents to their offspring, either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic information of their parents. Through heredity, variations between individuals can accumulate and cause species to evolve by natural selection; the study of heredity in biology is genetics. In humans, eye color is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype; the complete set of observable traits of the structure and behavior of an organism is called its phenotype. These traits arise from the interaction of its genotype with the environment; as a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's sunlight. However, some people tan more than others, due to differences in their genotype: a striking example is people with the inherited trait of albinism, who do not tan at all and are sensitive to sunburn.
Heritable traits are known to be passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long polymer; the sequence of bases along a particular DNA molecule specifies the genetic information: this is comparable to a sequence of letters spelling out a passage of text. Before a cell divides through mitosis, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. A portion of a DNA molecule that specifies a single functional unit is called a gene. Within cells, the long strands of DNA form condensed structures called chromosomes. Organisms inherit genetic material from their parents in the form of homologous chromosomes, containing a unique combination of DNA sequences that code for genes; the specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a particular locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations.
If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by multiple interacting genes within and among organisms. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlie some of the mechanics in developmental plasticity and canalization. Recent findings have confirmed important examples of heritable changes that cannot be explained by direct agency of the DNA molecule; these phenomena are classed as epigenetic inheritance systems that are causally or independently evolving over genes. Research into modes and mechanisms of epigenetic inheritance is still in its scientific infancy, this area of research has attracted much recent activity as it broadens the scope of heritability and evolutionary biology in general.
DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference, the three dimensional conformation of proteins are areas where epigenetic inheritance systems have been discovered at the organismic level. Heritability may occur at larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment; this generates a legacy of effect that modifies and feeds back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits, group heritability, symbiogenesis; these examples of heritability that operate above the gene are covered broadly under the title of multilevel or hierarchical selection, a subject of intense debate in the history of evolutionary science.
When Charles Darwin proposed his theory of evolution in 1859, one of its major problems was the lack of an underlying mechanism for heredity. Darwin believed in the inheritance of acquired traits. Blending inheritance would lead to uniformity across populations in only a few generations and would remove variation from a population on which natural selection could act; this led to Darwin adopting some Lamarckian ideas in editions of On the Origin of Species and his biological works. Darwin's primary approach to heredity was to outline how it appeared to work rather than suggesting mechanisms. Darwin's initial model of heredity was adopted by, heavily modified by, his cousin Francis Galton, who laid the framework for the biometric school of heredity. Galton found no evidence to support the aspects of Darwin's pangenesis model, which relied on acquired traits; the inheritance of acquired traits was shown to have little basis in the 1880s when August Weismann cut the tails off many generations of mice and found that their offspring continued to develop tails.
Scientists in Antiquity had a variety of ideas about heredity: Theophrastus proposed that male flowers caused f
G proteins known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells, are involved in transmitting signals from a variety of stimuli outside a cell to its interior. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate to guanosine diphosphate; when they are bound to GTP, they are'on', when they are bound to GDP, they are'off'. G proteins belong to the larger group of enzymes called GTPases. There are two classes of G proteins; the first function as monomeric small GTPases, while the second function as heterotrimeric G protein complexes. The latter class of complexes is made up of alpha and gamma subunits. In addition, the beta and gamma subunits can form a stable dimeric complex referred to as the beta-gamma complex. Heterotrimeric G proteins located within the cell are activated by G protein-coupled receptors that span the cell membrane. Signaling molecules bind to a domain of the GPCR located outside the cell, an intracellular GPCR domain in turn activates a particular G protein.
Some inactive-state GPCRs have been shown to be "pre-coupled" with G proteins. The G protein activates a cascade of further signaling events that results in a change in cell function. G protein-coupled receptor and G proteins working together transmit signals from many hormones, neurotransmitters, other signaling factors. G proteins regulate metabolic enzymes, ion channels, transporter proteins, other parts of the cell machinery, controlling transcription, motility and secretion, which in turn regulate diverse systemic functions such as embryonic development and memory, homeostasis. G proteins were discovered when Alfred G. Gilman and Martin Rodbell investigated stimulation of cells by adrenaline, they found that when adrenaline binds to a receptor, the receptor does not stimulate enzymes directly. Instead, the receptor stimulates a G protein, which stimulates an enzyme. An example is adenylate cyclase, which produces the second messenger cyclic AMP. For this discovery, they won the 1994 Nobel Prize in Medicine.
Nobel prizes have been awarded for many aspects of signaling by G GPCRs. These include receptor antagonists, neurotransmitters, neurotransmitter reuptake, G protein-coupled receptors, G proteins, second messengers, the enzymes that trigger protein phosphorylation in response to cAMP, consequent metabolic processes such as glycogenolysis. Prominent examples include: The 1947 Nobel Prize in Physiology or Medicine to Carl Cori, Gerty Cori and Bernardo Houssay, for their discovery of how glycogen is broken down to glucose and resynthesized in the body, for use as a store and source of energy. Glycogenolysis is stimulated by numerous neurotransmitters including adrenaline; the 1970 Nobel Prize in Physiology or Medicine to Julius Axelrod, Bernard Katz and Ulf von Euler for their work on the release and reuptake of neurotransmitters. The 1971 Nobel Prize in Physiology or Medicine to Earl Sutherland for discovering the key role of adenylate cyclase, which produces the second messenger cyclic AMP; the 1988 Nobel Prize in Physiology or Medicine to George H. Hitchings, Sir James Black and Gertrude Elion "for their discoveries of important principles for drug treatment" targeting GPCRs.
The 1992 Nobel Prize in Physiology or Medicine to Edwin G. Krebs and Edmond H. Fischer for describing how reversible phosphorylation works as a switch to activate proteins, to regulate various cellular processes including glycogenolysis; the 1994 Nobel Prize in Physiology or Medicine to Alfred G. Gilman and Martin Rodbell for their discovery of "G-proteins and the role of these proteins in signal transduction in cells"; the 2000 Nobel Prize in Physiology or Medicine to Eric Kandel, Arvid Carlsson and Paul Greengard, for research on neurotransmitters such as dopamine, which act via GPCRs. The 2004 Nobel Prize in Physiology or Medicine to Richard Axel and Linda B. Buck for their work on G protein-coupled olfactory receptors; the 2012 Nobel Prize in Chemistry to Brian Kobilka and Robert Lefkowitz for their work on GPCR function. G proteins are important signal transducing molecules in cells. "Malfunction of GPCR signaling pathways are involved in many diseases, such as diabetes, allergies, cardiovascular defects, certain forms of cancer.
It is estimated that about 30% of the modern drugs' cellular targets are GPCRs." The human genome encodes 800 G protein-coupled receptors, which detect photons of light, growth factors and other endogenous ligands. 150 of the GPCRs found in the human genome have still-unknown functions. Whereas G proteins are activated by G protein-coupled receptors, they are inactivated by RGS proteins. Receptors stimulate GTP binding. RGS proteins stimulate GTP hydrolysis. All eukaryotes has evolved a large diversity of G proteins. For instance, humans encode 18 different Gα proteins, 5 Gβ proteins, 12 Gγ proteins. G protein can refer to two distinct families of proteins. Heterotrimeric G proteins, sometimes referred to as the "large" G proteins, are activated by G protein-coupled receptors and are made up of alpha and gamma subunits. "Small" G proteins belong to the Ras superfamily of small GTPases. These proteins are homologous to the alpha subunit found in heterotrimers, but are in fact monomeric, consisting of only a single unit.
However, like their larger relatives, they al
Heterotrimeric G protein
"G protein" refers to the membrane-associated heterotrimeric G proteins, sometimes referred to as the "large" G proteins. These proteins are activated by G protein-coupled receptors and are made up of alpha and gamma subunits, the latter two referred to as the beta-gamma complex. There are four main families of G proteins: Gi/Go, Gq, Gs, G12. Reconstitution experiments carried out in the early 1980s showed that purified Gα subunits can directly activate effector enzymes; the GTP form of the α subunit of transducin activates the cyclic GMP phosphodiesterase from retinal rod outer segments, the GTP form of the α subunit of the stimulatory G protein activates hormone-sensitive adenylate cyclase. Gα subunits consist of two domains, the GTPase domain, the alpha-helical domain. There exist at least 20 different Gα subunits; this nomenclature is based on their sequence homologies: The β and γ subunits are bound to one another and are referred to as the G beta-gamma complex. Upon activation of the GPCR, the Gβγ complex is released from the Gα subunit after its GDP-GTP exchange.
The free Gβγ complex can act as a signaling molecule itself, by activating other second messengers or by gating ion channels directly. For example, the Gβγ complex, when bound to histamine receptors, can activate phospholipase A2. Gβγ complexes bound to muscarinic acetylcholine receptors, on the other hand, directly open G protein-coupled inward rectifying potassium channels, they can activate L-type calcium channels, as in H3 receptor pharmacology. Heterotrimeric+G-Proteins at the US National Library of Medicine Medical Subject Headings EC 126.96.36.199
GTPase-activating proteins or GTPase-accelerating proteins are a family of regulatory proteins whose members can bind to activated G proteins and stimulate their GTPase activity, with the result of terminating the signaling event. GAPs are known as RGS protein, or RGS proteins, these proteins are crucial in controlling the activity of G proteins. Regulation of G proteins is important because these proteins are involved in a variety of important cellular processes; the large G proteins, for example, are involved in transduction of signaling from the G protein-coupled receptor for a variety of signaling processes like hormonal signaling, small G proteins are involved in processes like cellular trafficking and cell cycling. GAP’s role in this function is to turn the G protein’s activity off. In this sense, GAPs function is opposite to that of guanine nucleotide exchange factors, which serve to enhance G protein signaling. GAP are linked to the G-protein linked receptor family; the activity of G proteins comes from their ability to bind guanosine triphosphate.
Binding of GTP inherently changes the activity of the G proteins and increases their activity, through the loss of inhibitory subunits. In this more active state, G proteins can bind other proteins and turn on downstream signalling targets; this whole process is regulated by GAPs. G proteins can weakly hydrolyse GTP, breaking a phosphate bond to make GDP. In the GDP-bound state, the G proteins are subsequently inactivated and can no longer bind their targets; this hydrolysis reaction, occurs slowly, meaning G proteins have a built-in timer for their activity. G proteins have a window of activity followed by slow hydrolysis. GAP accelerates this G protein timer by increasing the hydrolytic GTPase activity of the G proteins, hence the name GTPase-activating protein, it is thought that GAPs serve to make GTP on the G protein a better substrate for nucleophilic attack and lower the transition state energy for the hydrolysis reaction. For example, many GAPs of the small G proteins have a conserved finger-like domain an arginine finger, which changes the conformation of the GTP-bound G protein to orient the GTP for better nucleophilic attack by water.
This makes the GTP a better substrate for the reaction. GAPs seem to induce a GDP-like charge distribution in the bound GTP; because the change in charge distribution makes the GTP substrate more like the products of the reaction, GDP and monophosphate, along with opening the molecule for nucleophilic attack, lowers the transition state energy barrier of the reaction and allows GTP to be hydrolyzed more readily. GAPs work to enhance the GTP hydrolysis reaction of the G proteins. By doing so, they accelerate the G protein's built-in timer, which inactivates the G proteins more and along with the inactivation of GEFs, this keeps the G protein signal off. GAPs are critical in the regulation of G proteins. In general, GAPs tend to be pretty specific for their target G proteins; the exact mechanism of target specificity is not known, but it is that this specificity comes from a variety of factors. At the most basic level, GAP-to-G protein specificity may come from the timing and location of protein expression.
RGS9-1, for example, is expressed in the rod and cone photoreceptors in the eye retina, is the only one to interact with G proteins involved in phototransduction in this area. A certain GAP and a certain G protein happen to be expressed in the same time and place, and, how the cell ensures specificity. Meanwhile, scaffold proteins can sequester the proper GAP to its G protein and enhance the proper binding interactions; these binding interactions may be specific for G protein. GAPs may have particular amino acid domains that recognize only a particular G protein. Binding to other G proteins may not have the same favorable interactions, they therefore do not interact. GAPs can, regulate specific G proteins. EIF5 is a GTPase-activating protein. Furthermore, YopE is a protein domain, a Rho GTPase-activating protein, which targets small GTPases such as RhoA, Rac1, Rac2; the GAPs that act on small GTP-binding proteins of the Ras superfamily have conserved structures and use similar mechanisms, An example of a GTPase is the monomer Ran, found in the cytosol as well as the nucleus.
Hydrolysis of GTP by Ran is thought to provide the energy needed to transport nuclear proteins into the cell. Ran is turned off by GEFs and GAPs, respectively. Most GAPs that act on alpha subunits of heterotrimeric G proteins belong to a distinct family, the RGS protein family. While GAPs serve to regulate the G proteins, there is some level of regulation of the GAPs themselves. Many GAPs have allosteric sites that serve as interfaces with downstream targets of the particular path that they regulate. For example, RGS9-1, the GAP in the photoreceptors from above, interacts with cGMP phosphodiesterase, a downstream component of phototransduction in the retina. Upon binding with cGMP PDE, RGS9-1 GAP activity is enhanced. In other words, a downstream target of photoreceptor-induced signaling binds and activates the inhibitor of signaling, GAP; this positive regulatory binding of downstream targets to GAP serves as a negative feedback loop that turns off the signaling, activated. GAPs are regulated by targets of the G protein.
There are examples of negative regulatory mechanisms, where downstream targets of G protein signaling inhibit the GAPs. In G protein-gated potassium channels, phosphatidylinositol 3, 4, 5-triphosphate