An Autoantigen for Pancreatitis

Pancreatic Secretory Trypsin Inhibitor (PSTI) Has Internalization Basic Triplet

Pancreatitis is an inflammation of the pancreas resulting from lack of adequate inhibition of proteases. Autoantibodies against PSTI would explain some forms of pancreatitis.

I was researching the maintenance of baby gut flora by mother’s milk, when the reference discussed here was brought to my attention by my wife, who happens to be a lactation consultant. The paper showed that PSTI is present in colostrom, the first milk that a baby gets, before the true milk comes in. PSTI protects the new gut from digestion by its own pancreatic proteases, since PSTI is a protease inhibitor that sticks to the gut.

I naturally assumed that PSTI stuck to the gut by heparin-binding domains that would stick to the heparan sulfate proteoglycans on the gut surface. [Recall that it is via these HSPGs that viruses and bacteria infect the gut and the HSPGs in turn are protected during infections by the release of heparin from mast cells. The heparin in the guts of cattle and pigs are used to make commercial heparin to block blood clotting.] So I looked up the structure (above, with basic amino acids in blue and basic triplet on right) sequence of human PSTI at NCBI:

>gi|190694|gb|AAA36522.1| PSTI
MKVTGIFLLSALALLSLSGNTGADSLGREAKCYNELNGCTKIYD
PVCGTDGNTYPNECVLCFENRKRQTSILIQKSGPC

The basic triplet (RKR,arg-lys-arg), from my perspective, should result in presentation to the immune system during high levels of inflammation, and as a consequence result in autoantibodies against PSTI. The result would be the neutralization of the protease inhibitor and damaging production of active protease to attack the pancreas, i.e. pancreatitis.

It would be fairly easy to test this hypothesis by looking for the anti-PSTI antibodies in some people with pancreatitis. Other autoantibodies, e.g. against tissue transglutaminase, might also be checked, because the inflammation that produced one autoantibody may produce others and both PSTI and tTG are produced in the intestines. In fact, celiac may be the cause of some cases of autoimmune pancreatitis.

Note added in proof:

I just checked the literature on PubMed and found that PSTI is in fact an autoantigen in pancreatitis and produces antibodies against PSTI:
Raina A, Greer JB, Whitcomb DC. Serology in autoimmune pancreatitis. Minerva Gastroenterol Dietol. 2008 Dec;54(4):375-87.

and
I found that pancreatitis is often found associated with celiac (gluten intolerance):
Patel RS, Johlin FC Jr, Murray JA. Celiac disease and recurrent pancreatitis. Gastrointest Endosc. 1999 Dec;50(6):823-7.

ref:
Marchbank T, Weaver G, Nilsen-Hamilton M, Playford RJ. Pancreatic secretory trypsin inhibitor is a major motogenic and protective factor in human breast milk. Am J Physiol Gastrointest Liver Physiol. 2009 Apr;296(4):G697-703.

Lyme Spirochete Binds to Heparan in Blood Vessels

Borrelia burgdorferi Sticks to Host Cells via Heparin-binding Proteins

A research group at the University of Calgary has watched the binding of fluorescent Borrelia burgdorferi spirochetes, the Lyme disease pathogen, to the surface of blood vessels in mice. (ref. below) A small heparin molecule was shown to block this interaction between the spirochete surface protein BBK32 and the heparan sulfate proteoglycans of the endothelial cells of the skin blood vessels.

The heparin-binding domains in the spirochete protein, BBK32 are easy to spot in the amino acid sequence of this protein that I downloaded from the NCBI protein database:

>gi|19072701|gb|AAL84596.1| BBK32 [Borrelia burgdorferi]
MKKVKSKYLALGLLFGFISCDLFIRYEMKEESPGLFDKGNSILET
SEESIKKPMNKKGKKIARKKGKSKVSRKEPYIHSLKRDSANKSN
FLQKNVILEEESLKTELLKEQSETRKEKIQKQQDEYKGMTQGSL
NSLSGESGELKETIESNEIDITIDSDLRPKSSLQDIAGSNSISYTDE
IEEEDYARYYLDEDDEDDEYYEDDYEEIRLSNRYQSYLEGVKYNV
DSAINTINKIYDTYTLFSTKLTQMYSTRLDNLAKAKAKEEAAKFTK
EDLEKNFKTLLNYIQVSVKTAANFVYINDTHAKRKLENIEAEIKTL
IAKIKEQSNLYEAYKAIVTSILLMRDSLKEVQGIIDKNGVWY
Basic amino acids are K=lysine, R=arginine

The minimal heparin binding pairs, e.g. KKVKSK are shown in red and the strong heparin-binding triplets, e.g. KRK, are shown in blue. Notice that one triplet is augmented with several pairs to further enhance heparin binding.

I would also expect that BBK32 would be internalized into host cells and transported into the nucleus, where it may alter transcription, a la HIV-TAT. The existence of multiple, strong heparin-binding domains may also serve to bind the BBK32 (or the spirochetes) to multiple different heparan sulfate proteoglycans and interfere with the HSPG circulation system. This may have a toxic effect.

reference:
Norman MU, Moriarty TJ, Dresser AR, Millen B, Kubes P, Chaconas G. Molecular mechanisms involved in vascular interactions of the Lyme disease pathogen in a living host. PLoS Pathog. 2008 Oct 3;4(10):e1000169.

The Cause of Allegies and Autoimmune Diseases

Keyhole Limpet Hemocyanin (KLH): Internalized Antigen

Scanning the literature for a common protein that can be used as an experimental antigen, it becomes quickly obvious that a favorite is KLH. This would seem to be an odd choice -- why a keyhole limpet protein? But that is the wrong question.

Why is KLH such a good antigen, i.e. why is it readily presented to the host immune system? If you have been reading my posts, you might be thinking about triplets of basic amino acids and that is the answer.

As soon as I remembered the prominent use of KLH as an antigen, I checked the NCBI protein database and immediately found an unusual KKK (triple lysine) near the amino terminus of hemocyanin II ( it comes in two pieces). This triplet explains why KLH is such a good experimental antigen, because it is internalized into antigen presenting cells by its strong heparin-binding domain. Other components, adjuvants, are typically added to the KLH for injection to make sure that a strong local inflammation occurs.

Autoantigens Have Strong Heparin-Binding Triplet

I also learned that Hashimoto’s thyroiditis is an autoimmune disease mediated by the autoantigen thyroid peroxidase. A quick search reveals that thyroid peroxidase is an autoantigen, because it also has a triplet of basic amino acids that can enhance presentation under inflammatory conditions. Grave’s disease of hyperthyroidism is an autoimmune disease in which the thyroid receptor (with a basic triplet) is an autoantigen. The same kind of triplet of basic amino acids was found when I searched today for fire ant antigens and mosquito antigens.

I have also looked for the triplets in protein databases. The triplets are rare in cytoplasmic and extracellular proteins. The proteins that have triplets are usually identified as autoantigens in some disease. The triplets are common in nuclear proteins, since heparin-binding and nucleic acid-binding share the same basic amino acid domains. The nuclear internalization signal also results in rapid cellular internalization, e.g. HIV-TAT, heparanase, IGF-binding proteins. Nuclear proteins are common autoantigens in lupus.

Inflammation Plus Heparin-Binding Internalization: Allergy, Autoimmunity

Chronic inflammation can produce antibodies against proteins (foreign or self) with strong heparin-binding domains (triplets or sometimes neighboring pairs of basic amino acids, lysine or arginine). The generalization explains why particular proteins in pollens, foods, insects, pets, mites, asthma, MS, lupus, celiac, etc. produce antibody responses.

Insulin-like Growth Factor, Diabetes Autoantigen

IGF Binding to Heparin is Basis for Receptor Interaction, Internalization and Immunization

Examination of the protein sequence of insulin-like growth factors reveals strong heparin-binding domains (triplet of basic amino acids) that are also associated with internalization. Similar heparin internalization domains are also found on allergens and autoantigens. It was a small leap to expect that IGFs would also become autoantigens under inflammatory conditions that minimize heparan sulfate proteoglycan production.

Triplets of Basic Amino Acids Internalize Proteins

In several articles on this blog, I have discussed proteins that are internalized by their heparin binding domains. Heparin binding domains consistent only of a pair of basic amino acids, e.g. RK, flanked by one or more basic amino acids within a hydrophobic sequence of protein, are not sufficient to mediate internalization on heparan sulfate proteoglycans. A triplet of basic amino acids is usually required. Simple inspection of amino acid sequences is sufficient to identify these regions.

Internalization Triplet Identified in Insulin-like Growth Factor Binding Proteins

I noticed in a paper that insulin-like growth factors bind to epidermal growth factor receptors. I have previously written an article showing that EGF1 binds to its receptor via heparin, i.e. both the EGF and the receptor have heparin-binding domains. So I suspected that IGFs also had heparin binding domains. Inspection of the sequences readily identified simple heparin binding domains with pairs, but not triplets of basic amino acids. A search of the literature confirmed that heparin mediated IGF binding to receptors. A further search indicated that the heparin binding domains from proteins that bind and control the activity of IGFs could mediate internalization of proteins into cells and also into nuclei.

Internalization Triplets Are Associated with Allergens and Autoantigens

I have previously noted that all allergens and autoantigens have internalization triplets of basic amino acids. The presence of these triplets in IGF binding proteins suggested that IGF binding proteins might also be autoantigens. A quick check of the literature showed that antibodies against IGFs themselves frequently occur in type I diabetes. This suggests that the IGF-binding protein complexes are internalized and IGFs are immunologically presented during inflammation to produce anti-IGF antibodies. It is interesting that the other autoantigens for type I diabetes, e.g. transglutaminase, also have the expected internalization triplets.

references:
Maruyama T, Murayama H, Nagata A, Shimada A, Kasuga A, Saruta T.
Anti-insulin-like growth factor-1 autoantibodies in type 1 diabetes. Ann N Y Acad Sci. 2002 Apr;958:267-70.

Miao D, Yu L, Eisenbarth GS. Role of autoantibodies in type 1 diabetes. Front Biosci. 2007 Jan 1;12:1889-98.

Goda N, Tenno T, Inomata K, Shirakawa M, Tanaka T, Hiroaki H. Intracellular protein delivery activity of peptides derived from insulin-like growth factor binding proteins 3 and 5. Exp Cell Res. 2008 Aug 1;314(13):2352-61. Epub 2008 May 29.

Allergy, Asthma, Autoimmunity Start the Same Way

Inflammation is the current medical buzzword. Name the disease and inflammation is there.

Reproduction Requires Controlled Inflammation
Aspirin blocks many of the steps in triggering inflammation and thus, aspirin administration can be used to reveal a role of inflammation in many unexpected places. Aspirin is effective in blocking some forms of infertility, inhibiting miscarriages and ameliorating postpartum depression. So inflammation is a critical part of reproduction. But, also notice that depression is a symptom of chronic inflammation.

Cancer Requires Inflammation
High dose (IV) aspirin has been successfully used to treat cancer. Inflammation is required for cancer growth, because both use the same transcription factor, NFkB. The aberrant signaling of cancer cells would normally lead to programed cell death, apoptosis, but inflammation blocks apoptosis. Aspirin can in turn block NFkB and in the absence of inflammation, cancer cells die by apoptosis.

Inflammation is Self-Limiting
Aspirin also transforms the COX/lipoxidase system to produce anti-inflammatory prostaglandins/eicosinoids. Inflammation normally progresses into anti-inflammation. Blocking this progression leads to chronic inflammation and a shift from local to systemic inflammation with the rise of inflammatory interleukins in the blood stream.

Immune Response Requires Inflammation
The signal molecules (IL-1, IL-6, TNF) and transcription factor, NFkB, associated with inflammation were all initially identified in the development of lymphocytes. Hence, IL stands for interleukin, a hormone that triggers leukocyte (literally white blood cells or cells associated with the lymphatic immune system, i.e. lymphocytes) development. The nuclear factor, i.e. transcription factor, involved in expression of the large chain, kappa, of immunoglobulins in B cells, was called NFkB.

Genes Expressed by NFkB Cause Symptoms of Inflammation
About five dozen genes are under control of NFkB. Among these are COX-2, the enzyme that converts omega-6 arachidonic acid to inflammatory prostaglandins; iNOS, the enzyme that produces nitric oxide that dilates blood vessels to produce hot, red skin; and the inflammatory interleukins, IL-1, IL-6 and TNF, associated with autoimmune disease, fatigue and cachexia (wasting).

Autoimmunity and Allergy Start with Inflammation
Medical treatments focus on symptom abatement and ignore cause. What causes obesity, allergy or autoimmune disease? The answer appears to be chronic systemic inflammation plus exposure to unusual proteins. The unusual proteins are immunogenic, i.e. interact with the immune system to produce antibodies or reactive T-cell receptors, and are subsequently recognized as autoantigens or allergens, that are the targets for immune attack. Inspection of these autoantigens and allergens shows that they all have one thing in common, they bind to heparin via a strong heparin-binding protein domain that is typically a triplet of adjacent basic amino acids.

Heparin is a Short, Highly Sulfated Fragment of Heparan Sulfate
Commercial heparin is purified from the intestines of hogs and cattle. Heparin is released from mast cells (made fluorescent for microscopy using berberine) along with histamine and is released into the intestines to block pathogens from binding to the heparan sulfate that is part of the intestine surface. The heparin is anti-inflammatory and it contributes to minimizing the inflammatory response of the intestines to food.

Inflammation Reduces Heparan Sulfate Production
Pathogen-generated inflammation of the intestines reduces heparan sulfate production and increases immune response to food antigens. NFkB activation by inflammation turns off the production of some genes needed for heparan sulfate proteoglycan (HSPG) synthesis. Since HSPG is a major component of the basement membrane that holds tissues together, the reduction of HSPG results in protein loss (proteinuria) from kidneys, leaking of intestines, and disruption of the blood/brain barrier.

Reduction of HSPG Results in Immunological Presentation of Autoantigens/Allergens
Proteins are brought into cells by specific binding to protein receptors. In many cases, particularly involving signaling or growth factors, both the signal molecules and the receptors bind to heparin. In addition, there is a robust circulation of HSPG, which is secreted and internalized with a half-life of approximately six hours. The sweep of the HSPGs take heparin-binding proteins with them for internalization, e.g. HIV-TAT, heparanase, tissue transglutaminase. I think that this HSPG sweep under inflammatory conditions also internalizes basic autoantigens and allergens with strong heparin-binding domains. This internalization is the first step toward immunological presentation and the immune response to autoantigens and allergens.

Autoantigen/autoantibody/HSPG Complexes Kill Cells
Antibodies against self-antigens, autoantigens form antigen/antibody complexes that also bind to and cross-link HSPGs, because of the heparin-binding domains of the autoantigens. The large complexes may disrupt HSPG circulation and trigger apoptosis or abnormal physiology. There are many other examples of heparin-based complexes that are toxic, e.g. Alzheimer’s amyloid plaque, diabetic beta cell antibody complexes, celiac gluten/tRG antibody complexes, multiple sclerosis myelin antibody complexes, atherosclerotic plaque.

Anti-Inflammatory Diet and Lifestyle Protects
Dietary and lifestyle adjustments that minimize inflammation, e.g. low starch, no HFCS, low vegetable oil (except olive) and supplements of vitamins D & C, fish oil (omega-3) and glucosamine, reduce the risk of allergies/asthma, degenerative diseases and cancers. Simple, high level supplements with fish oil reduce numerous mental disorders, e.g. depression, ADHD; infertility, pre-eclampsia and postpartum depression; allergies, asthma; arthritis, atherosclerosis; burn recovery, septicemia and head injury.

Reducing Inflammation is a Panacea for Modern Diseases
Most modern diseases have an inflammatory component, because modern diets are rich in inflammatory components, e.g. starch/sugar, corn/soy oil, HFCS, trans fats, and exercise is minimal. The medical industry has not successfully promoted healthy eating and exercise; and in fact has promoted the devastating replacement of saturated fats with inflammatory polyunsaturated vegetable oils. Meat production has moved away from grazing on omega-3-rich plant vegetation to omega-6-rich corn and soy. Replacement of the corn/soy based agricultural economy would have predictably immense beneficial impact in reducing inflammation-based degenerative autoimmune diseases and cancers.

HIV TAT and Methamphetamine -- TNF

HIV infection and methamphetamine both cause inflammation of the brain and together they are paralyzing.

What’s worse than a TNF typhoon resulting from methamphetamine use? The answer is a TNF typhoon resulting in dementia from HIV infection of the brain.
Combine methamphetamine with HIV in the brain and the result is a Parkinson’s type of paralysis.

This sounds like very morbid subject matter to pursue out of curiosity, but if you put heparin into the equation, as I always do, it all becomes very interesting.

Here are pieces to the big picture:

HIV, the AIDS virus, infects cells of the immune system and causes chronic inflammation. The inflammation causes a disruption of heparin metabolism and since heparin is a major part of the matrix that holds together the endothelial cells that line the capillaries that feed the brain, the capillaries leak, i.e. there is a leak in the blood brain barrier. HIV-infected cells can pass out of the capillaries and into the brain. Here comes the insidious part, HIV produces a protein called TAT.

I drew a graphic of TAT with the basic amino acids in blue. The sequence of this nasty little protein shows how it gets around. It is secreted from cells, attached to heparan sulfate proteoglycans. It sticks tightly to heparin (yellow and red stick figures, sticking to ribbon of TAT), because of the patches with three and four adjacent basic amino acids. Frequently, the TAT will just be secreted and then sweep over the surface of the infected cell and be brought back into the cell on the circulating HSPG.

DPVDPNIEPWNHPGSQPKTACN
RCHCKKCCYHCQVCFIKKGLGI
SYGRKKRRQRRRPSQGGQTHQ
DPIPKQPSSQPRGDPTGPKE

A protein with three adjacent basic amino acids will get swept into a cell. All allergens that I have examined have this internalization triplet of basic amino acids. TAT is so powerful, that if it is chemically linked to the larger fluorescent protein from jelly fish (left with green, fluorescent amino acid derivative down the center), the whole fluorescent protein is dragged into cells.

The TAT can move from the HSPGs of an HIV-infected cell to neighboring cells with HSPGs. The TAT then gets taken into the cytoplasm of the next cell. Four adjacent basic amino acids are the signal that transports a protein to the nucleus and into the nucleus. It is in the nucleus that TAT really causes trouble. The TAT can move from an infected immune cell in the brain to neurons. TAT can kill neurons and stimulate other cells to produce TNF.

Methamphetamine also causes a TNF storm in the brain. This is a quick way to start the wasting symptoms that TNF in known for -- it is also call cachexin, after the wasting process of cachexia. If methamphetamine is given to someone with neurological symptoms of HIV, then the neuropathology is further exaggerated into a Parkinson’s type of paralysis. The TNF production of both is additive.

TNF production by methamphetamine brings up the consequences of the very closely related compound amphetamine (Adderall, Dexedrine) used by children and young adults (college age) as a treatment for ADHD.

reference:
Theodore S, Cass WA, Nath A, Maragos WF. 2007. Progress in understanding basal ganglia dysfunction as a common target for methamphetamine abuse and HIV-1 neurodegeneration. Curr HIV Res. May;5(3):301-13.

Inflammatory Proteins Bind Heparin

Particular amino acid sequences mark a protein for secretion, binding to heparin, uptake and internalization into the nucleus.

You can tell a lot about a protein from the sequence of its amino acids. Basic amino acids (arginine and lysine) arranged in groups, for example, usually mean (if it is an extracellular protein) that a protein binds to heparan sulfate proteoglycans.

It seemed strange to me that heparin-binding was so simple when I tried to determine the rules for heparin-binding by looking at the structures of several hundred proteins known to bind to heparin. Since heparin is heavily sulfated and the sulfates are negatively charged, at first I just color-coded the positively-charged , basic amino acids (blue) to look for oppositely charged heparin-binding sites on the surface of the proteins. Obvious blue patches were found on the surfaces of all of the proteins that bound to heparin and scattered blue spots were on the surfaces of other proteins. Moreover, similarly color-coded amino acid sequences showed that the blue patchs almost always had pairs of basic amino acids flanked within six amino acids by a third basic amino acid, i.e. BBxxxxB, where B is either arginine (R) or lysine (K) and x is a hydrophobic amino acid. It was surprisingly simple.

I was shocked at the simplicity, because most binding sites are made up of parts of regular secondary structures of helices or pleated sheets. If there were basic amino acids on these structures, which bound to heparin on one side, then the R/K would be repeated at specific intervals. For a helix, for example, the repeat would be BxxBxxB, because it takes three amino acids to return to the same side as the amino acids wind around in the helix. For the pleated sheet, the amino acids alternate on each side of the sheet, so the pattern is BxBxB. I found these kinds of heparin-binding domains also. The hardest patterns to find from sequences are groups formed as R/K’s on neighboring helices or sheets are brought together in the final folding of the protein.

One of the reasons that the simple pair plus one (BBxxxxB) was found so easily, is because the sequence is typically found on coils that only take shape in the presence of heparin. Thus the rigid binding of the domains to heparin is a result of the shape of the protein induced by the heparin. A related example of this phenomenon is the facilitation of the formation of amyloid fibers in the presence of heparin. The beta amyloid of Alzheimer’s disease for example, consists of a stack of small amyloid peptides with basic amino acids that line up and bind heparin along the length of the stack. Heparin is also an essential component in the amyloids of diabetes. Prions also seem to involve heparin. It is assumed that the cytoplasmic tau fibers of Alzheimer’s disease also have a similar facilitating polyanion (if not heparin), but it has not been identified.

Because of the essential nature of HSPG recycling, it is interesting that amyloid formation is toxic when the amyloid is in contact with cells. Perhaps the amyloid paralyzes HSPG recycling and thereby kills the cells. Treatments that disrupt amyloid binding to heparin, e.g. methylene blue, spare the neurons. This would also suggest the utility of berberine, a fluorescent dye for heparin, which is also a common herbal cure for arthritis, in treatment of many amyloid diseases.

The pair plus one is the minimal grouping of R/K’s that binds heparin, but larger groups bind more strongly and increase the complexity of the interaction between proteins and a cell. A triplet of R/K’s results in a protein binding to the heparan sulfate proteoglycans (HSPGs) on the surface of a cell, but as the HSPGs are recycled by being brought into vesicles within the ce)ll, the bound proteins are also internalized. These internalized proteins are then fused with lysosomes and the proteins are at least partially degraded by proteases. The proteins were released from the HSPGs by the degradation of the heparan. The modified proteins have a variety of fates. Some return to the Golgi for secretion, e.g.HSPGs and heparanase, whereas others are degraded in proteosomes and presented as potential antigen fragments on surface receptors, and still others are are transported to the nucleus. Those proteins transported into the nucleus have four R/K’s or to neighboring pairs of R/K’s, e.g. HIV-TAT, heparanase and transglutaminase 2 (?) Heparanase is intimately involved in cancer proliferation and transglutaminase is involved in Celiac and inflammation.

I have reproduced below the sequences of several human proteins from the National Center for Biotechnology Information. For simplicity, I have deleted the “uninteresting” amino acids between the heparin-binding domains. You will also see an occasional negatively charged amino acids (D/E) within the R/K groups and their hydrophobic neighbors. These amino acids bind to the amino sugars of the heparin.

transglutaminase 2
M---REKLVVRR---KFLKNAGRDCSRR---RRWK---KIRILGEPKQKRK

heparanase
M---REHYQKKFKNSTYSR---KLLRKSTFKNAK---RRKTAKMLKSFLK---RPGKK---KKLVGTK---KRRKLR

Tat [Human immunodeficiency virus 1]
M---KCYCKK---RKKRKHRRGTPQSSK---KEQKKTVASKAER

Chain A, Interleukin- 1 Beta
A---KKKMEKRFVFNK

lactoferrin
M---RRRR---RNMRKVR---RRAR---KGKK---KRKPVTEAR

Preventing Allergies

The cause of allergies and autoimmune degenerative diseases is inflammation.

As a scientist, I am concerned with how the body works at the molecular level. I try to understand how molecules of cells interact to cause disease. So if you tell me that you have an allergy, I want to understand how you became allergic and I am much less interested in how you avoid triggering your allergy. If you say that your allergy is triggered by ragweed pollen, I want to know the shape and structure of the proteins or carbohydrates of the pollen that actually come in contact with receptors on the surface of your cells and trigger the allergic response, but I also want to trace those interactions back to the original events that started the allergy.

Allergies are mistakes of your immune system. Your body should learn to ignore common food and environmental molecules as it ignores itself. There is an elaborate system used by cells of your body to disassemble and display fragments of dangerous pathogens on the surface of cells for evaluation by the immune system. Inappropriate display of innocuous or self molecules is part of the problem in allergies and autoimmunity.

Ragweed pollen, for example, will cause no reaction unless pollen proteins bind to antibodies (IgE) held in receptors on the surface of mast cells. We know that ragweed pollen binds to anti-ragweed antibodies on the surface of mast cells of allergic individuals and triggers the release of histamine and other molecules that give the symptoms of allergy. That’s why you take antihistamines to remediate the allergic symptoms. The first questions are what are the ragweed molecules to which the antibodies bind, i.e. the ragweed allergens and why is this allergic person producing anti-ragweed antibodies?

We know that the ragweed allergens are common pollen proteins, but why are they particularly prone to producing allergies? I tried to figure out this riddle by asking if there is something about these proteins that make their transport into cells more likely. I had just discovered that a particular amino acid sequence, a triplet of basic amino acids, lysine or arginine, resulted in transport of proteins into cells. This triplet that provides binding to heparin is found, for example in the nasty HIV protein, called TAT that moves on heparan sulfate proteoglycans (HSPGs) from infected to uninfected human cells and paves the way for the spread of infection. This triplet is also found in heparanase, that is first secreted by cells in an inactive form, is brought back into cells by binding to HSPGs, is activated by partial digestion and resecreted for action in the extracellular environment. This heparin-binding triplet can also be added to other proteins, e.g. the fluorescent jellyfish protein, to transport those proteins into cells.

Examination of ragweed pollen and subsequently dozens of other common allergens revealed that each one (or a close relative) possessed the unusual heparin-binding triplet of basic amino acids. The basic charged character of these sequences also determined that these parts of proteins would be present as accessible coils on the surface of the proteins. It is interesting that people suffering from the autoimmune disease of lupus produce antibodies to most of the proteins found in the nucleus of their cells. These nuclear proteins bind to nucleic acids, that mimic the structure of heparin and in many cases have triplets of heparin-binding basic amino acids. Thus, it appears that allergenic proteins enhance the chance of uptake by cells that can display them to the immune system, because of their triplet heparin-binding domains and the immune system subsequently produces antibodies that bind to other regions of the protein allergens. This explains how the antibodies are produced to these allergens, but it does not explain why some people produce antibodies to environmental antigens and healthy people do not.

Allergic people readily expand their allergies to include new allergens. What is it about these susceptible people that makes them allergic? I think that the answer is inflammation. Inflammation leads to a disruption of normal production of heparan sulfate proteoglycans and as a consequence to a change in how external proteins interact with cells involved in processing antigens for presentation to the immune system. This means that people with chronic inflammation, also called the metabolic syndrome, are not only increasingly susceptible to diabetes, arthritis, heart disease, etc. but they are also at risk for picking up new allergies. This also suggests that an anti-inflammatory diet and lifestyle changes would be of great benefit to those with allergies. Unfortunately, because of immunological memory, it will take years to deplete the population of antibody secreting cells that provide the basis for a specific allergy and during this depletion time, the allergen would have to be scrupulously avoided. It might also mean that autoimmune diseases such as type I diabetes might be treated by depletion of anti-beta cell antibodies and their secreting B cells along with a shift to an aggressively anti-inflammatory diet.

It is my belief that many of the genetic components of allergies and autoimmune diseases would not be experienced in the absence of chronic inflammation as a precipitating condition.