Investigating Alykl Hydoxylation in P450-can Using EVB

Investigating Alykl Hydoxylation in P450-can Using EVB Shen Ye Abstract Cytochrome P450s are a superfamily of haemoproteins1-3 which catalyse the oxidation of organic molecules4. One P450 enzyme studied for its hydroxylation mechanism is P450cam (CYP101) from the Pseudomonas putida bacteria, whose crystal structure (1DZ9) was solved by Schlichting et al.5. The active form of P450cam contains an oxyferryl species known as compound I(CPDI), where the iron has a formal oxidation state of Fe(V) 6, 7 in the plane of a porphyrin ring with a protruding oxygen atom. This oxygen atom is a tremendously potent oxidising agent and can readily abstract a hydrogen of a C-H bond from non-activated hydrocarbons with potentially high regioselectivity[REF]. Acknowledgements The author would like to thank: Patrick von Glehn Dr Richard Lonsdale Professor Adrian Mulholland Professor Jeremy Harvey Professor Neil Allan Table of Contents Abstract Acknowledgements Table of Contents Part I – Literature Review An introduction to haem oxygenases Cytochrome P450 enzymes P450 catalytic cycle P450cam An introduction to CHARMM and EVB Part II Methodology Part I – Literature Review An introduction to haem oxygenases After hydrogen and helium, oxygen is the third most abundant chemical element in the universe8 and makes up 20.9% of Earth’s atmosphere9. Oxygen accounts for 65% of the mass in humans8 as it is found in all biological systems including carbohydrates, proteins, lipids and water. Oxygen occurs in the atmosphere as dioxygen, with a triple ground state where the two unpaired electrons are occupying two degenerate molecular orbitals10. This makes incorporating atmospheric oxygen into organic molecules (predominantly singlet species) extremely difficult as it would be a spin forbidden process. Haem oxygenases are enzymes containing a prosthetic haem cofactor, an iron atom held by a porphyrin ring. Haem B is the most common prosthetic haem group, consisting of a protoporphyrin IX ring bound to the iron. It is most commonly found in the human body inside haemoglobin and myoglobin11, playing a major role when it comes to binding atmospheric dioxygen. There are two groups of haem oxygenases, monooxygenases and dioxygenases, one reacts using a single oxygen atom and the other using both oxygen atoms. The haem B cofactor and the apoenzyme are synthesised separately in different parts of a cell and they are connected via ligation to the iron atom on the proximal face12. The protoporphyrin ring is a tetrapyrrole macrocycle synthesised from basic biological precursors including succinyl CoA and the most basic amino acid, glycine13. Ferrochelatase coordinates the iron atom to the protoporphyrin, producing haem B14. In cytochrome P450 enzyme the iron is ligated to a proximal cysteine residue via the sulphur atom15, however in some other oxygenases and other haemoproteins such as haemoglobin and myoglobin the iron is coordinated to a proximal histidine residue16. In monooxygenases one of the dioxygen atoms is converted to H2O and the other is commonly inserted into an aliphatic position of the substrate, producing a hydroxyl group by oxidation of reducing agents such as NADH and NAD(P)H17, 18. The most studied haem-containing monooxygenases are the superfamily of cytochrome P450 enzymes due to their large diversity and versatility19, 20. Cytochrome P450 enzymes Cytochrome P450 enzymes (CYP) were first discovered by Axelrod21 and Brodie et al.22 in 1955 when they observed the oxidation of xenobiotic compounds in the endoplasmic reticulum of the liver, but the enzymes responsible were still unknown until 1962. Klingenberg23 and Garfinkel24 found a carbon monoxide binding pigment in the rat and pig livers, respectively, which had an absorption maximum at 450 nm. The CO molecule was bound to the centre of the haem and its 450 nm absorption maximum25 is prevalent in all CYPs26-28, an electron spin resonance spectrum identified this enzyme was a low spin haemoprotein29. This 450 nm Soret peak is the origin of the name P450. The superfamily of CYPs contain over a thousand haem monooxygenases30 and are present in nearly all living organisms and even viruses, a well-known exception is Escherichia coli4, 19 which is widely used to investigate CYPs by sequence insertion into plasmids and allow the E. coli to express the genes31, 32. CYPs typically con tain approximately 500 amino acids, the cysteine residue which ligates to the haem group is located near the carboxy-terminus and the amino-terminus region of CYPs are rich in hydrophobic residues and is believed to be responsible for binding the enzymes to the lipid bilayers of cells33. CYPs in mammals are a crucial part of catalysing the metabolism of organic compounds and the biosynthesis of steroid hormones34, such as oestrogen and testosterone, and are able to perform hydroxylation, epoxidations and other oxidation reactions at physiological temperatures35 extremely selectively. Such reactions when performed uncatalysed tend to require extremely high temperatures5. CYPs are tremendously versatile, they’re able to catalyse a wide range of foreign hydrophobic compounds, which helps to protect the organism if they have ingested potentially harmful substances including toxins and carcinogens36. This ability is often called â€Å"xenobiotic metabolism†37. There is a system for the nomenclature of P450 enzymes, which is â€Å"CYP† followed by a number, a latter and another number, e.g. CYP2J2. The first number relates to the family of the CYP, where all the CYPs in the family share a sequence identity of 40% or greater. The letter afterwards corresponds to the subfamily, where the CYPs in the subfamily share a sequence identity of 55% of greater. The final number is a label where all CYPs with this label share a sequence identity of 97% or greater38. CYPs with the same label are known as isoforms. Humans have 57 different CYP isoforms divided into 18 families and 42 subfamilies34. Most of the isoforms are found on membranes, including the inner membrane of mitochondria, the endoplasmic reticulum and the cell membrane. They all differ in roles but the processes they all catalyse are similar and a few are crucial for catalysing more than once process. For example CYP 17A1 is located in the endoplasmic reticulum and is shown to be both a hydrolase and lyase, a key enzyme in the biosynthetic pathway of steroids including oestrogens and progestins39. The most researched area of CYPs is the drug metabolising CYPs in the human hepatic system such as 3A440, 2C941, 2D642, 2E143, 1A2 and 2C1944. These CYPs are responsible for the xenobiotic metabolism against infested foreign compounds, breaking them down into more readily soluble products to aid excretion through the urinary system45. For this reason, a good understanding of the metabolic pathway of organic molecules inside the body al lows drug development to invent new methods of bioactivation of inert but bioavailable forms of an active compound, where the ingested compound is inactive but gets metabolised into the active form inside the body. The versatility of CYPs can sometimes cause unexpected side-effects in metabolising pharmaceutical drugs, for example some bioactive compounds in grapefruit juice have been found to inhibit CYP catalysed metabolism of certain cardiovascular drugs, causing an increased blood concentration of the bioactive drug, thus leaking to a risk of overdose46, 47. P450cam P450cam was the first CYP to have its three-dimensional structure determined. It displays a high region- and stereoselectivity when catalysing the hydroxylation of camphor, only the exo-hydroxyl at C5 position is produced. Despite the extensive research into P450s, there are still certain details of the mechanism which are not fully understood. References 1.T.K. D. R. Nelson, D. J. Waxman, F. P. Guengerich, R. W. Estabrook, R. Feyereisen, F. J. Gonzales, M. J. Coon, I. C. Gunsalus, O. Gotoh, K. Okuda and D. W. Nebert DNA Cell Biol, 1993. 12(1): p. 1-51. 2.C. Loannides and D. Parke, Drug metabolism reviews, 1990. 22(1): p. 1-85. 3.A. Altun, S. Shaik, and W. Thiel, Journal of the American Chemical Society, 2007. 129(29): p. 8978-8987. 4.P. Danielson, Current drug metabolism, 2002. 3(6): p. 561-597. 5.I. Schlichting, J. Berendzen, K. Chu, A.M. Stock, S.A. Maves, D.E. Benson, R.M. Sweet, D. Ringe, G.A. Petsko, and S.G. Sligar, Science, 2000. 287(5458): p. 1615-1622. 6.D. Dolphin, A. Forman, D. Borg, J. Fajer, and R. Felton, Proceedings of the National Academy of Sciences, 1971. 68(3): p. 614-618. 7.J.E. Penner-Hahn, K. Smith Eble, T.J. McMurry, M. Renner, A.L. Balch, J.T. Groves, J.H. Dawson, and K.O. Hodgson, Journal of the American Chemical Society, 1986. 108(24): p. 7819-7825. 8.R. Chang, Chemistry. 9th Edition ed. 2007: McGraw-Hill. 9.A. Murphy, Plasma Chemistry and Plasma Processing, 1995. 15(2): p. 279-307. 10.T.F. Slater, Free radical mechanisms in tissue injury, in Cell Function and Disease. 1988, Springer. p. 209-218. 11.A.R. Fanelu, E. Antonini, and A. Caputo, Advances In Protein Chemistry, 1964. 19: p. 73. 12.H.S. Marver, D.P. Tschudy, M.G. Perlroth, and A. Collins, Science, 1966. 154(3748): p. 501-503. 13.F.J. Leeper, Natural Products Reports, 1983. 19: p. 1137-1161. 14.T. Yoon and J. Cowan, Journal of Biological Chemistry, 2004. 279(25): p. 25943-25946. 15.A.W. Munro, D.G. Leys, K.J. McLean, K.R. Marshall, T.W. Ost, S. Daff, C.S. Miles, S.K. Chapman, D.A. Lysek, and C.C. Moser, Trends in biochemical sciences, 2002. 27(5): p. 250-257. 16.D.F. Brook and P.J. Large, European Journal of Biochemistry, 1975. 55(3): p. 601-609. 17.M.H.M. Eppink, C. Bunthof, H.A. Schreuder, and W.J.H. van Berkel, FEBS Letters, 1999. 443(3): p. 251-255. 18.S. Harayama, M. Kok, and E.L. Neidle, Annual Review of Microbiology, 1992. 46(1): p. 565-601. 19.A. Sigel, H. Sigel, and R.K. Sigel, The ubiquitous roles of cytochrome P450 proteins: metal ions in life sciences. Vol. 10. 2007: John Wiley Sons. 20.P.R.O. De Montellano, Cytochrome P450: structure, mechanism, and biochemistry. 2005: Springer. 21.J. Axelrod, Journal of Pharmacology and Experimental Therapeutics, 1956. 117(3): p. 322-330. 22.B.B. Brodie, J. Axelrod, J.R. Cooper, L. Gaudette, B.N. La Du, C. Mitoma, and S. Udenfriend, Science, 1955. 121(3147): p. 603-604. 23.M. Klingenberg, Archives of biochemistry and biophysics, 1958. 75(2): p. 376-386. 24.D. Garfinkel, Archives of biochemistry and biophysics, 1958. 77(2): p. 493-509. 25.R.W. Estabrook, D.Y. Cooper, and O. Rosenthal, Biochemische Zeitschrift, 1962. 338: p. 741-755. 26.T. Omura and R. Sato, J. Biol. Chem., 1962. 237: p. 1375-1376. 27.T. 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Seasonal Affective Disorder :: Disorders Expository Essays

Seasonal Affective Disorder It's wintertime, and you are gathered for the holidays with all of your family and friends. Everything seems like it should be perfect, yet you are feeling very distressed, lethargic and disconnected from everything and everyone around you. "Perhaps it is just the winter blues," you tell yourself as you delve into the holiday feast, aiming straight for the sugary fruitcake before collapsing from exhaustion. However, the depression and other symptoms that you feel continue to persist from the beginning of winter until the springtime, for years upon end without ceasing. Although you may be tempted to believe that you, like many millions of other Americans, are afflicted with a case of the winter blues, you are most likely suffering from a more severe form of seasonal depression known as Seasonal Affective Disorder, or SAD. This form of depression has been described as a form of a unipolar or bipolar mood disorder which, unlike other forms of depression, follows a strictly seasonal pattern. (5). During the winter, many of us suffer from "the winter blues", a less severe form of seasonal depression than SAD. Still others are sufferers have an already existent condition, such as pre-menstrual syndrome or depression, which is exacerbated by the coming of the winter. (2). In general, many people suffer from some form of sporadic depression during the wintertime. We may feel more tired and sad at times. We may even gain some weight or have trouble getting out of bed. Over 10 million people in America, however, may feel a more extreme form of these symptoms. They may constantly feel lethargic and depressed to an extent that social and work related activities are negatively affected. This more extreme form of the "winter blues" is SAD. Typical SAD symptoms include sugar cravings, lethargy, depression, an increase in body weight, and a greater need for sleep (1). Onset of these symptoms usually occurs in October or November, and the symptoms disappear in early spring. Frequentl y, people who suffer from SAD react strongly to variations in the amount of light in their surrounding environment. Most often, patients who suffer from SAD and live at more northern latitudes note that the more north they live, the more distinct and severe their SAD symptoms become. In addition, SAD patients note that their depressive symptoms increase in severity when the amount of light indoors decreases and the weather is cloudy. Seasonal Affective Disorder :: Disorders Expository Essays Seasonal Affective Disorder It's wintertime, and you are gathered for the holidays with all of your family and friends. Everything seems like it should be perfect, yet you are feeling very distressed, lethargic and disconnected from everything and everyone around you. "Perhaps it is just the winter blues," you tell yourself as you delve into the holiday feast, aiming straight for the sugary fruitcake before collapsing from exhaustion. However, the depression and other symptoms that you feel continue to persist from the beginning of winter until the springtime, for years upon end without ceasing. Although you may be tempted to believe that you, like many millions of other Americans, are afflicted with a case of the winter blues, you are most likely suffering from a more severe form of seasonal depression known as Seasonal Affective Disorder, or SAD. This form of depression has been described as a form of a unipolar or bipolar mood disorder which, unlike other forms of depression, follows a strictly seasonal pattern. (5). During the winter, many of us suffer from "the winter blues", a less severe form of seasonal depression than SAD. Still others are sufferers have an already existent condition, such as pre-menstrual syndrome or depression, which is exacerbated by the coming of the winter. (2). In general, many people suffer from some form of sporadic depression during the wintertime. We may feel more tired and sad at times. We may even gain some weight or have trouble getting out of bed. Over 10 million people in America, however, may feel a more extreme form of these symptoms. They may constantly feel lethargic and depressed to an extent that social and work related activities are negatively affected. This more extreme form of the "winter blues" is SAD. Typical SAD symptoms include sugar cravings, lethargy, depression, an increase in body weight, and a greater need for sleep (1). Onset of these symptoms usually occurs in October or November, and the symptoms disappear in early spring. Frequentl y, people who suffer from SAD react strongly to variations in the amount of light in their surrounding environment. Most often, patients who suffer from SAD and live at more northern latitudes note that the more north they live, the more distinct and severe their SAD symptoms become. In addition, SAD patients note that their depressive symptoms increase in severity when the amount of light indoors decreases and the weather is cloudy.

Protect Our Environment Essay

Losing my future is not like losing an election or a few points on the stock market. I am here to speak for all generations to come. I am here to speak on behalf of the starving children around the world whose cries go unheard. I am here to speak for the countless animals dying across this planet because they have nowhere left to go. We cannot afford to be not heard. I am afraid to go out in the sun now because of the holes in the ozone. I am afraid to breathe the air because I don’t know what chemicals are in it. In my life, I have dreamt of seeing the great herds of wild animals, jungles and rainforests full of birds and butterfilies, but now I wonder if they will even exist for my children to see. All this is happening before our eyes and yet we act as if we have all the time we want and all the solutions. I’m only a child and I don’t have all the solutions, but I want you to realise, neither do you! * You don’t know how to fix the holes in our ozone layer. * You don’t know how to bring salmon back up a dead stream. * You don’t know how to bring back an animal now extinct. And you can’t bring back forests that once grew where there is now desert. If you don’t know how to fix it, please stop breaking it! Here, you may be delegates of your governments, business people, organisers, reporters or poiticians – but really you are mothers and fathers, brothers and sister, aunts and uncles – and all of you are somebody’s child. Ià ¢â‚¬â„¢m only a child yet I know we are all part of a family, five billion strong, in fact, 30 million species strong and we all share the same air, water and soil — borders and governments will never change that. I’m only a child yet I know we are all in this together and should act as one single world towards one single goal. Many people say there is a need to protect the environment, but do not really make any effort to do anything about it. Are you one of these people? What can we do to encourage people to take action to protect the environment? Most people are increasingly aware of the need to protect our environment. Despite this, not many of us are really taking steps to reduce our impact on the planet. In this essay, I will suggest some steps each of us can take and some ways to motivate others to do the same. Many environmental problems seem so big that only governments, local authorities or big companies can deal with them. One example is global warming. We need government action to reduce emissions from coal and oil burning power stations and to develop safer sources of power. These require tough regulations and huge investment. The loss of forests and other habitat is another problem. How can we as individuals stop the destruction of the Amazon or Indonesian rain forests? Yet another example is waste. When people live in cities, they may not be able store or recycle waste, so huge landfills or incinerators are needed. However, as consumers, we are the ones responsible for all these problems. First of all, we all need to consume less power. We need to turn off lights, replace inefficient bulbs with low-power ones, and not leave equipment on standby. Secondly, we need to control our surging populations. Each of us can make a decision regarding family size. This has a huge impact on the size of our cities and the need for food and more agricultural land. In addition, we need to consider eating less meat and more vegetables and fruit, in order to reduce the amount of land needed for meat. Generally, the main step we need to take is to live more simply. We need to reduce our consumption, recycle, and reuse. In conclusion, our choices, however small, do have a real impact. If each of us made took two or three simple steps to live more simply, imagine the positive effect on the planet!

Potential Medical Benefits of Embryonic Stem Cells

Today’s society has involved many scientific advances and beneficial research. Scientists all over the world have been doing recent studies on embryonic stem cells. Embryonic stem cells are the cells that aid the process of child growth while in the womb. These cells have a specific function to reproduce into any body part, such as a heart or major organ to hair or something not so major. Research shows that these cells have many potential medical benefits in the future. Embryonic stem cell research should continue to be pursued in society today. Embryonic stem cell research has led to medical benefits to aid in curing diseases and many cancer cases that have grown in today’s society. Tissues throughout the body have a specific single layer of cells that can regenerate daughter cells. These daughter cells, or embryonic cells, have the capabilities to regenerate and build tissues or organs. These cells can aid in a lifelong regeneration process for tissues throughout th e body. In vitro studies have shown that these cells can be placed in a specific area where there is large amounts of tissue damage due to injury or disease and completely rebuild this tissue into a completely new, fully functioning tissue. (Weissman, 2005, p. 1). However, people will argue the fact that embryonic stem cells have not been cleared to work in the human body. This is true that Weisman has only found it to work in mice and in genetically made organs, tissues, and muscle. Facts have shown thatShow MoreRelatedSupport of Embryonic Stem Cell Research Essay769 Words   |  4 PagesEmbryonic stem cell is one of the most controversial, widely discussed medical issues in the United States today. The medical use of stem cell raises difficult moral and political questions. To understand about embryonic stem cell. I thought we should discuss what embryonic stem cells are. According to Scientific American; June 2004, embryonic stem are derived from the portion of a very early sta ge embryo that would eventually give rise to an entire body. Because embryonic stem cells originate inRead MoreThe Debate Over Embryonic Stem Cells851 Words   |  4 Pagescured with embryonic stem cell therapy. Some researchers regard this as the greatest potential for the alleviation of human suffering since the advent of antibiotics† (White). However, not everybody agrees with this. While embryonic stem cells offer much hope for medical advancement because of their ability to grow into almost any kind of cell, the moral debate of the destruction of an embryo continues. Embryonic stem cells are taken directly from an embryo before the embryo s cells begin to developRead MoreThe Debate Concerning Embryonic Stem Cell Research Essay1406 Words   |  6 Pagesmorality of embryonic stem cell research. 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Therefore, the usage of embryonic cells outweighs the ethicalRead MorePersuasive Essay : Stem Cell Research1489 Words   |  6 PagesPersuasive Essay Stem Cell research and its funding have caused a lot of controversy throughout the past years. Stem cells are cells that are present in all living organisms. These cells have the potential to grow into any type of cell, including blood cells, nerves, muscles, and pancreatic cells. Stem cell research is essential because of the beneficial aspects it has to offer. Stem cells could potentially treat conditions such as Alzheimer s, Parkinson s, birth defects, strokes, Diabetes, cancerRead MoreThe Debate Over Embryonic Stem Cell Research852 Words   |  4 Pageshistory lesson. Medical advancements have brought technology closer to making that world a reality. Recent advancements in knowledge of stem cell research has already created the ability for doctors to print a functional organ just as easily as people can print a persuasive research essay. 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If the stem cells are donated out of free will or were going to be destroyed anyway, how can putting them to better use be controversial? Sure, a potential life must be destroyed to save a life, but only before one can tell that it is a human. Should the use of stem cells for medical research and use be regulated? These questions and more will be di scussed and pondered throughout this paper. A stem cell is defined as a cell that can changeRead MoreThe Benefits Of Embryonic Stem Cell Research1184 Words   |  5 Pagesâ€Å"Embryonic stem cell research will prolong life, improve life and give hope for life to millions of people.† This quote by Jim Ramstad is about the benefits of Embryonic Stem Cell Research. Stem cells give us many opportunities to find the mechanisms that help regulate embryonic development, organ maintenance, and cellular differentiation. (Ramalho-Santos and Willenbring 35-38). Embryonic stem cell research has been around for many years. 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