{"id":5444,"date":"2019-10-31T12:04:21","date_gmt":"2019-10-31T19:04:21","guid":{"rendered":"http:\/\/www.wou.edu\/chemistry\/?page_id=5444"},"modified":"2020-06-09T06:26:24","modified_gmt":"2020-06-09T13:26:24","slug":"chapter-8-protein-regulation-and-degradation","status":"publish","type":"page","link":"https:\/\/wou.edu\/chemistry\/courses\/online-chemistry-textbooks\/ch450-and-ch451-biochemistry-defining-life-at-the-molecular-level\/chapter-8-protein-regulation-and-degradation\/","title":{"rendered":"Chapter 8 – Protein Regulation and Degradation"},"content":{"rendered":"

Chapter 8 – Protein Regulation and Degradation<\/span><\/strong><\/h2>\n

8.1 Isozymes<\/strong><\/a><\/h3>\n

8.2 Post-Translational Modifcations<\/strong><\/span><\/a><\/h3>\n

8.3 Allosteric Regulation<\/span><\/strong><\/a><\/h3>\n

8.4 Zymogen Activation<\/span><\/strong><\/a><\/h3>\n

8.5 Intracellular Protein Degradation<\/span><\/strong><\/a><\/h3>\n

8.6 References<\/span><\/strong><\/a><\/h3>\n
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Protein activity within cells is controlled by many different mechanisms. The primary sequence of a protein is a main determinant of protein folding and final conformation as well as biochemical activity, stability, and half-life. However, at any given moment in the life of an individual, its proteome is up to two or three orders of magnitude more complex than the encoding genomes would predict. This chapter gives an overview of the major mechanisms utilized by biological systems to regulate protein functions after the protein has been synthesized. Note that these mechanisms seldom work in isolation. There are usually multiple levels of protein control that are functioning at any given time and in response to many different environmental cues and signals.<\/span><\/p>\n

8.1 Isozymes<\/strong><\/h3>\n

Isozymes<\/b><\/em>\u00a0(also known as\u00a0isoenzymes<\/b><\/em>\u00a0or more generally as\u00a0multiple forms of enzymes<\/b><\/em>) are\u00a0enzymes\u00a0that differ in amino acid sequence but catalyze the same chemical reaction. These enzymes usually display different kinetic parameters (e.g. different\u00a0K<\/i>M<\/sub> or K<\/em>cat<\/sub> values), or different regulatory properties. The existence of isozymes permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage. \u00a0In many cases, isozymes<\/em><\/strong> are coded for by homologous genes that have been duplicated within the genome and have then diverged over time. Isozymes<\/em><\/strong> should not be confused with allozymes, <\/em><\/strong>which are allelic variants of the same gene locus that are found within a population. A<\/em><\/strong>llozymes<\/em><\/strong>\u00a0represent enzymes from different\u00a0alleles\u00a0of the same\u00a0gene, whereas isozymes<\/em><\/strong> represent enzymes from different genes that process or catalyse the same reaction, the two words should not be used interchangeably. We will focus on isozymes<\/em><\/strong> within this section.<\/span><\/p>\n

Isozymes<\/em><\/strong> are usually the result of\u00a0gene duplication. Over evolutionary time, if the function of the new variant remains\u00a0identical<\/i>\u00a0to the original, then it is likely that one or the other will be lost as\u00a0mutations\u00a0accumulate, resulting in a\u00a0pseudogene. However, if the mutations do not immediately prevent the enzyme from functioning, but instead modify either its function, or its pattern of\u00a0expression, then the two variants may both be favored by\u00a0natural selection\u00a0and become specialized to different functions.\u00a0For example, they may be expressed at different stages of development or in different tissues. Some isozymes may also arise from convergent evolution and may not share high sequence homology or common ancestry.<\/span><\/p>\n

The Cyclooxygenase Enzymes, Cox-1 and Cox-2 are Isozymes<\/strong><\/span><\/h4>\n

The Cyclooxygenases COX-1<\/b><\/em>\u00a0and\u00a0COX-2<\/b><\/em>, also called\u00a0Prostaglandin Synthases<\/b><\/em>, are examples of isoenzymes<\/em><\/strong>. They regulate a key step in prostaglandin and thromboxane synthesis and are the targets of nonsteroidal antiinflammatory drugs (NSAIDs), such as ibuprofen (Figure 8.1). The\u00a0prostaglandins<\/b>\u00a0(PG<\/b>)<\/em> are a group of\u00a0physiologically\u00a0active\u00a0lipid\u00a0compounds called\u00a0eicosanoids<\/sup>\u00a0having diverse\u00a0hormone-like effects in animals. Prostaglandins have been found in almost every\u00a0tissue\u00a0in humans and other animals. They are derived\u00a0enzymatically\u00a0from the\u00a0fatty acid\u00a0arachidonic acid.\u00a0Every prostaglandin contains 20\u00a0carbon\u00a0atoms, including a\u00a05-carbon ring. They are a subclass of\u00a0eicosanoids\u00a0and of the\u00a0prostanoid\u00a0class of fatty acid derivatives.<\/span><\/p>\n

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Figure 8.1 The Role of COX-1 and COX-2 in Prostaglandin Biosynthesis.<\/strong> (A) COX-1 and COX-2 are bifunctional enzymes that mediate the cyclooxygenase and peroxidase reactions that convert Arachidonic Acid to Prostaglandin H2<\/sub>. (B) Some of the physiological effects that prostaglandins, prostacyclins, and thromboxanes have on biological processes.<\/span><\/p>\n

Images from:<\/span> \u0410\u0434\u043c\u0438\u043d\u0438\u0441\u0442\u0440\u0430\u0446\u0438\u044f \u0412\u043e\u043b\u0433\u043e\u0433\u0440\u0430\u0434\u0441\u043a\u043e\u0439 <\/a>\u043e\u0431\u043b\u0430\u0441\u0442\u0438<\/a> , scientific animations<\/a>,<\/span> and<\/span> Fuzis<\/a><\/span><\/p>\n

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The structural differences between prostaglandins account for their different biological activities. A given prostaglandin may have different and even opposite effects in different tissues. The ability of the same prostaglandin to stimulate a reaction in one tissue and inhibit the same reaction in another tissue is determined by the type of\u00a0receptor\u00a0to which the prostaglandin binds. They act as\u00a0autocrine\u00a0or\u00a0paracrine\u00a0factors with their target cells present in the immediate vicinity of the site of their\u00a0secretion. Prostaglandins differ from\u00a0endocrine\u00a0hormones\u00a0in that they are not produced at a specific site but in many places throughout the human body and tend to act locally once secreted. Prostaglandins are implicated in various physiological processes such as gastrointestinal cytoprotection, hemostasis and thrombosis, as well as renal hemodynamics.<\/span><\/p>\n

Through their role in vasodilation, prostaglandins are also involved in\u00a0inflammation and can trigger the onset of a fever or the sensation of pain. They are synthesized in the walls of blood vessels and serve the physiological function of preventing needless clot formation, as well as regulating the contraction of\u00a0smooth muscle\u00a0tissue. The prostacyclins, a special class of prostaglandins, are powerful, locally-acting\u00a0vasodilators\u00a0and inhibit the aggregation of blood platelets. Conversely, thromboxanes (produced by platelet cells) are\u00a0vasoconstrictors\u00a0and facilitate platelet aggregation. Their name comes from their role in clot formation or thrombosis (Figure 8.1).<\/span><\/p>\n

The Cyclooxygenases COX-1<\/b>\u00a0and\u00a0COX-2<\/b> regulate the first two steps in prostaglandin and are bifunctional enzymes containing two active sites. The first active site performs the bis<\/em>-oxygenation and cyclization of arachidonic acid, whereas the second active site mediates a peroxidase reaction to form PGH2 <\/sub>(Figure 8.1). The COX-1 enzyme is widely distributed in many tissues where it is constitutively expressed. Expression of the COX-2 isoform (shown in Figure 8.2), on the otherhand, is normally undetectable in most tissues (except for the central nervous system, kidneys, and seminal vesicles). COX-2 is induced by various inflammatory and mitogenic stimuli. More recently, a third isoform named COX-3 was identified as a COX-1 splicing variant. This new variant may play a role in processes such as fever and pain. Additionally, a high level of COX-2 expression is found in several forms of cancer. For example, COX-2 overexpression is related to poor prognosis in certain breast cancers\u00a0and endometrial adenocarcinomas.<\/span><\/p>\n

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\"Pharmaceuticals<\/p>\n

Figure 8.2 NSAID Inhibition of COX-1 and COX-2 Enzymes.<\/strong> Upper panel<\/em> shows the crystal structure of the glycosylated, mouse COX-2 tetramer with heme group cofactor shown in red and gray. Lower left panel<\/em> shows the schematic representation of the COX-1 (large green figure) active site being inhibitied by a nonselective NSAID (central blue figure). The entrance channel to COX-1 is blocked by the NSAID. Binding and transformation of arachidonic acid (bottom yellow figure) within COX-1 is prevented. Middle Lower Panel<\/em> shows the inhibition of COX-2 by a nonselective NSAID (central blue figure). Nonselective binding uses an amino acid residue, Arg120, that is conserved in both enzymes. Lower right panel<\/em> shows the inhibition of COX-2 by COX-2 selective NSAIDs (central red figure). The COX-2 side pocket allows specific binding of the COX-2 selective NSAID\u2019s. The entrance channel to COX-2 is blocked. The bulkier COX-2-selective NSAID will not fit into the narrower COX-1 entrance channel, allowing COX-1 to remain active.<\/span><\/p>\n

Upper Figure by<\/span> Saiz, M., Gonzalez, R., & Garcia, E., (2019) Protopedia<\/span> \u00a0<\/a>and Lower Figure by<\/span> Meek, I.L., et al. (2010) Pharmaceuticals 3(7):2146-2162.<\/a><\/span><\/p>\n

back to the top<\/span><\/strong><\/em><\/a><\/h4>\n
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COX-2, unlike COX-1, is induced in inflammatory cells when they are activated by various inflammatory and mitogenic stimuli. Under these conditions, COX-2 activity leads to the production of prostanoid mediators that trigger important\u00a0inflammatory processes. \u00a0Although inflammation is initially a necessary process to fight infection or build up an efficacious inmmune response, if it is maintained or remains uncontrolled, it can provoke chronic pathologies and tissue damage. This is why the inhibition of COX proteins have created considerable interest as potent anti-inflammatory and pain-management targets and has resulted in the development and use of NSAIDs (Figure 8.2).<\/span><\/p>\n

Clinically available NSAIDs can be separated into 3 different classes based upon their mechanism of action:<\/span><\/p>\n