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Gilbert Ling's Theory Confirmed - ATP Required For Protein Solubility & Aggregation Control

Discussion in 'Scientific Studies' started by haidut, May 26, 2017.

  1. haidut

    haidut Member

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    As some of you know, the Wikipedia article on Gilbert Ling's AI hypothesis was removed due to being too "alternative" and not accepted as valid by the scientific "consensus". In the mainstream biochemical view, ATP is nothing but an energy currency for cells and has no role in maintaining cellular structure. In fact, mainstream biochemistry claims the cell has little structure, consisting instead of a bag of salty water solution containing electrolytes and proteins.
    This new study shows that ATP has a crucial role in allowing proteins to dissolve properly and stay inside the cell in a proper structure. As the study mentions, in aging and neurodegenerative conditions such as Alzheimer's Disease (AD) and Creutzfeldt–Jakob (mad cow) disease, these cellular proteins tend to aggregate in abnormally shaped clumps and ultimately cause cell death. If ATP was simply an energetic currency then the cell would maintain it in micromolar concentrations. But the cells go through great trouble to maintain millimolar concentrations of ATP and the only reasonable explanation is the role of ATP as hydrotrope and protein aggregation watchdog, as ATP function as such only in millimolar concentrations. So, keeping ATP levels high (aka high metabolism) is crucial for maintaining proper structure of the cell and preventing degeneration commonly seen in aging and diseases. As such, once again, "function and structure are interdependent --RP".
    Hey @Drareg, @aguilaroja and @Such_Saturation - you guys may want to look at this as I know you were interested in the confirmation of some of Ling's postulates.


    Journal Club: ATP could help proteins dissolve in cells, prompting a rethink about its function and evolution | National Academy of Sciences
    "...ATP’s protein-solubilizing role may be even more ancient than its energy storage functions, Krishnan says. Large molecules clumping together would have posed an early problem during the evolution of life, so it’s possible that ATP—as one of the basic building blocks of DNA and RNA—may have been deployed to solubilize proteins."

    “...This sort of turns ATP on its head, the idea that ATP evolved to solubilize proteins and only later to function as an energy source,” Weiss says. “One of the first examples of chemical energy we learn as kids is ATP, and it’s exciting to think we might have to re-teach that role.”


    ATP as a biological hydrotrope | Science

    "...We reconstituted FUS compartments in vitro at physiological concentration (7) using low salt (70 mM) buffer conditions (8) and tested the effect of ATP around its physiological concentration range of 2 to 8 mM (9), complexed with Mg2+ ions (ATP-Mg) (10). (For the chemical structures of all compounds used in this paper, see figs. S1A and S2A.) Indeed, 8 mM ATP-Mg prevented liquid-liquid phase separation and dissolved previously formed drops (Fig. 1, A and B). We observed similar effects of ATP with other proteins that form liquid compartments (11) (Fig. 1, A and B). A fluorescent tracer molecule confirmed that ATP was enriched in the liquid drops (Fig. 1C). Importantly, APPNP was as efficient as ATP in preventing the formation of liquid drops (Fig. 1, D and F). Thus, at millimolar concentrations, ATP dissolved drops independently of its role as an energy source."

    "...Given the similarities between classical hydrotropes and ATP (Fig. 2A), we sought to explore whether ATP might act like a hydrotrope in a classical hydrotrope assay, in which the solubility of a hydrophobic compound such as fluorescein diacetate (FDA) in water is quantified as a function of hydrotrope concentration (15). For a hydrotrope such as NaXS, as its concentration increases, FDA solubility in water increases and the latter is quantified by ultraviolet absorption at 480 nm of the aqueous medium (Fig. 2B, upper panel). NaXS required concentrations greater than ~1 M to effectively solubilize FDA (Fig. 2B). However, ATP achieved the same effect at concentrations as low as 100 mM (Fig. 2B, lower panel). Water-soluble assemblies comprising amphiphiles (e.g., hydrotropes and surfactants) (fig. S2A) structured around a hydrophobic molecule consist of relatively nonpolar interior microenvironment. An organic dye, ANS (8-anilino-1-naphthalenesulfonic acid) is commonly used to probe the polarity near the head group (hydrophilic) or interfacial region of such amphiphilic assemblies. The fluorescence emission maximum of ANS is blue-shifted in a hydrophobic microenvironment (Fig. 2C, upper panel). Thus, the concentration at which the blue shift of ANS is maximal is a widely used indicator of the effectiveness of a hydrotrope (15, 22). Classical hydrotropes such as NaXS and NaTO induce a blue shift in the emission spectrum of ANS (15). ATP altered the emission spectrum of ANS to the same degree as NaXS and NaTO, albeit at much lower concentrations (Fig. 2C, lower panel). This shows that ATP is much more efficient than classical hydrotropes for creating a solubilizing microenvironment for hydrophobic molecules that are unlike micelles (fig. S2B and supplementary text)."

    "...We next investigated whether high concentrations of ATP could also prevent protein aggregation. Using a centrifugation assay, we showed that millimolar concentrations of ATP kept FUS soluble and that higher concentrations of ATP prevent FUS aggregation (Fig. 3, A and B, and fig. S3, A to C). Notably, millimolar concentrations of ATP could also dissolve preformed FUS fibers, albeit at higher concentrations than were required to prevent aggregation (Fig. 3, C and D, and fig. S3, D to F). We also showed, using incorporation of thioflavin T, that ATP prevents the aggregation of two proteins that tend to cause amyloids: (i) synthetic Aß42 peptides, which aggregate to form Amyloid beta, associated with Alzheimer’s disease (25); and (ii) the prion domain of the yeast protein Mot3 (Mot3-PrD), which is thought to form functional aggregates in yeast cells (26) (Fig. 3, E and F)."

    "...To investigate the role of ATP in a more physiological mixture of biological molecules at physiological concentrations, we studied protein aggregation in chicken egg white. At high temperatures, egg proteins lose their native conformation, thus exposing hidden hydrophobic patches within the proteins, which drive the aggregation of egg-white proteins. ATP inhibited the aggregation of boiled egg white in a dose-dependent manner (Fig. 4, A to C; fig. S4, A and B; and movie S1). Thus, ATP appears to prevent aggregation of egg white by stabilizing the native globular state (fig. S4C). Taken together, our experiments suggest that ATP has two different chemical properties. At micromolar concentrations, it acts as an energy source to drive chemical reactions, whereas at millimolar concentrations it acts to solubilize proteins."

    "...The high concentration of ATP in cells has long been a puzzle, because ATP-dependent enzymes require micromolar concentrations of ATP. Why, then, would a cell invest so much energy into maintaining its cytoplasmic ATP concentration at ~5 mM? One explanation is that the free-energy difference between ATP and ADP is required to drive ATP-dependent reactions and that the 50-fold higher ATP/ADP ratio is necessary to fuel the myriad metabolic reactions taking place simultaneously in a cell. However, cytoplasm can have protein concentrations over 100 mg/mL (31–33), and it is extremely difficult to maintain such high protein concentrations in a test tube without spontaneous aggregation. The hydrotrope activity of ATP may help keep proteins soluble in the cytoplasm (34) and provide another, but not mutually exclusive, explanation for high ATP concentrations in cells. Possibly also, as the levels of ATP decline with age or mitochondrial impairment, this could lead to increased aggregation and consequently neurodegenerative decline during aging. Our work in this paper has focused on the role of ATP in keeping unstructured proteins soluble, because these are the types of proteins that have a propensity to form pathological aggregates (35). It will be interesting to examine the role of high ATP concentrations in stability and function of multimolecular protein machines."

    Some excerpts from Ray discussing the role of ATP in the cell.
    Age Pigment: Cause And Effect Of Aging And Stress
    "...In Ling's view, ATP causes cells to retain water in a tightly organized form, and when ATP is seriously depleted, adsorbed potassium is released to become osmotically active, and sodium and chloride enter along with water, which is then in the "loosely held" state of normal bulk water, lacking the special properties of water that had been dominated by polymer surfaces. This swelling has been called "depolarization swelling," and is partly responsible for the swelling of injured or dying cells. Presumably, less drastic energy changes will cause physiological changes in the amount of organized water , in which water is usefully retained in proportion to the energy level."

    "...Estrogen's early effects include activation of dehydrogenases and peroxidase (Jellinck and Lyttle, 1971 ; Talalay and Williams-Ashman, 1958; Temple, et al., 1960), and it participates in the interaction of NADH and NADPH as well as in the oxidation of NADH (Beard and Hollander, 1962, Hollander and Stephens, 1959; Yokota and Yamazaki, 1965; Lucas, et al., 1955; Villee, et al., 1965). The oxidation of NADH is involved in many harmful free radical processes. (McCay, 1971, an early study, but recently others have been published.) The most visible early effect of estrogen is to stimulate water-uptake by the cell. How it causes this immediate swelling isn't known, but it probably involves this consumption of oxygen, since simply cutting off the cell's supply of oxygen also causes water-uptake and edema. (Maybe ATP is needed to "extrude" water from the cell generally, as it is in the mitochondria.) The oxidation of NADH tends to raise the pH of the cell, and by increasing the electrical charge of the proteins this would be likely to cause swelling. I suspect that the normal (respiratory) function of oxygen is to adjust the electrical charge of the cell proteins, in a way that favors ATP synthesis and controls hydration. ATP (which is an acid, and is strongly adsorbed to proteins, influencing their charge) is known to cause swollen mitochondria to extrude water."
     
  2. Such_Saturation

    Such_Saturation Member

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    Holy crap that made it on Science?
     
  3. Drareg

    Drareg Member

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    Thanks,this is very interesting.

    Interesting because this may imply more protein in the diet may require more atp-mg or the opposite more atp-mg and protein is used more efficiently?
    Some may get the impression that too much ATP will make your proteins soluble.
     
  4. OP
    haidut

    haidut Member

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    I know, right? Probably because they can easily claim another "paradigm shift" or "scientific revolution" and explain their past ignorance/fraud away.
     
  5. OP
    haidut

    haidut Member

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    I agree, and incidentally there is plenty of evidence that better metabolism or magnesium supplementation (hence - more ATP) allow one to get by on much less protein probably due to increased efficiency or utilization due to increase solubility. Or if the diet is high protein then it protects the person's kidneys and liver.
     
  6. Travis

    Travis Member

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    An attack on the "high-energy phosphate bond" concept can be found here: Reassessment of the Role of ATP in Vivo

    Here are some quotes:
    You might wonder why most people think it's necessary for muscle contraction? Read on:
    I was questioning the role of ATP in muscle contraction myself after reading about microtubules. It seems silly that a diffusible molecule (ATP) would be the cause of muscle contraction. Why would the body rely on diffusion when there are microtubules carrying electrons through every myosin fiber? Perhaps ATP is involved in some way, but creatine is probably more important.
    Don't hold back Dr. Banks. I would have said, "Words fail to describe the idiocy of likening ATP synthesase to a vending machine."
    He then goes on to attack Mitchell, who would go on to win a Nobel Prize for his chemi-osmotic theory of ATP production which is still taught today in textbooks.
    Mitchell may have been on the right track. You really do need a proton (H⁺) to form ATP from ADP and phosphate.
    ADP + HPO₄²⁻ + H⁺ ⟹ ATP + H₂O
    I have seen a good experiment which measured ΔG° for ATP at –4.7 kcal/mol (Podolsky & Morales). Dr. Banks (who doesn't even think ΔG° is important) thinks the most reliable estimate is –5.6 kcal/mol. These values are little different than the Gibbs free energies of inorganic pyrophosphate. Gilbert Ling also thinks the concept of the "high-energy phosphate bond" is ridiculous: "In time it became established that while ATP does not carry so-called high-energy phosphate bonds, ATP has powerful affinity for the protein it interacts with, thereby affirming the unique role of this compound as the queen of cardinal adsorbents in maintaining the resting living state and in shifting between alternate states."–Ling
     
  7. yerrag

    yerrag Member

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    So, this is more reason then for arguing for oxidative metabolism right? Over and above it producing energy most efficiently, oxidative metabolism contributes to the integrity of our cells. If the body is further away from using this process, it will lose its structure that maintains the ionic balance. This ionic balance influences the electrical impulses, such as in the beating and pumping of the heart. Whether or not it does its job of distributing oxygen and sugar and nutrition to the cells, and of transporting out of the cell of its waste and by-products, is wholly dependent on enabling the body to run with all four cylinders - with efficiency and with integrity.
     
  8. Travis

    Travis Member

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    Yeah. There is something wrong the idea that ATP is "a fuel" which transfers energy in its "high-energy phosphate bond".

    It's still necessary, but Gilbert Ling and Barbara Banks (⇑) think that its misunderstood.

    Some textbooks, and Wikipedia, give the impression that the entire point of the electron transport chain, the citric acid cycle, glycolysis, and β-oxidation is merely to regenerate ATP. The cell purportedly can then take this "stored chemical energy" to other parts of the cell—notably muscle and Na⁺/K⁺ ATPase (another biological unicorn)—and "release it".

    But in the process of ATP generation, we already have electron flow within the cell. I think that instead electron flow is the main purpose of the the citric acid cycle, glycolysis, and β-oxidation. I think the production of ATP is to buffer the excess H⁺ created and to lower heat. The formation of ATP from ADP and P cools the cells as energy is taken from the environment (~4.7 kcal/mol) to form ATP. This is made apparent by the fact that uncoupling (from ATP synthesis) mitochondria leads to increased heat production.
     
  9. Mito

    Mito Member

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    Interesing thought. If true, supplementing exogenous ATP would not be beneficial.
     
  10. Ledo

    Ledo Member

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    Hi @Travis ,

    I have never closely studied these cellular energy mechanisms with the intent of really learning much or being able to question much. I have really only cared about what I can eat or do from the big perspective to optimize them as much as possible with the really few inputs we have as organisms.

    So no intent to challenge you at all but isn't what you suggest either absurd or alternatively, a sad state of affairs that the science consensus would have things so backwards some guy on the internet could so casually up end it all with a brief refitting of the entire theory of how our orgaanism makes energy?

    FWIW I hope you are right. Maybe we can make some progress for a change. LOL
     
  11. Travis

    Travis Member

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    It's not just me saying this, it's respectable biochemists Barbara Banks, C.A. Vernon, and Gilbert Ling.

    If I'm merely "some guy on the internet", then you're merely "that other guy on the internet".

    And Ray Peat quotes are always admissible here:
    You have to realize that the concept of the "high-energy phosphate bond" was formulated in 1941 based on imprecise caloric measurements. Lipmann probably didn't subtract the heat of ionization leading to excessive values. Almost every single measurement since then—in addition to quantum mechanical calculations—has given values little different that inorganic pyrophosphate.

    Most of the biochemistry taught in textbooks was elaborated in the 1960s. This was before the discovery of microtubules inside of nerves linked to mitochondria. There is simply no other biological structure capable of long-distance energy transfer.

    This isn't a "casual up-ending". The Banks & Vernon article is 26 pages of good information and my Gilbert Ling book is 600+ pages of good insight. Gilbert Ling did his own experiments. I have also read also Mitchell's papers on ATP.

    There isn't even a good theory on muscle contraction, and much less on how ATP purportedly "causes" it. The consensus is Andrew Huxley's mind-numbingly stupid Crossbridge Theory, which Harold Hillman says this about:
    As for ATP as an acid base buffer, see here:
    ATP formation caused by acid-base transition of spinach chloroplasts

    As for ADP⇒ATP as an entropic cooling device, see here:
    Table IV
    Uncoupled ATPase Activity and Heat Production by the Sarcoplasmic Reticulum Ca²⁺-ATPase
    REGULATION BY ADP
     
  12. OP
    haidut

    haidut Member

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    I suspect ATP is nothing but a sign/symptom of a well functioning electron flow. It by itself probably has a very minor role in muscle function or the function of any organ for that reason. Peat wrote about Szent-Gyorgyi making "dead" muscle contract like normal by supplying the proper ratios of electron donors and acceptors (quinones).
     
  13. Travis

    Travis Member

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    Yeah, I agree. It seems more like a "side-effect" than the primary agent. I need to read about those Szent-Györgyi experiments someday. Coenzyme Q₁₀ (coenzyme quinone) is way more important to muscle contraction in the heart than ATP seems to be. A deficiency in CoQ₁₀ can actually cause heart failure (this can be caused by statins through inhibiting CoQ₁₀ tail synthesis. The same isoprene units that make-up cholesterol also form the tail of CoQ₁₀.)

    If you look at the chemistry of ATP, you see that it buffers free H⁺ and lowers entropy. It does other things as well. It participates in numerous enzymatic kinase reactions.

    Everyone intuitively knows that electric potential is what causes muscle contraction, not ATP. But before the discovery of microtubules, chemists were puzzled because most proteins are non-conductive. Szent-Györgyi theorized that this was because chemists usually measure the conductivity of globular proteins (like casein) instead of long structural proteins. He hypothesized that methylglyoxal played a role in unsaturating the peptide backbone of structural proteins, making them electrically conductive.

    But the erroneous idea of the "high-energy phosphate bond" has been clouding people's perceptions about ATP and muscle contraction for over 80 years.

    Even when Mitchell formulated his chemiosmotic theory in the 60s that describes how H⁺ turns ADP into ATP, he was biased in this manner. He knew that the one of the only ways to do chemical work is to create an electric potential, or a proton gradient (in his words). But if the cell already has an electric gradient which can perform muscle contraction directly, then why do you need to use this gradient form ATP?

    I think ATP has a strong role in donating H⁺ to O₂ to form H₂O. In fact, this almost certainly has to be the case. Nicotinamide adenine dinucleotide (NADH) only differs from NAD⁺ by one H⁺ and 2e⁻, or hydride [:H⁻]. To make water from O₂ in cytochrome c oxidase, you need one additional H⁺ for every [:H⁻] donated by NADH which must come from somewhere.

    O₂=12e⁻
    2H₂O=16e⁻
    Δ=4e⁻

    O₂+4e⁻(2NADH)+2H⁺(2NADH)+2H⁺(which must come from somewhere)=2H₂O

    This is why you cannot permanently form and store ATP. Every H⁺ that is used to form ATP must be donated to O₂ at some point. Transporting ATP much further that it's source will cause a pH inbalance. Adenosine triphosphate must exist in a more-or-less steady-state.

    The more people think about the ATP phosphate bond as a source of "energy", the less they think about electrons or biophotons driving energy. Biophotons aren't woo. There are textbooks written on it and we have all seen glowing insects. Some animals even have light that emits from their eyes. This can be seen in the dark.

    There are only two main ways (that I'm aware) that you could use ATP to produce energy. Entropy is produced from breaking a bond and can manifest as heat. This comes from the additional kinetic energy of having two smaller molecules instead of one larger one. I haven't heard of anyone try to say that heat or entropy creates muscle contraction, although this function of ATP can be utilized during mitochondrial uncoupling to produce heat.

    The second way is to set-up an electric potential: the reverse of the Mitchell ATP-chemiosmotic gradient. This actually seems plausible, but would make molecules such as acetylcholine, creatine, and NADH every bit as energetic as ATP.

    The way I generally see energy production is that charges are separated during the citric acid cycle (H⁺, :H⁻) and then recombined in a manner that sets-up an electric potential. "High-energy phosphate bond" proponents can never explain how this imaginary energy is harnessed in a way that makes even the slightest bit of sense.
     
  14. OP
    haidut

    haidut Member

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    That was a great explanation, thanks. So, maybe the primary role of ATP is to generate heat/water, even in the non-uncoupled state?? I always wondered why ATP is one of the most potent downregulators of the enzyme PDH. If ATP was indeed an energy storage molecule why wouldn't the body want more, in fact as much as it can get? Instead, if ATP accumulates it downregulates its own synthesis AND activates the uncoupling proteins. But muscle contraction does not deteriorate the slightest bit, showing (as you said) that it is not ATP that drives the process.
    In regards to the above quote - by disrupting the CoQ10 synthesis statins can indeed do all kinds of damage to muscle fibers and affect the ability to contract. If statins can cause heart failure through this mechanism, what other muscle disorder do you think they can cause? How about ALS, Huntington, and myasthenia gravis?
    Medscape: Medscape Access
    http://www.medscape.org/viewarticle/581181
    STATINS MAY AGGRAVATE MYASTHENIA GRAVIS
    Statin-associated weakness in myasthenia gravis: a case report

    Given that statins also inhibit the synthesis of vitamin K2 (the alternative electron carrier then CoQ10 is low), their names should be changed to "quinone antagonists" to reflect the profound metabolic antagonism that occurs with the use of these drugs.
    Statins stimulate atherosclerosis and heart failure: pharmacological mechanisms. - PubMed - NCBI
    "...In contrast to the current belief that cholesterol reduction with statins decreases atherosclerosis, we present a perspective that statins may be causative in coronary artery calcification and can function as mitochondrial toxins that impair muscle function in the heart and blood vessels through the depletion of coenzyme Q10 and 'heme A', and thereby ATP generation. Statins inhibit the synthesis of vitamin K2, the cofactor for matrix Gla-protein activation, which in turn protects arteries from calcification. Statins inhibit the biosynthesis of selenium containing proteins, one of which is glutathione peroxidase serving to suppress peroxidative stress. An impairment of selenoprotein biosynthesis may be a factor in congestive heart failure, reminiscent of the dilated cardiomyopathies seen with selenium deficiency. Thus, the epidemic of heart failure and atherosclerosis that plagues the modern world may paradoxically be aggravated by the pervasive use of statin drugs. We propose that current statin treatment guidelines be critically reevaluated."

    Btw, there is a proposal that excessive ATP drive cancer appearance and progression.
    Does excessive adenosine 5'-triphosphate formation in cells lead to malignancy? A hypothesis on cancer. - PubMed - NCBI
     
  15. Travis

    Travis Member

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    Yeah. I would find it funny—it it wasn't so destructive—that a drug class (statins) mad to prevent cardiovascular events actually contributes to two of them: congestive heat failure from low CoQ₁₀ biosynthesis, and arterial calcification from low vitamin K₂ synthesis.

    These "opposing" effects (protection vs causation) might seem to balance eachother, which could then be used to argue that statins could have more a beneficial effect than a deleterious effect. However, I think we all here know that depressing cholesterol synthesis wouldn't be expected to improve cardiovascular disease anyhow. This makes statins one of the most Orwellian (triple-plus bad?) drug therapies ever conceived, although their discoverer (Eno) had good intentions.

    He was blinded by the Ancel Keyesian Lipid Hypothesis.
     
  16. lollipop

    lollipop Guest

  17. yerrag

    yerrag Member

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    That's good news, isn't it?

    The cancer treatment of the future:

    If you like your hair, you can keep your hair.

    I like marketing. I really do.
     
  18. lollipop

    lollipop Guest

    :lol
     
  19. Travis

    Travis Member

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    These people. I still haven't seen anything as safe effective as methylglyoxal or bromopyruvate for cancer. These two drugs (one is natural) reverse tumors in 90% to 100% of cases. I have rat studies that show this. The studies come out of India and China.

    This is why I don't get excited about most cancer drugs that only work about 20% of the time. Methylglyoxal is so effective that it captivated Albert Szent-Györgyi.

    And besides inhibiting synthesis of CoQ₁₀ and vitamin K₂, statins inhibit the production of heme. I can't see how this can be a good thing for normal cells, since you would expect this to inhibit respiration. Heme needs a "tail" (farnesyl) too, which is constructed from isoprene units.

    Statins inhibit every downstream event dependent on isoprene units, not just cholesterol synthesis.
     
  20. chispas

    chispas Member

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    That's what the scientific method has always aimed to achieve.
     
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