Ubiquitin and Ubiquitination
INTRODUCTION
General Understanding of Ubiquitin.
Ubiquitin is a regulatory protein that plays an important role in the regulation of eukaryotic cells. The word ubiquitin is derived from the Latin word, ubiquitous, which means everywhere, since this protein is found in all parts of the body. It was first isolated by Goldstein in 1975 from the thymus and was later found in all of the tissues and organs of the eukaryotic cells1. The protein has a molar mass of 8.5 kDa and consists of 76 amino acids that are highly conserved in all eukaryotic organisms1. There are four genes in the human genome that are responsible for the production of ubiquitin including UBB, UBC, UBA52 and RPS27A. Although Ubiquitin is only present in eukaryotes, prokaryotes have a similar protein that performs the same function as ubiquitin, known as ThiS 1.
Figure 1 Ubiquitin basic structure
The structure of Ubiquitin is characterized by an N terminal and C terminal as a regular protein. Lys 63 and Lys 48 (figure 1) play an important role in ubiquitination (shown below), the step in post translational modification where ubiquitin attaches to the target proteins. This process is incredibly important as it determines the protein function 2. Ubiquitination is the step in post translational modification where ubiquitin attaches to the target proteins. Ubiquitin plays an important role in post translation modification, the process that determines a protein function. Post translational modification can be phosphorylation, SUMOlation and ubiquitination 3.
Ubiquitination was initially only associated to protein degradation, now ubiquitination has been connected to other cellular functions. There are three enzymes that make possible ubiquitination which include E1 (the ubiquitin activating enzyme), E2 (ubiquitin conjugating enzyme) and E3 (ubiquitin ligase) 3. This paper will be a summary of the structure, function of ubiquitin, steps of ubiquitination and the application to cancer research.
2) Similarities and differences of the family of Ubiquitin;
Structure
The ubiquitin family is large, but shares a few characteristics. Some of these characteristics includes; the ubiquitin folding and the biochemical mechanism they use to bind to the target protein. The ubiquitin structure was analyzed as part of a larger NMR study to understand new techniques including H/D exchange. This technique contributed mostly on the information of the protein folding.
Recent genetic and biochemical study revealed that mutations in a unique PXX repeat region of UBQLN2 which is one of ubiquitin like protein family are causative in ALS. The different mutations of UBQLN2 are present in the typical skein-like inclusion which is a hallmark of ALS pathology. In detailed functional relevance of ubiquitin like domain (UBL) and ubiquitin association domain (UBA) of UBQLN2 still need further elucidation, degradation of UPS reporter slowed in neuroblastoma cells transfected with mutations of UBQLN2 (Deng et al., 2011). Interaction of another member of the ubiquilin family (UBQLN1) with polyubiquitylated TAR DNA-binding protein 43 (TDP43) which is also genetically linked to ALS may imply fundamental functions of ubiquilin family in ALS pathology (Kim et al., 2009).
A urinary tract infection (UTI) is an infection of the urinary tract. The urinary tract is the body's drainage system for removing wastes and extra water. Urinary tract infections can have different names, depending on what part of the urinary tract is infected. The infection can include the bladder, kidneys, ureters, or the urethra. If the infection is in the bladder it is called “cystitis” or a bladder infection. If the infection is in the kidneys is it called “pyelonephritis” or a kidney infection? If the infection is in the urethra it is called “urethritis”. Most urinary tract infections are bladder infections. Infections in the ureters are very rare. Everyone is at risk of getting a UTI allowing bacteria to grow in the urine that stays
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Thought to be an oncogene, a gene that has potential in transforming normal cells into tumor cells, p53 was regarded as the most prominent tumor suppressor gene [1]. P53 is a gene which signals apoptosis (programmed cell death) if a cell cannot be repaired due to an extensive amount of damage. As stated in the textbook, p53 regulation occurs by an E3 ubiquitin-protein ligase known as MDM2 [1]. "Controlling the controller" is a statement that describes the molecular interaction where the presence of MDM2 targets the p53 for proteosome via degradation. With three main checkpoints in cell cycle, the literature states p53 functioning from G1 into S phase in a chaotic cell [2]. The normal state of cells is to keep p53 levels low in order to prevent uncontrolled apoptosis and random cell cycle arrest from occurring. In a further note, although p53 promotes apoptosis and cell cycle arrest, cancer may result from p53 unable to recognize the problematic site. In turn, a mutation in p53 may result engaging in new activities. These activities include cellular transformation, tumor metastasis,...
... over normal proliferating cells (Figure 1) It is important to target events taking place at the same time in the cell cycle in order to boost effectiveness of the arrest and the results. In addition, it is important to characterize tumors precisely in order to clarify where the deficiencies on the cell cycle control are accrued and which of the phases have to be targeted for successful therapy. Furthermore, in the future, identification of new tumor specific isoenzymes will be necessary to characterize the cell cycle accurately and comprehend the differences between normal cells and cancer cells for the design of novel anticancer therapies (Diaz-Moralli, et al. 2013).
Myoglobin consist of single polypeptide chain that made up of 153 amino acid and ahs a size of 18 kDa. Its three-dimensional structure was first determined by X-ray crystallography by John Kendrew in 1957. Myoglobin is a typical globular protein in that it is a highly folded compact structure with most of the hydrophobic amino acid residues buried in the interior and many of the polar residues on the surface. X-ray crystallography revealed that the single polypeptide chain of myoglobin consist of entirely of eight (labelled A-H) alpha-helical. Within a hydrophobic crevice formed by the folding polypeptide chain is the heme prosthetic group. This nonopolypepetide unit is noncovalently bound to myoglobin and is essential for the biological activity of the protein.
It is known that one of the active constituents of the medicinal plant Couroupita guianensis, namely isatin, is known to exert cytotoxic activity against certain cancer cell lines, being a potential source of new chemotherapeutic agents (Gousia et al., 2013). Isatin is an endogenous compound identified in humans. Biological properties of isatin include the brain and offer protection against certain types of infections. Isatin constitutes an important class of bioactive compounds exhibiting caspase inhibitor, antibacterial and antiproliferative activity (Kiran et al., 2013).
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Fulda, K. G., and K. Lykens. "Abstract." National Center for Biotechnology Information. U.S. National Library of Medicine, 25 Aug. 0005. Web. 18 Mar. 2014. .
De-novo nucleotide biosynthesis pathway is shown to cross talk with Ara-C activation pathway through the enzyme ribonucleotide reductase (RR). dNTPs generated by RR acts as competitive inhibitor against the active metabolite Ara-CTP and prevents them from incorporating into the DNA. Furthermore, high intracellular dNTP pools inhibit dCK activity, thereby reducing Ara-C activation. The RR holoenzyme is a dimeric protein and comprises of large and small subunits, ribonucleotide reductase M1 (RRM1) and ribonucleotide reductase M2 (RRM2). In patients with advanced non small cell lung cancer treated with gemcitabine, a drug that has similar metabolic pathway like Ara-C, low RRM1 mRNA expression levels was associated with significantly longer median survival than those with high levels [28] [29].
For example, some of the proteins contain pleckstrin homology domains that bind phosphoinositide and others contain C2 domains that bind membrane lipids in the presence of Ca2+, some proteins contain positively charged regions that bind to negatively charged phosphoglycerides and others contain covalently attached fatty acyl groups or prenyl groups that anchor them to membranes. Another example is Annexin shows Ca2+ dependent binding to the cytosolic surfaces of cell membranes. Ca2+ ions bind to the iface of each annexin and this promote protein–lipid interactions through a combination of electrostatic and hydrophobic mechanisms. The same result has been shown by crystallographic studies with phosphoglyceride analogs, suggested that some of the bound Ca2+ ions may bind directly to the oxygens of phospholipid head groups. Addition to this, adjacent membrane lipids that do not bind proteins directly may modulate the protein–lipid interactions, the binding of proteins to membrane surfaces may promote further changes in the structure and function of the proteins, and groups of proteins that bind to the same membrane surface may interact with each other to produce complex membrane
The biological approach emphasizes physical and biological bases of behaviour. It looks at how brain functions influence different behaviours and personality. The study of nervous system has played a major role in the development of biological approach to psychology. On the other hand, the psychoanalytic approach explains personality, motivation and psychological disorders by focusing on the influence of early childhood experiences, unconscious motives and conflicts. This essay attempts to explain biological and psychoanalytic approaches to psychology with focus on their core assumptions, key features, similarities and differences.
Proteins are considered to be the most versatile macromolecules in a living system. This is because they serve crucial functions in all biological processes. Proteins are linear polymers, and they are made up of monomer units that are called amino acids. The sequence of the amino acids linked together is referred to as the primary structure. A protein will spontaneously fold up into a 3D shape caused by the hydrogen bonding of amino acids near each other. This 3D structure is determined by the sequence of the amino acids. The 3D structure is referred to as the secondary structure. There is also a tertiary structure, which is formed by the long-range interactions of the amino acids. Protein function is directly dependent on this 3D structure.
Domains may be considered to be connected units, which are to varying extents independent in terms of their structure, function and folding behaviour. Each domain can be described by its fold. While some proteins consist of a single domain, others consist of several or many. A number of globular protein chains consist of two or three domains appearing as 'lobes'. In other cases the domains may be of very different nature- for example some proteins located in cell membranes have a globular intracellular or extracellular domain distinct from that which spans the membrane.