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Monday, June 11, 2018

Allergy

From Wikipedia, the free encyclopedia
Allergy
Hives2010.JPG
Hives are a common allergic symptom
Specialty Allergy and immunology
Symptoms Red eyes, itchy rash, runny nose, shortness of breath, swelling, sneezing[1]
Types Hay fever, food allergies, atopic dermatitis, allergic asthma, anaphylaxis[2]
Causes Genetic and environmental factors[3]
Diagnostic method Based on symptoms, skin prick test[4]
Differential diagnosis Food intolerances, food poisoning[5]
Prevention Early exposure to potential allergens[6]
Treatment Avoiding known allergens, medications, allergen immunotherapy[7]
Medication Steroids, antihistamines, epinephrine[8][7]
Frequency Common[9]

Allergies, also known as allergic diseases, are a number of conditions caused by hypersensitivity of the immune system to typically harmless substances in the environment.[10] These diseases include hay fever, food allergies, atopic dermatitis, allergic asthma, and anaphylaxis.[2] Symptoms may include red eyes, an itchy rash, sneezing, a runny nose, shortness of breath, or swelling.[1] Food intolerances and food poisoning are separate conditions.[5][4]

Common allergens include pollen and certain food.[10] Metals and other substances may also cause problems.[10] Food, insect stings, and medications are common causes of severe reactions.[3] Their development is due to both genetic and environmental factors.[3] The underlying mechanism involves immunoglobulin E antibodies (IgE), part of the body's immune system, binding to an allergen and then to a receptor on mast cells or basophils where it triggers the release of inflammatory chemicals such as histamine.[11] Diagnosis is typically based on a person's medical history.[4] Further testing of the skin or blood may be useful in certain cases.[4] Positive tests, however, may not mean there is a significant allergy to the substance in question.[12]

Early exposure to potential allergens may be protective.[6] Treatments for allergies include avoiding known allergens and the use of medications such as steroids and antihistamines.[7] In severe reactions injectable adrenaline (epinephrine) is recommended.[8] Allergen immunotherapy, which gradually exposes people to larger and larger amounts of allergen, is useful for some types of allergies such as hay fever and reactions to insect bites.[7] Its use in food allergies is unclear.[7]

Allergies are common.[9] In the developed world, about 20% of people are affected by allergic rhinitis,[13] about 6% of people have at least one food allergy,[4][6] and about 20% have atopic dermatitis at some point in time.[14] Depending on the country about 1–18% of people have asthma.[15][16] Anaphylaxis occurs in between 0.05–2% of people.[17] Rates of many allergic diseases appear to be increasing.[8][18] The word "allergy" was first used by Clemens von Pirquet in 1906.[3]

Signs and symptoms

Many allergens such as dust or pollen are airborne particles. In these cases, symptoms arise in areas in contact with air, such as eyes, nose, and lungs. For instance, allergic rhinitis, also known as hay fever, causes irritation of the nose, sneezing, itching, and redness of the eyes.[19] Inhaled allergens can also lead to increased production of mucus in the lungs, shortness of breath, coughing, and wheezing.[20]

Aside from these ambient allergens, allergic reactions can result from foods, insect stings, and reactions to medications like aspirin and antibiotics such as penicillin. Symptoms of food allergy include abdominal pain, bloating, vomiting, diarrhea, itchy skin, and swelling of the skin during hives. Food allergies rarely cause respiratory (asthmatic) reactions, or rhinitis.[21] Insect stings, food, antibiotics, and certain medicines may produce a systemic allergic response that is also called anaphylaxis; multiple organ systems can be affected, including the digestive system, the respiratory system, and the circulatory system.[22][23][24] Depending on the rate of severity, anaphylaxis can include skin reactions, bronchoconstriction, swelling, low blood pressure, coma, and death. This type of reaction can be triggered suddenly, or the onset can be delayed. The nature of anaphylaxis is such that the reaction can seem to be subsiding, but may recur throughout a period of time.[24]

Skin

Substances that come into contact with the skin, such as latex, are also common causes of allergic reactions, known as contact dermatitis or eczema.[25] Skin allergies frequently cause rashes, or swelling and inflammation within the skin, in what is known as a "weal and flare" reaction characteristic of hives and angioedema.[26]

With insect stings a large local reaction may occur (an area of skin redness greater than 10 cm in size).[27] It can last one to two days.[27] This reaction may also occur after immunotherapy.[28]

Cause

Risk factors for allergy can be placed in two general categories, namely host and environmental factors.[29] Host factors include heredity, sex, race, and age, with heredity being by far the most significant. However, there have been recent increases in the incidence of allergic disorders that cannot be explained by genetic factors alone. Four major environmental candidates are alterations in exposure to infectious diseases during early childhood, environmental pollution, allergen levels, and dietary changes.[30]

Foods

A wide variety of foods can cause allergic reactions, but 90% of allergic responses to foods are caused by cow's milk, soy, eggs, wheat, peanuts, tree nuts, fish, and shellfish.[31] Other food allergies, affecting less than 1 person per 10,000 population, may be considered "rare".[32] The use of hydrolysed milk baby formula versus standard milk baby formula does not appear to change the risk.[33]

The most common food allergy in the US population is a sensitivity to crustacea.[32] Although peanut allergies are notorious for their severity, peanut allergies are not the most common food allergy in adults or children. Severe or life-threatening reactions may be triggered by other allergens, and are more common when combined with asthma.[31]

Rates of allergies differ between adults and children. Peanut allergies can sometimes be outgrown by children. Egg allergies affect one to two percent of children but are outgrown by about two-thirds of children by the age of 5.[34] The sensitivity is usually to proteins in the white, rather than the yolk.[35]

Milk-protein allergies are most common in children.[36] Approximately 60% of milk-protein reactions are immunoglobulin E-mediated, with the remaining usually attributable to inflammation of the colon.[37] Some people are unable to tolerate milk from goats or sheep as well as from cows, and many are also unable to tolerate dairy products such as cheese. Roughly 10% of children with a milk allergy will have a reaction to beef. Beef contains a small amount of protein that is present in cow's milk.[38] Lactose intolerance, a common reaction to milk, is not a form of allergy at all, but rather due to the absence of an enzyme in the digestive tract.

Those with tree nut allergies may be allergic to one or to many tree nuts, including pecans, pistachios, pine nuts, and walnuts.[35] Also seeds, including sesame seeds and poppy seeds, contain oils in which protein is present, which may elicit an allergic reaction.[35]

Allergens can be transferred from one food to another through genetic engineering; however genetic modification can also remove allergens. Little research has been done on the natural variation of allergen concentrations in the unmodified crops.[39][40]

Latex

Latex can trigger an IgE-mediated cutaneous, respiratory, and systemic reaction. The prevalence of latex allergy in the general population is believed to be less than one percent. In a hospital study, 1 in 800 surgical patients (0.125 percent) reported latex sensitivity, although the sensitivity among healthcare workers is higher, between seven and ten percent. Researchers attribute this higher level to the exposure of healthcare workers to areas with significant airborne latex allergens, such as operating rooms, intensive-care units, and dental suites. These latex-rich environments may sensitize healthcare workers who regularly inhale allergenic proteins.[41]

The most prevalent response to latex is an allergic contact dermatitis, a delayed hypersensitive reaction appearing as dry, crusted lesions. This reaction usually lasts 48–96 hours. Sweating or rubbing the area under the glove aggravates the lesions, possibly leading to ulcerations.[41]  Anaphylactic reactions occur most often in sensitive patients who have been exposed to a surgeon's latex gloves during abdominal surgery, but other mucosal exposures, such as dental procedures, can also produce systemic reactions.[41]

Latex and banana sensitivity may cross-react. Furthermore, those with latex allergy may also have sensitivities to avocado, kiwifruit, and chestnut.[42] These people often have perioral itching and local urticaria. Only occasionally have these food-induced allergies induced systemic responses. Researchers suspect that the cross-reactivity of latex with banana, avocado, kiwifruit, and chestnut occurs because latex proteins are structurally homologous with some other plant proteins.[41]

Medications

About 10% of people report that they are allergic to penicillin; however, 90% turn out not to be.[43] Serious allergies only occur in about 0.03%.[43]

Toxins interacting with proteins

Another non-food protein reaction, urushiol-induced contact dermatitis, originates after contact with poison ivy, eastern poison oak, western poison oak, or poison sumac. Urushiol, which is not itself a protein, acts as a hapten and chemically reacts with, binds to, and changes the shape of integral membrane proteins on exposed skin cells. The immune system does not recognize the affected cells as normal parts of the body, causing a T-cell-mediated immune response.[44] Of these poisonous plants, sumac is the most virulent.[45] The resulting dermatological response to the reaction between urushiol and membrane proteins includes redness, swelling, papules, vesicles, blisters, and streaking.[46]

Estimates vary on the percentage of the population that will have an immune system response. Approximately 25 percent of the population will have a strong allergic response to urushiol. In general, approximately 80 percent to 90 percent of adults will develop a rash if they are exposed to .0050 milligrams (7.7×10−5 gr) of purified urushiol, but some people are so sensitive that it takes only a molecular trace on the skin to initiate an allergic reaction.[47]

Genetics

Allergic diseases are strongly familial: identical twins are likely to have the same allergic diseases about 70% of the time; the same allergy occurs about 40% of the time in non-identical twins.[48] Allergic parents are more likely to have allergic children,[49] and those children's allergies are likely to be more severe than those in children of non-allergic parents. Some allergies, however, are not consistent along genealogies; parents who are allergic to peanuts may have children who are allergic to ragweed. It seems that the likelihood of developing allergies is inherited and related to an irregularity in the immune system, but the specific allergen is not.[49]

The risk of allergic sensitization and the development of allergies varies with age, with young children most at risk.[50] Several studies have shown that IgE levels are highest in childhood and fall rapidly between the ages of 10 and 30 years.[50] The peak prevalence of hay fever is highest in children and young adults and the incidence of asthma is highest in children under 10.[51]

Overall, boys have a higher risk of developing allergies than girls,[49] although for some diseases, namely asthma in young adults, females are more likely to be affected.[52] These differences between the sexes tend to decrease in adulthood.[49]

Ethnicity may play a role in some allergies; however, racial factors have been difficult to separate from environmental influences and changes due to migration.[49] It has been suggested that different genetic loci are responsible for asthma, to be specific, in people of European, Hispanic, Asian, and African origins.[53]

Hygiene hypothesis

Allergic diseases are caused by inappropriate immunological responses to harmless antigens driven by a TH2-mediated immune response. Many bacteria and viruses elicit a TH1-mediated immune response, which down-regulates TH2 responses. The first proposed mechanism of action of the hygiene hypothesis was that insufficient stimulation of the TH1 arm of the immune system leads to an overactive TH2 arm, which in turn leads to allergic disease.[54] In other words, individuals living in too sterile an environment are not exposed to enough pathogens to keep the immune system busy. Since our bodies evolved to deal with a certain level of such pathogens, when they are not exposed to this level, the immune system will attack harmless antigens and thus normally benign microbial objects—like pollen—will trigger an immune response.[55]

The hygiene hypothesis was developed to explain the observation that hay fever and eczema, both allergic diseases, were less common in children from larger families, which were, it is presumed, exposed to more infectious agents through their siblings, than in children from families with only one child. The hygiene hypothesis has been extensively investigated by immunologists and epidemiologists and has become an important theoretical framework for the study of allergic disorders. It is used to explain the increase in allergic diseases that have been seen since industrialization, and the higher incidence of allergic diseases in more developed countries. The hygiene hypothesis has now expanded to include exposure to symbiotic bacteria and parasites as important modulators of immune system development, along with infectious agents.

Epidemiological data support the hygiene hypothesis. Studies have shown that various immunological and autoimmune diseases are much less common in the developing world than the industrialized world and that immigrants to the industrialized world from the developing world increasingly develop immunological disorders in relation to the length of time since arrival in the industrialized world.[56] Longitudinal studies in the third world demonstrate an increase in immunological disorders as a country grows more affluent and, it is presumed, cleaner.[57] The use of antibiotics in the first year of life has been linked to asthma and other allergic diseases.[58] The use of antibacterial cleaning products has also been associated with higher incidence of asthma, as has birth by Caesarean section rather than vaginal birth.[59][60]

Stress

Chronic stress can aggravate allergic conditions. This has been attributed to a T helper 2 (TH2)-predominant response driven by suppression of interleukin 12 by both the autonomic nervous system and the hypothalamic–pituitary–adrenal axis. Stress management in highly susceptible individuals may improve symptoms.[61]

Other environmental factors

International differences have been associated with the number of individuals within a population have allergy. Allergic diseases are more common in industrialized countries than in countries that are more traditional or agricultural, and there is a higher rate of allergic disease in urban populations versus rural populations, although these differences are becoming less defined.[62]

Alterations in exposure to microorganisms is another plausible explanation, at present, for the increase in atopic allergy.[30] Endotoxin exposure reduces release of inflammatory cytokines such as TNF-α, IFNγ, interleukin-10, and interleukin-12 from white blood cells (leukocytes) that circulate in the blood.[63] Certain microbe-sensing proteins, known as Toll-like receptors, found on the surface of cells in the body are also thought to be involved in these processes.[64]

Gutworms and similar parasites are present in untreated drinking water in developing countries, and were present in the water of developed countries until the routine chlorination and purification of drinking water supplies.[65] Recent research has shown that some common parasites, such as intestinal worms (e.g., hookworms), secrete chemicals into the gut wall (and, hence, the bloodstream) that suppress the immune system and prevent the body from attacking the parasite.[66] This gives rise to a new slant on the hygiene hypothesis theory—that co-evolution of humans and parasites has led to an immune system that functions correctly only in the presence of the parasites. Without them, the immune system becomes unbalanced and oversensitive.[67] In particular, research suggests that allergies may coincide with the delayed establishment of gut flora in infants.[68] However, the research to support this theory is conflicting, with some studies performed in China and Ethiopia showing an increase in allergy in people infected with intestinal worms.[62] Clinical trials have been initiated to test the effectiveness of certain worms in treating some allergies.[69] It may be that the term 'parasite' could turn out to be inappropriate, and in fact a hitherto unsuspected symbiosis is at work.[69] For more information on this topic, see Helminthic therapy.

Pathophysiology


A summary diagram that explains how allergy develops.

Tissues affected in allergic inflammation

Acute response


Degranulation process in allergy. Second exposure to allergen. 1 – antigen; 2 – IgE antibody; 3 – FcεRI receptor; 4 – preformed mediators (histamine, proteases, chemokines, heparin); 5granules; 6mast cell; 7 – newly formed mediators (prostaglandins, leukotrienes, thromboxanes, PAF)

In the early stages of allergy, a type I hypersensitivity reaction against an allergen encountered for the first time and presented by a professional antigen-presenting cell causes a response in a type of immune cell called a TH2 lymphocyte; a subset of T cells that produce a cytokine called interleukin-4 (IL-4). These TH2 cells interact with other lymphocytes called B cells, whose role is production of antibodies. Coupled with signals provided by IL-4, this interaction stimulates the B cell to begin production of a large amount of a particular type of antibody known as IgE. Secreted IgE circulates in the blood and binds to an IgE-specific receptor (a kind of Fc receptor called FcεRI) on the surface of other kinds of immune cells called mast cells and basophils, which are both involved in the acute inflammatory response. The IgE-coated cells, at this stage, are sensitized to the allergen.[30]

If later exposure to the same allergen occurs, the allergen can bind to the IgE molecules held on the surface of the mast cells or basophils. Cross-linking of the IgE and Fc receptors occurs when more than one IgE-receptor complex interacts with the same allergenic molecule, and activates the sensitized cell. Activated mast cells and basophils undergo a process called degranulation, during which they release histamine and other inflammatory chemical mediators (cytokines, interleukins, leukotrienes, and prostaglandins) from their granules into the surrounding tissue causing several systemic effects, such as vasodilation, mucous secretion, nerve stimulation, and smooth muscle contraction. This results in rhinorrhea, itchiness, dyspnea, and anaphylaxis. Depending on the individual, allergen, and mode of introduction, the symptoms can be system-wide (classical anaphylaxis), or localized to particular body systems; asthma is localized to the respiratory system and eczema is localized to the dermis.[30]

Late-phase response

After the chemical mediators of the acute response subside, late-phase responses can often occur. This is due to the migration of other leukocytes such as neutrophils, lymphocytes, eosinophils and macrophages to the initial site. The reaction is usually seen 2–24 hours after the original reaction.[70] Cytokines from mast cells may play a role in the persistence of long-term effects. Late-phase responses seen in asthma are slightly different from those seen in other allergic responses, although they are still caused by release of mediators from eosinophils and are still dependent on activity of TH2 cells.[71]

Allergic contact dermatitis

Although allergic contact dermatitis is termed an "allergic" reaction (which usually refers to type I hypersensitivity), its pathophysiology actually involves a reaction that more correctly corresponds to a type IV hypersensitivity reaction.[72] In type IV hypersensitivity, there is activation of certain types of T cells (CD8+) that destroy target cells on contact, as well as activated macrophages that produce hydrolytic enzymes.

Diagnosis


An allergy testing machine being operated in the diagnostic immunology lab

Effective management of allergic diseases relies on the ability to make an accurate diagnosis.[73] Allergy testing can help confirm or rule out allergies.[74][75] Correct diagnosis, counseling, and avoidance advice based on valid allergy test results reduces the incidence of symptoms and need for medications, and improves quality of life.[74] To assess the presence of allergen-specific IgE antibodies, two different methods can be used: a skin prick test, or an allergy blood test. Both methods are recommended, and they have similar diagnostic value.[75][76]

Skin prick tests and blood tests are equally cost-effective, and health economic evidence shows that both tests were cost-effective compared with no test.[74] Also, early and more accurate diagnoses save cost due to reduced consultations, referrals to secondary care, misdiagnosis, and emergency admissions.[77]

Allergy undergoes dynamic changes over time. Regular allergy testing of relevant allergens provides information on if and how patient management can be changed, in order to improve health and quality of life. Annual testing is often the practice for determining whether allergy to milk, egg, soy, and wheat have been outgrown, and the testing interval is extended to 2–3 years for allergy to peanut, tree nuts, fish, and crustacean shellfish.[75] Results of follow-up testing can guide decision-making regarding whether and when it is safe to introduce or re-introduce allergenic food into the diet.[78]

Skin prick testing


Skin testing on arm

Skin testing on back

Skin testing is also known as "puncture testing" and "prick testing" due to the series of tiny punctures or pricks made into the patient's skin. Small amounts of suspected allergens and/or their extracts (e.g., pollen, grass, mite proteins, peanut extract) are introduced to sites on the skin marked with pen or dye (the ink/dye should be carefully selected, lest it cause an allergic response itself). A small plastic or metal device is used to puncture or prick the skin. Sometimes, the allergens are injected "intradermally" into the patient's skin, with a needle and syringe. Common areas for testing include the inside forearm and the back.

If the patient is allergic to the substance, then a visible inflammatory reaction will usually occur within 30 minutes. This response will range from slight reddening of the skin to a full-blown hive (called "wheal and flare") in more sensitive patients similar to a mosquito bite. Interpretation of the results of the skin prick test is normally done by allergists on a scale of severity, with +/− meaning borderline reactivity, and 4+ being a large reaction. Increasingly, allergists are measuring and recording the diameter of the wheal and flare reaction. Interpretation by well-trained allergists is often guided by relevant literature.[79] Some patients may believe they have determined their own allergic sensitivity from observation, but a skin test has been shown to be much better than patient observation to detect allergy.[80]

If a serious life-threatening anaphylactic reaction has brought a patient in for evaluation, some allergists will prefer an initial blood test prior to performing the skin prick test. Skin tests may not be an option if the patient has widespread skin disease, or has taken antihistamines in the last several days.

Patch testing



Patch testing is a method used to determine if a specific substance causes allergic inflammation of the skin. It tests for delayed reactions. It is used to help ascertain the cause of skin contact allergy, or contact dermatitis. Adhesive patches, usually treated with a number of common allergic chemicals or skin sensitizers, are applied to the back. The skin is then examined for possible local reactions at least twice, usually at 48 hours after application of the patch, and again two or three days later.

Blood testing

An allergy blood test is quick and simple, and can be ordered by a licensed health care provider (e.g., an allergy specialist), GP, or PED. Unlike skin-prick testing, a blood test can be performed irrespective of age, skin condition, medication, symptom, disease activity, and pregnancy. Adults and children of any age can take an allergy blood test. For babies and very young children, a single needle stick for allergy blood testing is often more gentle than several skin tests.

An allergy blood test is available through most laboratories. A sample of the patient's blood is sent to a laboratory for analysis, and the results are sent back a few days later. Multiple allergens can be detected with a single blood sample. Allergy blood tests are very safe, since the person is not exposed to any allergens during the testing procedure.

The test measures the concentration of specific IgE antibodies in the blood. Quantitative IgE test results increase the possibility of ranking how different substances may affect symptoms. A rule of thumb is that the higher the IgE antibody value, the greater the likelihood of symptoms. Allergens found at low levels that today do not result in symptoms can nevertheless help predict future symptom development. The quantitative allergy blood result can help determine what a patient is allergic to, help predict and follow the disease development, estimate the risk of a severe reaction, and explain cross-reactivity.[81][82]

A low total IgE level is not adequate to rule out sensitization to commonly inhaled allergens.[83] Statistical methods, such as ROC curves, predictive value calculations, and likelihood ratios have been used to examine the relationship of various testing methods to each other. These methods have shown that patients with a high total IgE have a high probability of allergic sensitization, but further investigation with allergy tests for specific IgE antibodies for a carefully chosen of allergens is often warranted.

Laboratory methods to measure specific IgE antibodies for allergy testing include enzyme-linked immunosorbent assay (ELISA, or EIA),[84] radioallergosorbent test (RAST)[84] and fluorescent enzyme immunoassay (FEIA).[85]

Other testing

Challenge testing: Challenge testing is when small amounts of a suspected allergen are introduced to the body orally, through inhalation, or via other routes. Except for testing food and medication allergies, challenges are rarely performed. When this type of testing is chosen, it must be closely supervised by an allergist.

Elimination/challenge tests: This testing method is used most often with foods or medicines. A patient with a suspected allergen is instructed to modify his diet to totally avoid that allergen for a set time. If the patient experiences significant improvement, he may then be "challenged" by reintroducing the allergen, to see if symptoms are reproduced.

Unreliable tests: There are other types of allergy testing methods that are unreliable, including applied kinesiology (allergy testing through muscle relaxation), cytotoxicity testing, urine autoinjection, skin titration (Rinkel method), and provocative and neutralization (subcutaneous) testing or sublingual provocation.[86]

Differential diagnosis

Before a diagnosis of allergic disease can be confirmed, other possible causes of the presenting symptoms should be considered.[87] Vasomotor rhinitis, for example, is one of many maladies that shares symptoms with allergic rhinitis, underscoring the need for professional differential diagnosis.[88] Once a diagnosis of asthma, rhinitis, anaphylaxis, or other allergic disease has been made, there are several methods for discovering the causative agent of that allergy.

Prevention

Some foods during pregnancy has been linked to allergies in the child. Vegetable oil, nuts and fast food may increase the risk while fruits, vegetables and fish may decrease it.[89] Another review found no effect of eating fish during pregnancy on allergy risk.[90] Fish oil supplementation during pregnancy and breast feeding is associated with a lower risk.[91]
Probiotic supplements taken during pregnancy or infancy may help to prevent atopic dermatitis.[92]

Management

Management of allergies typically involves avoiding what triggers the allergy and medications to improve the symptoms.[7] Allergen immunotherapy may be useful for some types of allergies.[7]

Medication

Several medications may be used to block the action of allergic mediators, or to prevent activation of cells and degranulation processes. These include antihistamines, glucocorticoids, epinephrine (adrenaline), mast cell stabilizers, and antileukotriene agents are common treatments of allergic diseases.[93] Anti-cholinergics, decongestants, and other compounds thought to impair eosinophil chemotaxis, are also commonly used. Though rare, the severity of anaphylaxis often requires epinephrine injection, and where medical care is unavailable, a device known as an epinephrine autoinjector may be used.[24]

Immunotherapy


Anti-allergy immunotherapy

Allergen immunotherapy is useful for environmental allergies, allergies to insect bites, and asthma.[7][94] Its benefit for food allergies is unclear and thus not recommended.[7] Immunotherapy involves exposing people to larger and larger amounts of allergen in an effort to change the immune system's response.[7]

Meta-analyses have found that injections of allergens under the skin is effective in the treatment in allergic rhinitis in children[95][96] and in asthma.[94] The benefits may last for years after treatment is stopped.[97] It is generally safe and effective for allergic rhinitis and conjunctivitis, allergic forms of asthma, and stinging insects.[98]

The evidence also supports the use of sublingual immunotherapy for rhinitis and asthma but it is less strong.[97] For seasonal allergies the benefit is small.[99] In this form the allergen is given under the tongue and people often prefer it to injections.[97] Immunotherapy is not recommended as a stand-alone treatment for asthma.[97]

Alternative medicine

An experimental treatment, enzyme potentiated desensitization (EPD), has been tried for decades but is not generally accepted as effective.[100] EPD uses dilutions of allergen and an enzyme, beta-glucuronidase, to which T-regulatory lymphocytes are supposed to respond by favoring desensitization, or down-regulation, rather than sensitization. EPD has also been tried for the treatment of autoimmune diseases but evidence does not show effectiveness.[100]

A review found no effectiveness of homeopathic treatments and no difference compared with placebo. The authors concluded that, based on rigorous clinical trials of all types of homeopathy for childhood and adolescence ailments, there is no convincing evidence that supports the use of homeopathic treatments.[101]

According to the NCCIH, the evidence is relatively strong that saline nasal irrigation and butterbur are effective, when compared to other alternative medicine treatments, for which the scientific evidence is weak, negative, or nonexistent, such as honey, acupuncture, omega 3's, probiotics, astragalus, capsaicin, grape seed extract, Pycnogenol, quercetin, spirulina, stinging nettle, tinospora or guduchi. [102][103]

Epidemiology

The allergic diseases—hay fever and asthma—have increased in the Western world over the past 2–3 decades.[104] Increases in allergic asthma and other atopic disorders in industrialized nations, it is estimated, began in the 1960s and 1970s, with further increases occurring during the 1980s and 1990s,[105] although some suggest that a steady rise in sensitization has been occurring since the 1920s.[106] The number of new cases per year of atopy in developing countries has, in general, remained much lower.[105]

Allergic conditions: Statistics and epidemiology
Allergy type United States United Kingdom[107]
Allergic rhinitis 35.9 million[108] (about 11% of the population[109]) 3.3 million (about 5.5% of the population[110])
Asthma 10 million have allergic asthma (about 3% of the population). The prevalence of asthma increased 75% from 1980 to 1994. Asthma prevalence is 39% higher in African Americans than in Europeans.[111] 5.7 million (about 9.4%). In six- and seven-year-olds asthma increased from 18.4% to 20.9% over five years, during the same time the rate decreased from 31% to 24.7% in 13- to 14-year-olds.
Atopic eczema About 9% of the population. Between 1960 and 1990 prevalence has increased from 3% to 10% in children.[112] 5.8 million (about 1% severe).
Anaphylaxis At least 40 deaths per year due to insect venom. About 400 deaths due to penicillin anaphylaxis. About 220 cases of anaphylaxis and 3 deaths per year are due to latex allergy.[113] An estimated 150 people die annually from anaphylaxis due to food allergy.[114] Between 1999 and 2006, 48 deaths occurred in people ranging from five months to 85 years old.
Insect venom Around 15% of adults have mild, localized allergic reactions. Systemic reactions occur in 3% of adults and less than 1% of children.[115] Unknown
Drug allergies Anaphylactic reactions to penicillin cause 400 deaths per year. Unknown
Food allergies About 6% of US children under age 3 and 3.5–4% of the overall US population.[citation needed] Peanut and/or tree nut (e.g. walnut) allergy affects about three million Americans, or 1.1% of the population.[114] 5–7% of infants and 1–2% of adults. A 117.3% increase in peanut allergies was observed from 2001 to 2005, an estimated 25,700 people in England are affected.
Multiple allergies (Asthma, eczema and allergic rhinitis together) Unknown 2.3 million (about 3.7%), prevalence has increased by 48.9% between 2001 and 2005.[116]

Changing frequency

Although genetic factors govern susceptibility to atopic disease, increases in atopy have occurred within too short a time frame to be explained by a genetic change in the population, thus pointing to environmental or lifestyle changes.[105] Several hypotheses have been identified to explain this increased rate; increased exposure to perennial allergens due to housing changes and increasing time spent indoors, and changes in cleanliness or hygiene that have resulted in the decreased activation of a common immune control mechanism, coupled with dietary changes, obesity and decline in physical exercise.[104] The hygiene hypothesis maintains[117] that high living standards and hygienic conditions exposes children to fewer infections. It is thought that reduced bacterial and viral infections early in life direct the maturing immune system away from TH1 type responses, leading to unrestrained TH2 responses that allow for an increase in allergy.[67][118]

Changes in rates and types of infection alone however, have been unable to explain the observed increase in allergic disease, and recent evidence has focused attention on the importance of the gastrointestinal microbial environment. Evidence has shown that exposure to food and fecal-oral pathogens, such as hepatitis A, Toxoplasma gondii, and Helicobacter pylori (which also tend to be more prevalent in developing countries), can reduce the overall risk of atopy by more than 60%,[119] and an increased rate of parasitic infections has been associated with a decreased prevalence of asthma.[120] It is speculated that these infections exert their effect by critically altering TH1/TH2 regulation.[121] Important elements of newer hygiene hypotheses also include exposure to endotoxins, exposure to pets and growing up on a farm.[121]

History

The concept of "allergy" was originally introduced in 1906 by the Viennese pediatrician Clemens von Pirquet, after he noted that some of his patients were hypersensitive to normally innocuous entities such as dust, pollen, or certain foods.[122] Pirquet called this phenomenon "allergy" from the Ancient Greek words ἄλλος allos meaning "other" and ἔργον ergon meaning "work".[123]

All forms of hypersensitivity used to be classified as allergies, and all were thought to be caused by an improper activation of the immune system. Later, it became clear that several different disease mechanisms were implicated, with the common link to a disordered activation of the immune system. In 1963, a new classification scheme was designed by Philip Gell and Robin Coombs that described four types of hypersensitivity reactions, known as Type I to Type IV hypersensitivity.[124] With this new classification, the word allergy, sometimes clarified as a true allergy, was restricted to type I hypersensitivities (also called immediate hypersensitivity), which are characterized as rapidly developing reactions involving IgE antibodies.[125]

A major breakthrough in understanding the mechanisms of allergy was the discovery of the antibody class labeled immunoglobulin E (IgE). IgE was simultaneously discovered in 1966–67 by two independent groups:[126] Ishizaka's team at the Children's Asthma Research Institute and Hospital in Denver, Colorado,[127] and by Gunnar Johansson and Hans Bennich in Uppsala, Sweden.[128] Their joint paper was published in April 1969.[129]

Diagnosis

Radiometric assays include the radioallergosorbent test (RAST test) method, which uses IgE-binding (anti-IgE) antibodies labeled with radioactive isotopes for quantifying the levels of IgE antibody in the blood.[130] Other newer methods use colorimetric or fluorescence-labeled technology in the place of radioactive isotopes.[citation needed]

The RAST methodology was invented and marketed in 1974 by Pharmacia Diagnostics AB, Uppsala, Sweden, and the acronym RAST is actually a brand name. In 1989, Pharmacia Diagnostics AB replaced it with a superior test named the ImmunoCAP Specific IgE blood test, which uses the newer fluorescence-labeled technology.[citation needed]

American College of Allergy Asthma and Immunology (ACAAI) and the American Academy of Allergy Asthma and Immunology (AAAAI) issued the Joint Task Force Report "Pearls and pitfalls of allergy diagnostic testing" in 2008, and is firm in its statement that the term RAST is now obsolete:
The term RAST became a colloquialism for all varieties of (in vitro allergy) tests. This is unfortunate because it is well recognized that there are well-performing tests and some that do not perform so well, yet they are all called RASTs, making it difficult to distinguish which is which. For these reasons, it is now recommended that use of RAST as a generic descriptor of these tests be abandoned.[131]
The new version, the ImmunoCAP Specific IgE blood test, is the only specific IgE assay to receive FDA approval to quantitatively report to its detection limit of 0.1kU/l.[citation needed]

Medical specialty

An allergist is a physician specially trained to manage and treat allergies, asthma and the other allergic diseases. In the United States physicians holding certification by the American Board of Allergy and Immunology (ABAI) have successfully completed an accredited educational program and evaluation process, including a proctored examination to demonstrate knowledge, skills, and experience in patient care in allergy and immunology.[132] Becoming an allergist/immunologist requires completion of at least nine years of training. After completing medical school and graduating with a medical degree, a physician will undergo three years of training in internal medicine (to become an internist) or pediatrics (to become a pediatrician). Once physicians have finished training in one of these specialties, they must pass the exam of either the American Board of Pediatrics (ABP), the American Osteopathic Board of Pediatrics (AOBP), the American Board of Internal Medicine (ABIM), or the American Osteopathic Board of Internal Medicine (AOBIM). Internists or pediatricians wishing to focus on the sub-specialty of allergy-immunology then complete at least an additional two years of study, called a fellowship, in an allergy/immunology training program. Allergist/immunologists listed as ABAI-certified have successfully passed the certifying examination of the ABAI following their fellowship.[133]

In the United Kingdom, allergy is a subspecialty of general medicine or pediatrics. After obtaining postgraduate exams (MRCP or MRCPCH), a doctor works for several years as a specialist registrar before qualifying for the General Medical Council specialist register. Allergy services may also be delivered by immunologists. A 2003 Royal College of Physicians report presented a case for improvement of what were felt to be inadequate allergy services in the UK.[134] In 2006, the House of Lords convened a subcommittee. It concluded likewise in 2007 that allergy services were insufficient to deal with what the Lords referred to as an "allergy epidemic" and its social cost; it made several recommendations.[135]

Research

Low-allergen foods are being developed, as are improvements in skin prick test predictions; evaluation of the atopy patch test; in wasp sting outcomes predictions and a rapidly disintegrating epinephrine tablet, and anti-IL-5 for eosinophilic diseases.[136]

Aerobiology is the study of the biological particles passively dispersed through the air. One aim is the prevention of allergies due to pollen.[137][138]

Did Life On Earth Actually Originate On Mars?

Jun 10, 2018



, I cover over-the-
horizon technology, aerospace and astronomy. 
Opinions expressed by Forbes Contributors are their own.

With last week’s news that NASA’s Mars Curiosity rover detected "tough" organic molecules in 3-billion-year-old sedimentary rocks within five centimeters of the surface, at least one prominent planetary scientist thinks that the debate over whether Mars first seeded Earth with life or vice-versa will only intensify.

Credits: NASA/JPL-Caltech/MSSS
 
This low-angle self-portrait of NASA's Curiosity Mars rover shows the vehicle at the site from which it reached down to drill into a rock target called "Buckskin" on lower Mount Sharp.

The findings appeared in last week’s issue of the journal Science along with a second paper which noted that Curiosity has also detected seasonal variations in minuscule amounts of Mars’ atmospheric methane.

But the $64,000 question remains: if life arose on Mars did it do so independently? Or did one planet seed the other through the meteoritic exchange of organics or even biota? This is the ultimate conundrum, Cornell University planetary scientist Jonathan Lunine, told me.


For as some astrobiologists have long argued, if we find evidence that life arose independently on Mars --- only the next planet out, then it’s only logical to conclude that life in the cosmos is very common indeed.

Curiosity struck organic gold in Gale Crater because it was once a lake environment, where organics would have been concentrated and preserved in sediments,” Lunine told me.

NASA reports that some of the molecules identified include thiophenes, benzene, toluene, and small carbon chains, such as propane or butene.

The sulfur that is dominant in these organics stabilizes them, greatly enhancing the possibility that they would survive in the soil for billions of years,” Lunine told me.

And given the evidence for habitable environments that may have lasted for hundreds of millions of years, life may have begun on Mars, Lunine says. But the exchange of microbes with Earth through large impacts, early in Mars’ history, might have cross-contaminated the two planets, he says.

But did life on our two planets actually first originate on Mars?

“This is the dilemma,” said Lunine. “Mars and Earth are close enough to have exchanged lots of material over the age of the solar system.”

But as I (Bruce) noted here previously, some researchers think that both ultraviolet radiation from the young Sun and galactic cosmic rays would have likely destroyed microbial life in the unprotected vacuum of space. And even if microbial life survived the journey to Earth, it’s doubtful it would have survived the trip through Earth’s atmosphere and then adapted to its new home.

Even so, Lunine counters that it’s too soon to say whether or not biota were shared. And even if we find life, these arguments will persist unless we find a living cell. Although he notes that is very unlikely, he says it would be required for researchers to be able to study the biochemistry of putative Martian life.

This is why I am keenly interested in Saturn’s moon of Enceladus; it’s far enough away that interplanetary transfer of any such ancient life into the inner solar system would have been much less likely, says Lunine.

Although NASA says that while Curiosity has not determined the source of the organic molecules, data collected by the rover reveals that Gale Crater once held all the ingredients needed for life.

What are we missing in our current search for ancient and/or extant life on Mars?

Measuring the isotopic ratio of carbon in the gaseous methane—a measurement that requires great sensitivity---would help to constrain whether that methane is produced by water reacting with carbon dioxide and rock or by biology, says Lunine.

As for future missions?

NASA’s Mars 2020 rover which should land on Mars in 2021, says Lunine, has an instrument payload that can detect organic compounds and look for chemical and imaging indications of life on millimeter scales. And the European Space Agency’s (ESA) ExoMars program includes ongoing orbital measurements to help map Mars’ methane, he says. The ExoMars rover will also look for life in samples that will be recovered from six-foot drills.

“This will be an excellent follow-on to Curiosity,” said Lunine.

Credit: NASA/JPL-Caltech/MSSS

The interior of Gale Crater from Vera Rubin Ridge, as seen by Curiosity’s mastcam.

As for what Gale Crater’s ancient lakeshore might have looked like?

Some 3.1 to 3.billion years ago; Lunine says the area would have been filled with liquid water, with streams feeding the lake caldera from the surrounding region. Mars would have had a bluer sky and a thicker atmosphere , but by how much is still under debate, he says. But even in Mars’ astrobiological heyday, he notes Gale Crater would hardly evoke images of a “Caribbean vacay.”

Even so, the discovery of near-surface complex organics that survived over billion-year timescales is “stunning,” Mark Lemmon, atmospheric scientist at Texas A&M University in College Station and a member of the Curiosity science team, told me.

“I imagine most organics wouldn't have [survived], so the implication is that there could have been much more,” Lemmon told me.

Follow Bruce on Facebook, Twitter and Google +. And like like 'Distant Wanderers' exoplanet Facebook page.

Protein folding

From Wikipedia, the free encyclopedia


Protein before and after folding.

Results of protein folding.
Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil.[1] Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three dimensional structure. Folding begins to occur even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure (Anfinsen's dogma).[2] The energy landscape describes the folding pathways in which the unfolded protein is able to assume its native state.

The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded,[3] so that protein dynamics is important. Failure to fold into native structure generally produces inactive proteins, but in some instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins.[4] Many allergies are caused by incorrect folding of some proteins, because the immune system does not produce antibodies for certain protein structures.[5]

Denaturation of proteins is a process of transition from the folded to the unfolded state.

Process of protein folding

Primary structure

The primary structure of a protein, its linear amino-acid sequence, determines its native conformation.[6] The specific amino acid residues and their position in the polypeptide chain are the determining factors for which portions of the protein fold closely together and form its three dimensional conformation. The amino acid composition is not as important as the sequence.[7] The essential fact of folding, however, remains that the amino acid sequence of each protein contains the information that specifies both the native structure and the pathway to attain that state. This is not to say that nearly identical amino acid sequences always fold similarly.[8] Conformations differ based on environmental factors as well; similar proteins fold differently based on where they are found.

Secondary structure


The alpha helix spiral formation.

An anti-parallel beta pleated sheet displaying hydrogen bonding within the backbone.

Formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure. Characteristic of secondary structure are the structures known as alpha helices and beta sheets that fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability.[9] α-helices are formed by hydrogen bonding of the backbone to form a spiral shape (refer to figure on the right).[7] The β pleated sheet is a structure that forms with the backbone bending over itself to form the hydrogen bonds (as displayed in the figure to the left). The hydrogen bonds are between the amide hydrogen and carbonyl oxygen of the peptide bond. There exists anti-parallel β pleated sheets and parallel β pleated sheets where the stability of the hydrogen bonds is stronger in the anti-parallel β sheet as it hydrogen bonds with the ideal 180 degree angle compared to the slanted hydrogen bonds formed by parallel sheets.[7]

Tertiary structure

The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic portion and a hydrophobic portion. This property of secondary structures aids in the tertiary structure of a protein in which the folding occurs so that the hydrophilic sides are facing the aqueous environment surrounding the protein and the hydrophobic sides are facing the hydrophobic core of the protein.[10] Secondary structure hierarchically gives way to tertiary structure formation. Once the protein's tertiary structure is formed and stabilized by the hydrophobic interactions, there may also be covalent bonding in the form of disulfide bridges formed between two cysteine residues. Tertiary structure of a protein involves a single polypeptide chain; however, additional interactions of folded polypeptide chains give rise to quaternary structure formation.[11]

Quaternary structure

Tertiary structure may give way to the formation of quaternary structure in some proteins, which usually involves the "assembly" or "coassembly" of subunits that have already folded; in other words, multiple polypeptide chains could interact to form a fully functional quaternary protein.[7]

Driving forces of protein folding


All forms of protein structure summarized.

Folding is a spontaneous process that is mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, van der Waals forces, and it is opposed by conformational entropy.[12] The process of folding often begins co-translationally, so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still being synthesized by the ribosome; however, a protein molecule may fold spontaneously during or after biosynthesis. While these macromolecules may be regarded as "folding themselves", the process also depends on the solvent (water or lipid bilayer),[13] the concentration of salts, the pH, the temperature, the possible presence of cofactors and of molecular chaperones. Proteins will have limitations on their folding abilities by the restricted bending angles or conformations that are possible. These allowable angles of protein folding are described with a two-dimensional plot known as the Ramachandran plot, depicted with psi and phi angles of allowable rotation.[14]

Hydrophobic effect


Hydrophobic collapse. In the compact fold (to the right), the hydrophobic amino acids (shown as black spheres) collapse toward the center to become shielded from aqueous environment.

Protein folding must be thermodynamically favorable within a cell in order for it to be a spontaneous reaction. Since it is known that protein folding is a spontaneous reaction, then it must assume a negative Gibbs free energy value. Gibbs free energy in protein folding is directly related to enthalpy and entropy.[7] For a negative delta G to arise and for protein folding to become thermodynamically favorable, then either enthalpy, entropy, or both terms must be favorable.

Entropy is decreased as the water molecules become more orderly near the hydrophobic solute.

Minimizing the number of hydrophobic side-chains exposed to water is an important driving force behind the folding process.[15] The hydrophobic effect is the phenomenon in which the hydrophobic chains of a protein collapse into the core of the protein (away from the hydrophilic environment).[7] In an aqueous environment, the water molecules tend to aggregate around the hydrophobic regions or side chains of the protein, creating water shells of ordered water molecules.[16] An ordering of water molecules around a hydrophobic region increases order in a system and therefore contributes a negative change in entropy (less entropy in the system). The water molecules are fixed in these water cages which drives the hydrophobic collapse, or the inward folding of the hydrophobic groups. The hydrophobic collapse introduces entropy back to the system via the breaking of the water cages which frees the ordered water molecules.[7] The multitude of hydrophobic groups interacting within the core of the globular folded protein contributes a significant amount to protein stability after folding, because of the vastly accumulated van der Waals forces (specifically London Dispersion forces).[7] The hydrophobic effect exists as a driving force in thermodynamics only if there is the presence of an aqueous medium with an amphiphilic molecule containing a large hydrophobic region.[17] The strength of hydrogen bonds depends on their environment; thus, H-bonds enveloped in a hydrophobic core contribute more than H-bonds exposed to the aqueous environment to the stability of the native state.[18]

Chaperones


Example of a small eukaryotic heat shock protein.

Molecular chaperones are a class of proteins that aid in the correct folding of other proteins in vivo. Chaperones exist in all cellular compartments and interact with the polypeptide chain in order to allow the native three-dimensional conformation of the protein to form; however, chaperones themselves are not included in the final structure of the protein they are assisting in.[19] Chaperones may assist in folding even when the nascent polypeptide is being synthesized by the ribosome.[20] Molecular chaperones operate by binding to stabilize an otherwise unstable structure of a protein in its folding pathway, but chaperones do not contain the necessary information to know the correct native structure of the protein they are aiding; rather, chaperones work by preventing incorrect folding conformations.[20] In this way, chaperones do not actually increase the rate of individual steps involved in the folding pathway toward the native structure; instead, they work by reducing possible unwanted aggregations of the polypeptide chain that might otherwise slow down the search for the proper intermediate and they provide a more efficient pathway for the polypeptide chain to assume the correct conformations.[19] Chaperones are not to be confused with folding catalysts, which actually do catalyze the otherwise slow steps in the folding pathway. Examples of folding catalysts are protein disulfide isomerases and peptidyl-prolyl isomerases that may be involved in formation of disulfide bonds or interconversion between cis and trans stereoisomers, respectively.[20] Chaperones are shown to be critical in the process of protein folding in vivo because they provide the protein with the aid needed to assume its proper alignments and conformations efficiently enough to become "biologically relevant".[21] This means that the polypeptide chain could theoretically fold into its native structure without the aid of chaperones, as demonstrated by protein folding experiments conducted in vitro;[21] however, this process proves to be too inefficient or too slow to exist in biological systems; therefore, chaperones are necessary for protein folding in vivo. Along with its role in aiding native structure formation, chaperones are shown to be involved in various roles such as protein transport, degradation, and even allow denatured proteins exposed to certain external denaturant factors an opportunity to refold into their correct native structures.[22]

A fully denatured protein lacks both tertiary and secondary structure, and exists as a so-called random coil. Under certain conditions some proteins can refold; however, in many cases, denaturation is irreversible.[23] Cells sometimes protect their proteins against the denaturing influence of heat with enzymes known as heat shock proteins (a type of chaperone), which assist other proteins both in folding and in remaining folded. Some proteins never fold in cells at all except with the assistance of chaperones which either isolate individual proteins so that their folding is not interrupted by interactions with other proteins or help to unfold misfolded proteins, allowing them to refold into the correct native structure.[24] This function is crucial to prevent the risk of precipitation into insoluble amorphous aggregates. The external factors involved in protein denaturation or disruption of the native state include temperature, external fields (electric, magnetic),[25] molecular crowding,[26] and even the limitation of space, which can have a big influence on the folding of proteins.[27] High concentrations of solutes, extremes of pH, mechanical forces, and the presence of chemical denaturants can contribute to protein denaturation, as well. These individual factors are categorized together as stresses. Chaperones are shown to exist in increasing concentrations during times of cellular stress and help the proper folding of emerging proteins as well as denatured or misfolded ones.[19]

Under some conditions proteins will not fold into their biochemically functional forms. Temperatures above or below the range that cells tend to live in will cause thermally unstable proteins to unfold or denature (this is why boiling makes an egg white turn opaque). Protein thermal stability is far from constant, however; for example, hyperthermophilic bacteria have been found that grow at temperatures as high as 122 °C,[28] which of course requires that their full complement of vital proteins and protein assemblies be stable at that temperature or above.

Computational methods for studying protein folding

The study of protein folding includes three main aspects related to the prediction of protein stability, kinetics, and structure. A recent review summarizes the available computational methods for protein folding. [29]

Energy landscape of protein folding


The energy funnel by which an unfolded polypeptide chain assumes its native structure.

The protein folding phenomenon was largely an experimental endeavor until the formulation of an energy landscape theory of proteins by Joseph Bryngelson and Peter Wolynes in the late 1980s and early 1990s. This approach introduced the principle of minimal frustration.[30] This principle says that nature has chosen amino acid sequences so that the folded state of the protein is very stable. In addition, the undesired interactions between amino acids along the folding pathway are reduced, making the acquisition of the folded state a very fast process. Even though nature has reduced the level of frustration in proteins, some degree of it remains up to now as can be observed in the presence of local minima in the energy landscape of proteins. A consequence of these evolutionarily selected sequences is that proteins are generally thought to have globally "funneled energy landscapes" (coined by José Onuchic)[31] that are largely directed toward the native state. This "folding funnel" landscape allows the protein to fold to the native state through any of a large number of pathways and intermediates, rather than being restricted to a single mechanism. The theory is supported by both computational simulations of model proteins and experimental studies,[30] and it has been used to improve methods for protein structure prediction and design.[30] The description of protein folding by the leveling free-energy landscape is also consistent with the 2nd law of thermodynamics.[32] Physically, thinking of landscapes in terms of visualizable potential or total energy surfaces simply with maxima, saddle points, minima, and funnels, rather like geographic landscapes, is perhaps a little misleading. The relevant description is really a high-dimensional phase space in which manifolds might take a variety of more complicated topological forms.[33]

The unfolded polypeptide chain begins at the top of the funnel where it may assume the largest number of unfolded variations and is in its highest energy state. Energy landscapes such as these indicate that there are a large number of initial possibilities, but only a single native state is possible; however, it does not reveal the numerous folding pathways that are possible. A different molecule of the same exact protein may be able to follow marginally different folding pathways, seeking different lower energy intermediates, as long as the same native structure is reached.[34] Different pathways may have different frequencies of utilization depending on the thermodynamic favorability of each pathway. This means that if one pathway is found to be more thermodynamically favorable than another, it is likely to be used more frequently in the pursuit of the native structure.[34] As the protein begins to fold and assume its various conformations, it always seeks a more thermodynamically favorable structure than before and thus continues through the energy funnel. Formation of secondary structures is a strong indication of increased stability within the protein, and only one combination of secondary structures assumed by the polypeptide backbone will have the lowest energy and therefore be present in the native state of the protein.[34] Among the first structures to form once the polypeptide begins to fold are alpha helices and beta turns, where alpha helices can form in as little as 100 nanoseconds and beta turns in 1 microsecond.[19]

There exists a saddle point in the energy funnel landscape where the transition state for a particular protein is found.[19] The transition state in the energy funnel diagram is the conformation that must be assumed by every molecule of that protein if the protein wishes to finally assume the native structure. No protein may assume the native structure without first passing through the transition state.[19] The transition state can be referred to as a variant or premature form of the native state rather than just another intermediary step.[35] The folding of the transition state is shown to be rate-determining, and even though it exists in a higher energy state than the native fold, it greatly resembles the native structure. Within the transition state, there exists a nucleus around which the protein is able to fold, formed by a process referred to as "nucleation condensation" where the structure begins to collapse onto the nucleus.[35]

Two models of protein folding are currently being confirmed:
  • The diffusion collision model, in which first a nucleus forms, then the secondary structure, and finally these secondary structures collide and pack tightly together.
  • The nucleation-condensation model, in which the secondary and tertiary structures of the protein are made at the same time.
Recent studies have shown that some proteins show characteristics of both of these folding models.

For the most part, scientists have been able to study many identical molecules folding together en masse. At the coarsest level, it appears that in transitioning to the native state, a given amino acid sequence takes roughly the same route and proceeds through roughly the same intermediates and transition states. Often folding involves first the establishment of regular secondary and supersecondary structures, in particular alpha helices and beta sheets, and afterward tertiary structure.

Modeling of protein folding


Folding@home uses Markov state models, like the one diagrammed here, to model the possible shapes and folding pathways a protein can take as it condenses from its initial randomly coiled state (left) into its native 3D structure (right).

De novo or ab initio techniques for computational protein structure prediction are related to, but strictly distinct from, experimental studies of protein folding. Molecular Dynamics (MD) is an important tool for studying protein folding and dynamics in silico.[36] First equilibrium folding simulations were done using implicit solvent model and umbrella sampling.[37] Because of computational cost, ab initio MD folding simulations with explicit water are limited to peptides and very small proteins.[38][39] MD simulations of larger proteins remain restricted to dynamics of the experimental structure or its high-temperature unfolding. Long-time folding processes (beyond about 1 millisecond), like folding of small-size proteins (about 50 residues) or larger, can be accessed using coarse-grained models.[40][41][42]

The 100-petaFLOP distributed computing project Folding@home created by Vijay Pande's group at Stanford University simulates protein folding using the idle processing time of CPUs and GPUs of personal computers from volunteers. The project aims to understand protein misfolding and accelerate drug design for disease research.

Long continuous-trajectory simulations have been performed on Anton, a massively parallel supercomputer designed and built around custom ASICs and interconnects by D. E. Shaw Research. The longest published result of a simulation performed using Anton is a 2.936 millisecond simulation of NTL9 at 355 K.[43]

Experimental techniques for studying protein folding

While inferences about protein folding can be made through mutation studies, typically, experimental techniques for studying protein folding rely on the gradual unfolding or folding of proteins and observing conformational changes using standard non-crystallographic techniques.

X-ray crystallography


Steps of x-ray crystallography.

X-ray crystallography is one of the more efficient and important methods for attempting to decipher the three dimensional configuration of a folded protein.[44] To be able to conduct X-ray crystallography, the protein under investigation must be located inside a crystal lattice. To place a protein inside a crystal lattice, one must have a suitable solvent for crystallization, obtain a pure protein at supersaturated levels in solution, and precipitate the crystals in solution.[45] Once a protein is crystallized, x-ray beams can be concentrated through the crystal lattice which would diffract the beams or shoot them outwards in various directions. These exiting beams are correlated to the specific three-dimensional configuration of the protein enclosed within. The x-rays specifically interact with the electron clouds surrounding the individual atoms within the protein crystal lattice and produce a discernible diffraction pattern.[10] Only by relating the electron density clouds with the amplitude of the x-rays can this pattern be read and lead to assumptions of the phases or phase angles involved that complicate this method.[46] Without the relation established through a mathematical basis known as Fourier transform, the "phase problem" would render predicting the diffraction patterns very difficult.[10] Emerging methods like multiple isomorphous replacement use the presence of a heavy metal ion to diffract the x-rays into a more predictable manner, reducing the number of variables involved and resolving the phase problem.[44]

Fluorescence spectroscopy

Fluorescence spectroscopy is a highly sensitive method for studying the folding state of proteins. Three amino acids, phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp), have intrinsic fluorescence properties, but only Tyr and Trp are used experimentally because their quantum yields are high enough to give good fluorescence signals. Both Trp and Tyr are excited by a wavelength of 280 nm, whereas only Trp is excited by a wavelength of 295 nm. Because of their aromatic character, Trp and Tyr residues are often found fully or partially buried in the hydrophobic core of proteins, at the interface between two protein domains, or at the interface between subunits of oligomeric proteins. In this apolar environment, they have high quantum yields and therefore high fluorescence intensities. Upon disruption of the protein’s tertiary or quaternary structure, these side chains become more exposed to the hydrophilic environment of the solvent, and their quantum yields decrease, leading to low fluorescence intensities. For Trp residues, the wavelength of their maximal fluorescence emission also depend on their environment.

Fluorescence spectroscopy can be used to characterize the equilibrium unfolding of proteins by measuring the variation in the intensity of fluorescence emission or in the wavelength of maximal emission as functions of a denaturant value.[47][48] The denaturant can be a chemical molecule (urea, guanidinium hydrochloride), temperature, pH, pressure, etc. The equilibrium between the different but discrete protein states, i.e. native state, intermediate states, unfolded state, depends on the denaturant value; therefore, the global fluorescence signal of their equilibrium mixture also depends on this value. One thus obtains a profile relating the global protein signal to the denaturant value. The profile of equilibrium unfolding may enable one to detect and identify intermediates of unfolding.[49][50] General equations have been developed by Hugues Bedouelle to obtain the thermodynamic parameters that characterize the unfolding equilibria for homomeric or heteromeric proteins, up to trimers and potentially tetramers, from such profiles.[47] Fluorescence spectroscopy can be combined with fast-mixing devices such as stopped flow, to measure protein folding kinetics,[51] generate a chevron plot and derive a Phi value analysis.

Circular dichroism

Circular dichroism is one of the most general and basic tools to study protein folding. Circular dichroism spectroscopy measures the absorption of circularly polarized light. In proteins, structures such as alpha helices and beta sheets are chiral, and thus absorb such light. The absorption of this light acts as a marker of the degree of foldedness of the protein ensemble. This technique has been used to measure equilibrium unfolding of the protein by measuring the change in this absorption as a function of denaturant concentration or temperature. A denaturant melt measures the free energy of unfolding as well as the protein's m value, or denaturant dependence. A temperature melt measures the melting temperature (Tm) of the protein.[47] As for fluorescence spectroscopy, circular-dichroism spectroscopy can be combined with fast-mixing devices such as stopped flow to measure protein folding kinetics and to generate chevron plots.

Vibrational circular dichroism of proteins

The more recent developments of vibrational circular dichroism (VCD) techniques for proteins, currently involving Fourier transform (FFT) instruments, provide powerful means for determining protein conformations in solution even for very large protein molecules. Such VCD studies of proteins are often combined with X-ray diffraction of protein crystals, FT-IR data for protein solutions in heavy water (D2O), or ab initio quantum computations to provide unambiguous structural assignments that are unobtainable from CD.[citation needed]

Protein nuclear magnetic resonance spectroscopy

Protein folding is routinely studied using NMR spectroscopy, for example by monitoring hydrogen-deuterium exchange of backbone amide protons of proteins in their native state, which provides both the residue-specific stability and overall stability of proteins.[52]

Dual polarisation interferometry

Dual polarisation interferometry is a surface-based technique for measuring the optical properties of molecular layers. When used to characterize protein folding, it measures the conformation by determining the overall size of a monolayer of the protein and its density in real time at sub-Angstrom resolution,[53] although real-time measurement of the kinetics of protein folding are limited to processes that occur slower than ~10 Hz. Similar to circular dichroism, the stimulus for folding can be a denaturant or temperature.

Studies of folding with high time resolution

The study of protein folding has been greatly advanced in recent years by the development of fast, time-resolved techniques. Experimenters rapidly trigger the folding of a sample of unfolded protein and observe the resulting dynamics. Fast techniques in use include neutron scattering,[54] ultrafast mixing of solutions, photochemical methods, and laser temperature jump spectroscopy. Among the many scientists who have contributed to the development of these techniques are Jeremy Cook, Heinrich Roder, Harry Gray, Martin Gruebele, Brian Dyer, William Eaton, Sheena Radford, Chris Dobson, Alan Fersht, Bengt Nölting and Lars Konermann.

Proteolysis

Proteolysis is routinely used to probe the fraction unfolded under a wide range of solution conditions (e.g. Fast parallel proteolysis (FASTpp).[55][56]

Optical tweezers

Single molecule techniques such as optical tweezers and AFM have been used to understand protein folding mechanisms of isolated proteins as well as proteins with chaperones.[57] Optical tweezers have been used to stretch single protein molecules from their C- and N-termini and unfold them to allow study of the subsequent refolding.[58] The technique allows one to measure folding rates at single-molecule level; for example, optical tweezers have been recently applied to study folding and unfolding of proteins involved in blood coagulation. von Willebrand factor (vWF) is a protein with an essential role in blood clot formation process. It discovered – using single molecule optical tweezers measurement – that calcium-bound vWF acts as a shear force sensor in the blood. Shear force leads to unfolding of the A2 domain of vWF, whose refolding rate is dramatically enhanced in the presence of calcium.[59] Recently, it was also shown that the simple src SH3 domain accesses multiple unfolding pathways under force.[60]

Other information

Incorrect protein folding and neurodegenerative disease

A protein is considered to be misfolded if it cannot achieve its normal native state. This can be due to mutations in the amino acid sequence or a disruption of the normal folding process by external factors.[61] The misfolded protein typically contains β-sheets that are organized in a supramolecular arrangement known as a cross-β structure. These β-sheet-rich assemblies are very stable, very insoluble, and generally resistant to proteolysis.[62] The structural stability of these fibrillar assemblies is caused by extensive interactions between the protein monomers, formed by backbone hydrogen bonds between their β-strands.[62] The misfolding of proteins can trigger the further misfolding and accumulation of other proteins into aggregates or oligomers. The increased levels of aggregated proteins in the cell leads to formation of amyloid-like structures which can cause degenerative disorders and cell death.[61] The amyloids are fibrillary structure that contain intermolecular hydrogen bonds, which are highly insoluble, and made from converted protein aggregates.[61] Therefore, the proteasome pathway may not be efficient enough to degrade the misfolded proteins prior to aggregation. Misfolded proteins can interact with one another and form structured aggregates and gain toxicity through intermolecular interactions.[61]

Aggregated proteins are associated with prion-related illnesses such as Creutzfeldt–Jakob disease, bovine spongiform encephalopathy (mad cow disease), amyloid-related illnesses such as Alzheimer's disease and familial amyloid cardiomyopathy or polyneuropathy,[63] as well as intracellular aggregation diseases such as Huntington's and Parkinson's disease.[4][64] These age onset degenerative diseases are associated with the aggregation of misfolded proteins into insoluble, extracellular aggregates and/or intracellular inclusions including cross-β amyloid fibrils. It is not completely clear whether the aggregates are the cause or merely a reflection of the loss of protein homeostasis, the balance between synthesis, folding, aggregation and protein turnover. Recently the European Medicines Agency approved the use of Tafamidis or Vyndaqel (a kinetic stabilizer of tetrameric transthyretin) for the treatment of transthyretin amyloid diseases. This suggests that the process of amyloid fibril formation (and not the fibrils themselves) causes the degeneration of post-mitotic tissue in human amyloid diseases.[65] Misfolding and excessive degradation instead of folding and function leads to a number of proteopathy diseases such as antitrypsin-associated emphysema, cystic fibrosis and the lysosomal storage diseases, where loss of function is the origin of the disorder. While protein replacement therapy has historically been used to correct the latter disorders, an emerging approach is to use pharmaceutical chaperones to fold mutated proteins to render them functional.

Levinthal's paradox and kinetics

In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. An estimate of 3300 or 10143 was made in one of his papers.[66] Levinthal's paradox[67] is a thought experiment based on the observation that if a protein were folded by sequentially sampling of all possible conformations, it would take an astronomical amount of time to do so, even if the conformations were sampled at a rapid rate (on the nanosecond or picosecond scale). Based upon the observation that proteins fold much faster than this, Levinthal then proposed that a random conformational search does not occur, and the protein must, therefore, fold through a series of meta-stable intermediate states.

The duration of the folding process varies dramatically depending on the protein of interest. When studied outside the cell, the slowest folding proteins require many minutes or hours to fold primarily due to proline isomerization, and must pass through a number of intermediate states, like checkpoints, before the process is complete.[68] On the other hand, very small single-domain proteins with lengths of up to a hundred amino acids typically fold in a single step.[69] Time scales of milliseconds are the norm and the very fastest known protein folding reactions are complete within a few microseconds.[70]

Computer-aided software engineering

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