108-471: 1CK7 , 1CXW , 1EAK , 1GEN , 1GXD , 1HOV , 1J7M , 1KS0 , 1QIB , 1RTG , 3AYU 4313 17390 ENSG00000087245 ENSMUSG00000031740 P08253 P33434 NM_004530 NM_001127891 NM_001302508 NM_001302509 NM_001302510 NM_008610 NP_001121363 NP_001289437 NP_001289438 NP_001289439 NP_004521 NP_032636 72 kDa type IV collagenase also known as matrix metalloproteinase-2 (MMP-2) and gelatinase A
216-512: A Gram stained specimen of H. influenzae will show Gram-negative coccobacillus . The cultured organism can be further characterized using catalase and oxidase tests, both of which should be positive. Further serological testing is necessary to distinguish the capsular polysaccharide and differentiate between H. influenzae b and nonencapsulated strains. Although highly specific, bacterial culture of H. influenzae lacks sensitivity. Use of antibiotics prior to sample collection greatly reduces
324-487: A catalytic triad , stabilize charge build-up on the transition states using an oxyanion hole , complete hydrolysis using an oriented water substrate. Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a protein loop or unit of secondary structure , or even an entire protein domain . These motions give rise to
432-489: A conformational ensemble of slightly different structures that interconvert with one another at equilibrium . Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme dihydrofolate reductase are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle, consistent with catalytic resonance theory . Substrate presentation
540-533: A few other possible diseases and conditions that can arise from the H. influenzae depending on the areas that they exist in within the human body. This bacterium can exist in the nasal passages (especially the nasopharynx), the ear canal, and the lungs. The bacterium's presence in these areas can lead to some conditions such as otitis media, chronic obstructive pulmonary disorder (COPD), epiglottitis, and asthma which can become severe. Effective vaccines for Haemophilus influenzae serotype b have been available since
648-474: A first step and then checks that the product is correct in a second step. This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases. Similar proofreading mechanisms are also found in RNA polymerase , aminoacyl tRNA synthetases and ribosomes . Conversely, some enzymes display enzyme promiscuity , having broad specificity and acting on
756-454: A history of allergy to beta-lactam antibiotics. However, macrolide resistance has also been observed. The serious complications of HiB are brain damage, hearing loss , and even death. While non-typable H. influenzae strains rarely cause serious disease, they are more likely to cause chronic infections because they have the ability to change their surface antigens. Chronic infections are usually not as serious as acute infections. There are
864-415: A host organism. Colonization occurs when a microorganism continues to multiply within the host, without interaction, causing no visible signs of illness or infection. H. influenzae colonizes differently in adults than it does young children. Because this bacterium colonizes more rapidly in young children, they are capable of carrying more than one strain of the same bacterium. Once in the adult stage of life,
972-524: A human is likely to only be carrying one strain as this bacterium does not colonize as aggressively in adults. Nearly all infants will undergo colonization of this bacteria within their first year of life. H. influenzae is generally found within and upon the human body, but can also live on various dry, hard surfaces for up to 12 days. Most strains of H. influenzae are opportunistic pathogens; that is, they usually live in their host without causing disease, but cause problems only when other factors (such as
1080-462: A key process involved in cancer metastasis. MMP degradation of the ECM affects cellular behavior through changes in integrin -cell binding, by releasing growth factors harbored by the ECM, by generating ECM degradation products, and by revealing cryptic binding sites in ECM molecules. For instance, MMP-2 degradation of collagen type I can reveal a previously inaccessible cryptic binding site that binds with
1188-493: A lower affinity for penicillin, and therefore cannot cause resistance alone. Beta-lactamase emergence in the 1970s caused the therapy for severe cases of H. influenzae to be changed from ampicillin to cephalosporins , however further resistance to cephalosporins has occurred due to changes in the transpeptidase domain of penicillin binding protein 3 (PBP3). H. influenzae isolates were initially characterized as either encapsulated (having an extracellular polysaccharide layer,
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#17328837120201296-524: A major cause of lower respiratory tract infections in infants and children in developing countries where the vaccine is not widely used. Unencapsulated H. influenzae strains are unaffected by the Hib vaccine and cause ear infections ( otitis media ), eye infections ( conjunctivitis ), and sinusitis in children, and are associated with pneumonia. Some strains of H. influenzae produce beta-lactamases, and are also able to modify its penicillin-binding proteins , so
1404-634: A process known as angiogenesis . This process is essential for tumor progression, because as tumors grow they need increasing supplies of oxygen and nutrients. Localized MMP-2 activity plays an important role in endothelial cell migration, a key feature of angiogenesis . Additionally, MMP-9 and other MMPs have been suggested to also play a complex, indirect role in angiogenesis by promoting VEGF mobilization and generating antiangiogenic factors. For instance, when studying carcinogenesis of pancreatic islets in transgenic mice, Bergers et al. showed that MMP-2 and MMP-9 were upregulated in angiogenic lesions and that
1512-464: A quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics . The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis–Menten complex in their honor. The enzyme then catalyzes the chemical step in
1620-439: A range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. neutrally ), which may be the starting point for the evolutionary selection of a new function. To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This
1728-437: A role in maintaining tissue homeostasis and preventing tumor progression. However, genetically unstable cancer cells can often evade regulation by TGF-β by altering TGF-β receptors in downstream signaling processes. Furthermore, expression of TGF-β is also correlated with immune tolerance and may help shield cancer cells from immune regulation. MMP-2 also plays an important role in the formation of new blood vessels within tumors,
1836-451: A species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate. Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase , to over 2,500 residues in
1944-446: A steady level inside the cell. For example, NADPH is regenerated through the pentose phosphate pathway and S -adenosylmethionine by methionine adenosyltransferase . This continuous regeneration means that small amounts of coenzymes can be used very intensively. For example, the human body turns over its own weight in ATP each day. As with all catalysts, enzymes do not alter the position of
2052-442: A thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates. For example, the hydrolysis of ATP is often used to drive other chemical reactions. Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays . In 1913 Leonor Michaelis and Maud Leonora Menten proposed
2160-462: A variety of attachment techniques, such as pili, adhesins, or Hia and Hap proteins. Though the bacteria possess pili, they are not used for traditional movement or motility, and the bacterium is still considered to be non-motile. The cell wall of H. influenzae bacterium contains various proteins, referred to as autotransporters, for adherence and colony formation. H. influenzae prefers to bind to mucus linings or non-ciliated epithelial cells, which
2268-451: A viral infection, reduced immune function or chronically inflamed tissues, e.g. from allergies) create an opportunity. They infect the host by sticking to the host cell using trimeric autotransporter adhesins . The pathogenesis of H. influenzae infections is not completely understood, although the presence of the polyribosyl ribitol phosphate (PRP) capsule in encapsulated type b (Hib), a serotype causing conditions such as epiglottitis ,
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#17328837120202376-600: A viral infection, usually associated with low-grade fevers. This may progress to the lower respiratory tract within a few days, with features often resembling those of wheezy bronchitis. Sputum may be difficult to expectorate and is often grey or creamy in color. The cough may persist for weeks without appropriate treatment. Many cases are diagnosed after presenting chest infections that do not respond to penicillins or first-generation cephalosporins. A chest X-ray can identify alveolar consolidation. Clinical diagnosis of invasive H. influenzae infection (infection that has spread to
2484-457: Is k cat , also called the turnover number , which is the number of substrate molecules handled by one active site per second. The efficiency of an enzyme can be expressed in terms of k cat / K m . This is also called the specificity constant and incorporates the rate constants for all steps in the reaction up to and including the first irreversible step. Because the specificity constant reflects both affinity and catalytic ability, it
2592-838: Is orotidine 5'-phosphate decarboxylase , which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH , and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties. Some enzymes are used commercially, for example, in
2700-501: Is a homolog of recA , rec1 likely plays a key role in recombinational repair of DNA damage. Thus, H. influenzae may protect its genome against the reactive oxygen species produced by the host's phagocytic cells through recombinational repair of oxidative DNA damages. Recombinational repair of a damaged site of a chromosome requires, in addition to rec1 , a second homologous undamaged DNA molecule. Individual H. influenzae cells are capable of taking up homologous DNA from other cells by
2808-421: Is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol. Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate
2916-646: Is an enzyme that in humans is encoded by the MMP2 gene . The MMP2 gene is located on chromosome 16 at position 12.2. Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix (ECM) in normal physiological processes, such as embryonic development , reproduction , and tissue remodeling, as well as in disease processes, such as arthritis and metastasis . Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases . This gene encodes an enzyme which degrades type IV collagen ,
3024-437: Is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity (from very general to very specific). That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity. The top-level classification is: These sections are subdivided by other features such as the substrate, products, and chemical mechanism . An enzyme
3132-517: Is difficult for researchers to determine whether the inhibitors have successfully reached their targets. However, initial clinical trials using broad spectrum MMP inhibitors did show some positive results. Phase I clinical trials showed that MMP inhibitors are generally safe with minimal adverse side effects. Additionally, trials with marimastat did show a slight increase in survival of patients with gastric or pancreatic cancer. Various research groups have already suggested many strategies for improving
3240-511: Is facilitated by Hap𝘴 autotransporters in the cell wall binding with unknown receptors within the epithelium. The Hap𝘴 autotransporters also facilitate the formation of microcolonies of the bacteria. These microcolonies are likely responsible for the formation of various biofilms within the body, such as those responsible for middle ear or lung infections. Penicillin binding proteins (PBPs) catalyze steps in peptidoglycan metabolism. They carry out essential processes needed to build and modify
3348-749: Is fully specified by four numerical designations. For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1). Sequence similarity . EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam . Non-homologous isofunctional enzymes . Unrelated enzymes that have
MMP2 - Misplaced Pages Continue
3456-558: Is known to be a major factor in virulence. Their capsule allows them to resist phagocytosis and complement -mediated lysis in the nonimmune host. The unencapsulated strains are almost always less invasive; however, they can produce an inflammatory response in humans, which can lead to many symptoms. Vaccination with Hib conjugate vaccine is effective in preventing Hib infection but does not prevent infection with NTHi strains. H. influenzae can cause respiratory tract infections including pneumonia, otitis media, epiglottitis (swelling in
3564-473: Is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase . Examples are lactase , alcohol dehydrogenase and DNA polymerase . Different enzymes that catalyze the same chemical reaction are called isozymes . The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers (for "Enzyme Commission") . Each enzyme
3672-627: Is often excessive in tumor environments and can provide a route of metastasis for cancer cells. Detry, et al. showed that knocking down mmp2 in zebrafish prevented the formation of lymphatic vessels without altering angiogenesis, while MMP-2 inhibition slowed the migration of lymphatic endothelial cells and altered the morphology of new vessels. These results suggest that MMP-2 may alter tumor viability and invasion by regulating lymphangiogenesis in addition to angiogenesis. Clinical trials for cancer therapies using MMP inhibitors have yielded generally unsuccessful results. These poor results are likely due to
3780-418: Is often referred to as "the lock and key" model. This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve. In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with
3888-465: Is often resistant to the penicillin family, but amoxicillin/clavulanic acid can be used in mild cases. Serotype B H. influenzae have been a major cause of meningitis in infants and small children, frequently causing deafness and mental retardation. However, the development in the 1980s of a vaccine effective in this age group (the Hib vaccine ) has almost eliminated this in developed countries. This species
3996-462: Is only one of several important kinetic parameters. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis–Menten constant ( K m ), which is the substrate concentration required for an enzyme to reach one-half its maximum reaction rate; generally, each enzyme has a characteristic K M for a given substrate. Another useful constant
4104-404: Is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES complex. At the maximum reaction rate ( V max ) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme. V max
4212-403: Is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical reaction catalysed. Specificity is achieved by binding pockets with complementary shape, charge and hydrophilic / hydrophobic characteristics to
4320-433: Is their role in ECM degradation, which allows cancer cells to migrate out of the primary tumor to form metastases. More specifically, MMP-2 (along with MMP-9 ) is capable of degrading type IV collagen , the most abundant component of the basement membrane . The basement membrane is important for maintaining tissue organization, providing structural support for cells, and influencing cell signaling and polarity. Degradation of
4428-790: Is useful for comparing different enzymes against each other, or the same enzyme with different substrates. The theoretical maximum for the specificity constant is called the diffusion limit and is about 10 to 10 (M s ). At this point every collision of the enzyme with its substrate will result in catalysis, and the rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes with this property are called catalytically perfect or kinetically perfect . Example of such enzymes are triose-phosphate isomerase , carbonic anhydrase , acetylcholinesterase , catalase , fumarase , β-lactamase , and superoxide dismutase . The turnover of such enzymes can reach several million reactions per second. But most enzymes are far from perfect:
MMP2 - Misplaced Pages Continue
4536-481: Is ~5%. However adequate growth is often seen on brain-heart infusion agar supplemented with hemin and nicotinamide adenine dinucleotide (NAD) Colonies of H. influenzae appear as convex, smooth, pale, grey, or transparent colonies with a mild odor . H. influenzae will only grow on blood agar if other bacteria are present to release these factors from the red blood cells, forming 'satellite' colonies around these bacteria. For example, H. influenzae will grow in
4644-611: The DNA polymerases ; here the holoenzyme is the complete complex containing all the subunits needed for activity. Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme. Coenzymes transport chemical groups from one enzyme to another. Examples include NADH , NADPH and adenosine triphosphate (ATP). Some coenzymes, such as flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), thiamine pyrophosphate (TPP), and tetrahydrofolate (THF), are derived from vitamins . These coenzymes cannot be synthesized by
4752-616: The Embden–Meyerhof–Parnas (EMP) pathway for glycolysis and the pentose phosphate pathway , which is anabolic rather than catabolic . The citric acid cycle is incomplete and lacks several enzymes that are found in a fully functioning cycle. The enzymes missing from the TCA cycle are citrate synthase , aconitate hydratase , and isocitrate dehydrogenase . H. influenzae has been found in both aerobic and anaerobic environments, as well as environments with different pH's. H. influenzae
4860-415: The H. influenzae bacterium, which then allows the plasmid to transfer among H. influenzae strands via conjugation. H. influenzae mutants defective in their rec1 gene (a homolog of recA ) are very susceptible to being killed by the oxidizing agent hydrogen peroxide. This finding suggests that rec1 expression is important for H. influenzae survival under conditions of oxidative stress. Since it
4968-582: The bacterial capsule ) or unencapsulated. Encapsulated strains were further classified on the basis of the immune response to the type of polysaccharides in their capsule. The six generally recognized types of encapsulated H. influenzae are: a, b, c, d, e, and f. H. Influenzae type b, also known as Hib, is the most common form, recognizable by its polyribosyl ribitol phosphate (PRP) capsule, and found mostly in children. Types a, e, and f have been isolated infrequently, while types d and c are rarely isolated. Unencapsulated strains are more genetically diverse than
5076-511: The law of mass action , which is derived from the assumptions of free diffusion and thermodynamically driven random collision. Many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding and constrained molecular movement. More recent, complex extensions of the model attempt to correct for these effects. Enzyme reaction rates can be decreased by various types of enzyme inhibitors. A competitive inhibitor and substrate cannot bind to
5184-548: The ECM, MMPs release growth factors that were previously bound to the ECM, allowing them to bind with cell receptors and influence cell signaling. Furthermore, many MMPs also activate other proMMPs along with growth factors. MMP-2 has also been shown to cleave other non-ECM substrates including growth factors such as TGF-β , FGF receptor-1 , pro TNF , IL-1β and various chemokines . For instance, MMP-2 has been implicated, along with MMP-9 in cleaving latent TGF-β, which has complex interactions with cancer cells. TGF-β generally plays
5292-466: The MMP2 gene cause a rare type of skeletal dysplasia Multicentric Osteolysis, Nodulosis, and Arthropathy syndrome. Abnormal mutations cause defective collagen remodelling. The disease manifestations include bone destruction especially of the wrists and tarsus, generalized osteoporosis and joint stiffness and eventually destruction. Altered expression and activity levels of MMPs have been strongly implicated in
5400-455: The [Hib] vaccine. In infants and young children, H. influenzae type b (Hib) causes bacteremia , pneumonia , epiglottitis and acute bacterial meningitis . On occasion, it causes cellulitis , osteomyelitis , and infectious arthritis . It is one cause of neonatal infection . Due to routine use of the Hib vaccine in the U.S. since 1990, the incidence of invasive Hib disease has decreased to 1.3/100,000 in children. However, Hib remains
5508-400: The ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules , also called ribozymes . They are sometimes described as a type of enzyme rather than being like an enzyme, but even in
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#17328837120205616-544: The activation of MMP-2 is cell-cell clustering. A wild-type activated leukocyte cell adhesion molecule ( ALCAM ) is also required to activate MMP-2. Mutations in the MMP2 gene are associated with Torg-Winchester syndrome , multicentric osteolysis , arthritis syndrome, and possibly keloids. Activity of MMP-2 relative to the other gelatinase ( MMP-9 ) has been associated with severity of chronic airway diseases including Idiopathic interstitial pneumonia and Bronchiectasis . In idiopathic interstitial pneumonia, MMP-2 activity
5724-437: The active site and are involved in catalysis. For example, flavin and heme cofactors are often involved in redox reactions. Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins . An enzyme together with the cofactor(s) required for activity is called a holoenzyme (or haloenzyme). The term holoenzyme can also be applied to enzymes that contain multiple protein subunits, such as
5832-502: The active site. Organic cofactors can be either coenzymes , which are released from the enzyme's active site during the reaction, or prosthetic groups , which are tightly bound to an enzyme. Organic prosthetic groups can be covalently bound (e.g., biotin in enzymes such as pyruvate carboxylase ). An example of an enzyme that contains a cofactor is carbonic anhydrase , which uses a zinc cofactor bound as part of its active site. These tightly bound ions or molecules are usually found in
5940-407: The animal fatty acid synthase . Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site. This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site . The remaining majority of the enzyme structure serves to maintain
6048-578: The average values of k c a t / K m {\displaystyle k_{\rm {cat}}/K_{\rm {m}}} and k c a t {\displaystyle k_{\rm {cat}}} are about 10 5 s − 1 M − 1 {\displaystyle 10^{5}{\rm {s}}^{-1}{\rm {M}}^{-1}} and 10 s − 1 {\displaystyle 10{\rm {s}}^{-1}} , respectively. Michaelis–Menten kinetics relies on
6156-561: The bacteria have gained resistance to the penicillin family of antibiotics. In severe cases, cefotaxime and ceftriaxone delivered directly into the bloodstream are the elected antibiotics, and, for the less severe cases, an association of ampicillin and sulbactam , cephalosporins of the second and third generation, or fluoroquinolones are preferred. (Fluoroquinolone-resistant strains of H. influenzae have been observed). Macrolides and fluoroquinolones have activity against non-typeable H. influenzae and could be used in patients with
6264-654: The basement membrane is an essential step for the metastatic progression of most cancers. Cancer cell invasion, ECM degradation, and metastasis are highly linked with the presence of invadopodia , protrusive and adhesive structures on cancer cells. Invadopodia have been shown to concentrate MMPs (including MT1-MMP , MMP-2, and MMP-9) for localized release and activation. Furthermore, degradation products of MMP activity may further promote invadopodia formation and MMP activity. Finally, MMP-2 and several other MMPs have been shown to proteolytically activate TGF-β , which has been shown to promote epithelial mesenchymal transition (EMT),
6372-577: The bloodstream and internal tissues) is typically confirmed by bacterial culture , latex particle agglutination tests , or polymerase chain reaction tests on clinical samples obtained from an otherwise sterile body site. In this respect, H. influenzae cultured from the nasopharyngeal cavity or throat would not indicate H. influenzae disease, because these sites are colonized in disease-free individuals. However, H. influenzae isolated from cerebrospinal fluid or blood or joint fluid would indicate invasive H. influenzae infection. Microscopic observation of
6480-502: The body de novo and closely related compounds (vitamins) must be acquired from the diet. The chemical groups carried include: Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 1000 enzymes are known to use the coenzyme NADH. Coenzymes are usually continuously regenerated and their concentrations maintained at
6588-469: The cell wall. These proteins are the targets blocked by penicillin and other beta-lactam antibiotics that bind to PBPs, hence their name. Some antibiotic-resistant isolates of H. Influenzae contain modified PBPs that resist beta-lactam action by producing beta-lactamases to degrade these antibiotics. This resistance is likely due to a N526K mutation, or R517H substitution in conjunction with another unknown mutation. The R517H substitution alone did not have
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#17328837120206696-471: The chemical equilibrium of the reaction. In the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants: The rate of a reaction is dependent on the activation energy needed to form the transition state which then decays into products. Enzymes increase reaction rates by lowering
6804-425: The conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase , in 1833. A few decades later, when studying the fermentation of sugar to alcohol by yeast , Louis Pasteur concluded that this fermentation was caused by a vital force contained within
6912-444: The decades since ribozymes' discovery in 1980–1982, the word enzyme alone often means the protein type specifically (as is used in this article). An enzyme's specificity comes from its unique three-dimensional structure . Like all catalysts, enzymes increase the reaction rate by lowering its activation energy . Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example
7020-501: The detection of tumors before they spread. Though initial trials yielded disappointing results, MMP inhibitors offer significant potential for improving cancer treatment by slowing the process of cancer cell invasion and metastasis. MMP2 has been shown to interact with: Enzyme Enzymes ( / ˈ ɛ n z aɪ m z / ) are proteins that act as biological catalysts by accelerating chemical reactions . The molecules upon which enzymes may act are called substrates , and
7128-401: The early 1990s, and are recommended for children under age 5 and asplenic patients. The World Health Organization recommends a pentavalent vaccine , combining vaccines against diphtheria , tetanus , pertussis , hepatitis B and Hib. There is not yet sufficient evidence on how effective this pentavalent vaccine is in relation to the individual vaccines. Hib vaccines cost about seven times
7236-474: The effectiveness of MMP inhibitors in cancer treatment. First, highly specific MMP inhibitors could be used to target the functions of specific MMPs, which should allow doctors to increase the treatment dosage while minimizing adverse side effects. MMP inhibitors could also be administered along with cytotoxic agents or other proteinase inhibitors. Finally, MMP inhibitors could be used during earlier stages of cancer to prevent invasion and metastasis. Additionally,
7344-429: The encapsulated group. Unencapsulated strains are termed nontypable (NTHi) because they lack capsular serotypes; however, all H. influenzae isolates can now be classified by multilocus sequence typing and other molecular methods. Most NTHi strains are considered to be part of the normal human flora in the upper and lower respiratory tract, genitals, and conjunctivae (mucous membranes of the eye). H. influenzae uses
7452-433: The energy of the transition state. First, binding forms a low energy enzyme-substrate complex (ES). Second, the enzyme stabilises the transition state such that it requires less energy to achieve compared to the uncatalyzed reaction (ES ). Finally the enzyme-product complex (EP) dissociates to release the products. Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive"
7560-587: The enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley , who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin . These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography . This
7668-483: The enzyme at the same time. Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, the drug methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase , which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of dihydrofolate and this drug are shown in the accompanying figure. This type of inhibition can be overcome with high substrate concentration. In some cases,
7776-422: The enzyme converts the substrates into different molecules known as products . Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost
7884-403: The enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side-chains that make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases , the substrate molecule also changes shape slightly as it enters the active site. The active site continues to change until
7992-427: The enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane. Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects
8100-451: The fact that MMPs play complex roles in tissue formation and cancer progression, and indeed many MMPs have both pro and anti-tumorogenic properties. Furthermore, most clinical studies involve advanced stages of cancer, where MMP inhibitors are not particularly effective. Finally, there are no reliable biomarkers available for assessing the efficacy of MMP inhibitors and MMPs are not directly cytotoxic (so they do not cause tumor shrinkage), so it
8208-582: The family Pasteurellaceae . The bacteria are mesophilic and grow best at temperatures between 35 and 37 °C. H. influenzae was first described in 1893 by Richard Pfeiffer during an influenza pandemic when he incorrectly identified it as the causative microbe, which is why the bacteria was given the name "influenzae". H. influenzae is responsible for a wide range of localized and invasive infections, typically in infants and children, including pneumonia, meningitis, or bloodstream infections. Treatment consists of antibiotics; however, H. influenzae
8316-404: The hemolytic zone of Staphylococcus aureus on blood agar plates; the hemolysis of cells by S. aureus releases NAD which is needed for its growth. H. influenzae will not grow outside the hemolytic zone of S. aureus due to the lack of nutrients in these areas. Clinical features of a respiratory tract infection may include initial symptoms of an upper respiratory tract infection mimicking
8424-413: The inhibitor can bind to a site other than the binding-site of the usual substrate and exert an allosteric effect to change the shape of the usual binding-site. Haemophilus influenzae Haemophilus influenzae (formerly called Pfeiffer's bacillus or Bacillus influenzae ) is a Gram-negative , non-motile , coccobacillary , facultatively anaerobic , capnophilic pathogenic bacterium of
8532-399: The isolation rate by killing the bacteria before identification is possible. Recent work has shown that H. influenzae uses a highly specialized spectrum of nutrients where lactate is a preferred carbon source. The latex particle agglutination test (LAT) is a more sensitive method to detect H. influenzae than is culture. Because the method relies on antigen rather than viable bacteria,
8640-575: The major structural component of basement membranes . The enzyme plays a role in endometrial menstrual breakdown, regulation of vascularization and the inflammatory response. Activation of MMP-2 requires proteolytic processing. A complex of membrane type 1 MMP (MT1-MMP/MMP14) and tissue inhibitor of metalloproteinase 2 recruits pro-MMP 2 from the extracellular milieu to the cell surface. Activation then requires an active molecule of MT1-MMP and auto catalytic cleavage. Clustering of integrin chains promotes activation of MMP-2. Another factor that will support
8748-468: The mixture. He named the enzyme that brought about the fermentation of sucrose " zymase ". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate (e.g., lactase is the enzyme that cleaves lactose ) or to
8856-497: The overexpression of MMPs in tumors can potentially be leveraged to direct the release of chemotherapeutic agents specifically to tumor sites. For example, cytotoxic agents or siRNA could be encapsulated in liposomes or viral vectors that become activated only upon proteolytic cleavage by a target MMP. Moreover, the tumor-targeting characteristics of MMP inhibitors provide a promising strategy for identifying small tumors. Researchers could link MMP inhibitors to imaging agents to facilitate
8964-528: The precise orientation and dynamics of the active site. In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors . Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity. A small number of RNA -based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these
9072-401: The process of transformation . Transformation in H. influenzae involves at least 15 gene products, and is likely an adaptation for repairing DNA damage in the resident chromosome. Bacterial culture of H. influenzae is performed on agar plates. The strongest growth is seen on chocolate agar at 37 °C in a CO 2 -enriched incubator. The ideal CO 2 concentration for the culture
9180-533: The progression and metastasis of many forms of cancer. Increased MMP-2 activity has also been linked with a poor prognosis in multiple forms of cancer including colorectal , melanoma , breast , lung , ovarian , and prostate . Furthermore, changes in MMP-2 activity can come from alterations in levels of transcription , MMP secretion, MMP activation, or MMP inhibition. MMP production in many cancers may be upregulated in surrounding stromal tissue rather than simply in
9288-406: The reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane , who derived kinetic equations that are still widely used today. Enzyme rates depend on solution conditions and substrate concentration . To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation
9396-733: The reaction rate of the enzyme. In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause feedback regulation, altering the activity of the enzyme according to the flux through the rest of the pathway. Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and iron–sulfur clusters ) or organic compounds (e.g., flavin and heme ). These cofactors serve many purposes; for instance, metal ions can help in stabilizing nucleophilic species within
9504-494: The results are not disrupted by prior antibiotic use. It also has the added benefit of being quicker than culture methods. However, antibiotic sensitivity testing is not possible with LAT alone, so a parallel culture is necessary. Polymerase chain reaction (PCR) assays have been proven to be more sensitive than either LAT or culture tests and are highly specific. These PCR tests can be used for capsular typing of encapsulated H. influenzae strains. Many microbes colonize within
9612-410: The same enzymatic activity have been called non-homologous isofunctional enzymes . Horizontal gene transfer may spread these genes to unrelated species, especially bacteria where they can replace endogenous genes of the same function, leading to hon-homologous gene displacement. Enzymes are generally globular proteins , acting alone or in larger complexes . The sequence of the amino acids specifies
9720-404: The shape of the bacterium is variable, however it is typically coccobacillus or rod-shaped. H. Influenzae contains pili, which are specialized to adhere to the human nasopharynx. The H. Influenzae pili, unlike those of E. coli, resist unwinding, allowing for stronger adhesion to resist expulsion when coughing or sneezing. A minority of non-typeable, or unencapsulated, H. influenzae employ
9828-412: The structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone. Enzyme structures unfold ( denature ) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above
9936-519: The substrate is completely bound, at which point the final shape and charge distribution is determined. Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism. Enzymes can accelerate reactions in several ways, all of which lower the activation energy (ΔG , Gibbs free energy ) Enzymes may use several of these mechanisms simultaneously. For example, proteases such as trypsin perform covalent catalysis using
10044-405: The substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective , regioselective and stereospecific . Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome . Some of these enzymes have " proof-reading " mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in
10152-399: The synthesis of antibiotics . Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew. By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and
10260-403: The throat), eye infections and bloodstream infection, meningitis. It can also cause cellulitis (skin infection) and infectious arthritis (inflammation of the joint). Naturally acquired disease caused by H. influenzae seems to occur in humans only. In healthy children under the age of 5, H. influenzae type b was responsible for more than 80% of aggressive infections, before the introduction of
10368-602: The total cost of vaccines against measles, polio, tuberculosis, diphtheria, tetanus, and pertussis. Consequently, whereas 92% of the populations of developed countries were vaccinated against Hib as of 2003, vaccination coverage was 42% for developing countries, and only 8% for least-developed countries. The Hib vaccines do not provide cross-protection to any other H. influenzae serotypes like Hia, Hic, Hid, Hie or Hif. An oral vaccination has been developed for non-typeable H. influenzae (NTHi) for patients with chronic bronchitis , but it has not shown to be effective in reducing
10476-428: The tumor lesion. For instance, Mook, et al. showed that MMP-2 mRNA levels are strikingly similar between metastatic and non-metastatic lesions in colorectal cancer, but metastatic cases are correlated with higher levels of MMP-2 mRNA in surrounding healthy tissue. For this reason, it is difficult to fully understand the complex role of MMPs in cancer progression. One of the major implications of MMPs in cancer progression
10584-454: The two species ranges from 18% to 98% protein sequence identity, with the majority sharing 40–80% of their amino acids (with an average of 59%). Conjugative plasmids (DNA molecules that are capable of horizontal transfer between different species of bacteria) can frequently be found in H. influenzae . It is common that the F+ plasmid of a competent Escherichia coli bacterium conjugates into
10692-438: The type of reaction (e.g., DNA polymerase forms DNA polymers). The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate Richard Willstätter ) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner showed that
10800-547: The upregulation of these MMPs triggered the release of bioactive VEGF, a potent stimulator of angiogenesis. Additionally, the group determined that MMP-2 knockout mice showed decreased rates of tumor growth relative to tumor growth rates in wild type mice. Furthermore, increased expression and activity of MMP-2 has been tied to increased vascularization of lung carcinoma metastases in the central nervous system, which likely increases survival rate of these metastases. Finally, MMP-2 has been also shown to drive lymphangiogenesis , which
10908-486: The yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme , which comes from Ancient Greek ἔνζυμον (énzymon) ' leavened , in yeast', to describe this process. The word enzyme
11016-428: The α v β 3 integrin expressed by human melanoma cells. Signaling through this integrin is necessary for melanoma cell viability and growth in a collagen matrix and can potentially rescue the cells from apoptosis . As another example, cleavage of laminin-5, a component of the basement membrane, by MMP-2 has been shown to reveal a cryptic site inducing migration of breast epithelial cells. More generally, by degrading
11124-514: Was whole-genome shotgun , which was completed and published in Science in 1995. The genome of strain Rd KW20 consists of 1,830,138 base pairs of DNA in a single circular chromosome that contains 1604 protein-coding genes, 117 pseudogenes, 57 tRNA genes, and 23 other RNA genes. About 90% of the genes have homologs in E. coli , another gamma-proteobacterium . In fact, the similarity between genes of
11232-450: Was elevated in patients with the less severe disease phenotype which is more responsive and reversible with corticosteroid therapy. In non-cystic fibrosis bronchiectasis, MMP-2 concentration was elevated in patients with Haemophilus influenzae airway infection compared to Pseudomonas aeruginosa airway infection. Bronchiectasis patients with P. aeruginosa infection have a more rapid decline in lung function. Disease-causing mutations in
11340-581: Was first done for lysozyme , an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail. Enzymes can be classified by two main criteria: either amino acid sequence similarity (and thus evolutionary relationship) or enzymatic activity. Enzyme activity . An enzyme's name
11448-476: Was the first free-living organism to have its entire genome sequenced. The sequencing was completed by Craig Venter and his team at the Institute for Genomic Research , now part of the J. Craig Venter Institute . Haemophilus was chosen because one of the project leaders, Nobel laureate Hamilton Smith , had been working on it for decades and was able to provide high-quality DNA libraries. The sequencing method used
11556-485: Was the first organism to have its entire genome sequenced. H. influenzae is a small Gram-negative bacterium, approximately 0.3 micrometer to 1 micrometer. Like other Gram-negative bacteria, H. influenzae has a thin peptidoglycan layer surrounded by an outer membrane containing lipopolysaccharide . Some types of H. influenzae contain a polysaccharide capsule around the outer membrane to aid in protection and colonization. The bacteria are pleomorphic , meaning
11664-451: Was used later to refer to nonliving substances such as pepsin , and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin , he found that sugar was fermented by yeast extracts even when there were no living yeast cells in
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