- DNA bases stack.
- Heparin binding sites of proteins are basic amino acids (Arg, Lys).
- Sugar binding sites in enzymes and lectins are hydrophobic amino acids (Trp, Tyr, Phe).
- Nuclear translocation signals, quartets of basic amino acids, bind to receptors with tryptophans.
- Tryptophans are the most highly conserved amino acids in the same proteins across great evolutionary distances.
- Hydrophobic bonding between tryptophan and a sugar or basic amino acid is ten times greater than hydrogen or ionic bonds.
- Tryptophan/Arginine ladders zip regions of proteins together.
- Polyphenols can disrupt cellular protein interactions by binding to receptors for carbohydrates/heparin, steroid hormones, amyloids, etc.
- Heparin holds dozens of hormones to receptors and changes the shapes of proteins, e.g. clotting and complement.
- Most nucleic acid binding proteins will also bind to the more negatively charged heparin.
- Bacteria use a pair of lysines to mark proteins for export.
- Peptides containing the basic amino acids of heparin binding domains (also produced by the specificity of gastric proteases) are antimicrobial, e.g. defensins, and so are plant polyphenols.
- Many drugs are active because they are domesticated plant polyphenols.
Monday, March 24, 2014
— all 200 Posts —
I started posting to Cooling Inflammation on 21 Aug, 2008 with How Your Diet Makes You Sick or Healthy. My impetus for writing was my growing awareness that diet was the major reason why people were sick, and that health myths were preventing people from being healthy. Inflammation originated by diet-inflicted injury and people attributed their sickness to genetics, environmental toxins and pervasive pathogens.
My Path to the Obvious
My research background started with plant biochemistry, including carbohydrate structural analysis and polyphenol chemistry. At that stage I was interested in understanding how plants protected (phytoalexins) themselves from pathogens, and I expected to use this perspective to explore human innate immunity. From there, I went on to enzymology and protein characterization, biofilm structure, plant genetic engineering and breeding, monoclonal antibody production, mycotoxin detection, stem cell analysis, passive immunity in neonates, computational modeling of collagen and heparin binding, and heparan sulfate proteoglycan inhibition by inflammation. These were temporary foci and the research imperatives, in retrospect, prevented me from seeing the bigger pictures, although they did leave me with a broad skill set.
Perspective: Water and Surface Tension
When I finally decided to slow down, smell the flowers and start having kids, I switched from research to teaching, from university to small liberal arts college. For the first time, I actually thought about what I was teaching and my first revelation was that after teaching biochemistry for twenty years, I didn’t understand water and surface tension. I could provide the platitudes from the Molecular Biology of the Cell, but I couldn’t do it mechanistically with colliding, sticky, energetic water molecules in my mind or at the blackboard. I had to develop functional explanations of hydrogen bonds, entropy and thermal energy, that translated into the structuring of a layer of water molecules responsible for hydrophobic interactions and surface tension. I extended that to include an explanation of the two layers of water holding together cytoplasmic membranes, the tube of structured water that holds together the cylinder of stacked bases in DNA or the shrink wrapping water layer surrounding proteins.
Perspective: Heparin Binding and Amphipathy of Sugars and Basic Amino Acids
As the kids got older, I started to dabble in research again and my expertise in carbohydrate chemistry led me into cartilage (mostly the glycosaminoglycan, GAG, chondroitin sulfate) synthesis and ultimately another GAG, heparan sulfate proteoglycans (HSPGs). I was attracted to the dynamic HSPGs, that recycled with a half-life of six hours and formed layers around chondrocytes that secreted cartilage as they burrowed/ate through living cartilage. I learned that the heparin filled granules of mast cells could be stained with berberine, which similarly stained the heparin in basement membranes of tissues and amyloids of Alzheimer’s, atherosclerosis and diabetes. I was led by protein modeling of collagens to the binding of heparin to proteins and the revelation that basic amino acids (heparin binding domains) and sugars (heparin) are amphipathic, i.e. they have both hydrophobic and hydrophilic regions. This is also true of plant polyphenolics. Thus, polyphenolics, “basic” amino acids, “hydrophobic” amino acids, and sugars will all stack together.
From Heparin Binding to Antigen Presentation
As soon as I realized that basic amino acids were involved in heparin binding, I started to look for the basic amino acids (R for arginine and K for lysine in amino acid sequences) in proteins known to bind heparin. After study of hundreds of structures, it became obvious that heparin binding domains were simply a pair of basic amino acids (RR or KK or RK) with another within a distance of six amino acids. No particular structure was necessary, as I later deduced, since binding to the heparin provided the structure. In fact, in many X-ray crystallographic structures, the heparin binding regions on the surface of the protein are missing, because they are not in a defined shape. I suspected that protein antigens involved in autoimmunity and allergy might be brought into cells for presentation to the immune system by interacting with HSPGs on the surface and so started to check them out for heparin binding domains. I was very skillful at picking out pairs of Ks or Rs within sequences of hundreds of amino acids by that time, so I was shocked to see that the first dozen antigens that I checked, all had a triplet of basic amino acids. I had discovered that autoantigens and allergens utilize a basic triplet analogous to the basic quartet used in nuclear translocation! This also explained why proteins that interact with nucleic acids and are transported into the nucleus with a basic quartet are also prominent autoantigens.
Gut Flora and Immunity
Twenty years ago I read a curious description of leprosy that said that the course of infection could be either innocuous or devastating depending on whether the aggressive or the suppressive part of the immune system dominated. I remained perplexed until I realized that diet and gut flora were the major determinants. I was aware of the importance of diet at the outset of this blog, because it was clear that diet trumped genetics. I was also aware thirty years ago in my studies of passive immunity, that milk contained bifidus factor, now known to be milk oligosaccharides, that controlled the growth of Lactobacilli that in turn controlled the development of the neonate immune system. It was also known that bacteria-free mice had impaired immune systems. It still took me several years for the relationship between diet, gut flora and immunity to make sense. I began searching the literature for connections between gut flora and development of the immune system and soon noted experiments that linked filamentous bacteria with aggressive components and Clostridium spp. with Tregs. A further refinement was linking resistant starch, a soluble fiber, with Clostridium.
My Current Views are Summarized in Three Health Diagrams
Diet, Gut Flora, Inflammation, Antigen Presentation, Tregs and Autoimmunity
Protein from the body and from food don’t normally stimulate the immune system, because there in no inflammation, the proteins lack basic triplets that enhance presentation, and antibody production and aggressive T cells are suppressed by Tregs. Diet can throw the balance toward autoimmunity and allergy, by producing inflammation, e.g. hyperglycemia/AGE or high omega-6 fatty acids/prostaglandins, and starving gut flora needed for Treg production by eating processed food lacking soluble fiber. The combination of inflammation and Treg deficiency causes proteins, either self or potential allergens, which have basic triplets to be presented to the immune system and stimulates attack by the immune system.
The Cure is to Cool Inflammation and Stimulate Tregs with Diet and Bacteria
I have provided an outline with The Anti-Inflammatory Diet to avoid inflammation, to stimulate existing gut flora with soluble fiber and encourage Treg production. Mark Sisson, on Mark’s Daily Apple has provided an excellent dietary guide that also provides starch guidelines. If you already have symptoms of autoimmune disease or allergies, then Richard Nikoley provides gut flora repair advice on Free the Animal, and Dr. B G provides more details on Animal Pharm.
Autoimmunity and allergies are not genetic destiny and they can be cured with diet and bacteria.