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Prof Trevor Marshall
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Well, I guess you may have noticed that I don't spend a lot of time on the board these days:X I have been busy working on firming up the final bits of the Marshall Pathogenesis - the bits that the skeptics still point fingers at:):)

Some of you will know that human protein molecules are in constant motion. Indeed, the NMR/MRI scanners rely upon this motion to image inside your body. They scan the resonant frequencies of water, and several other smaller molecules.

There is a branch of molecular biology which focuses on exploring this motion, and simulating the proteins down to the level of the interatomic forces, as they vary femptosecond by femptosecond (a femptosecond is 10 ** -15 of a second). It takes big computers to play this game, the compute times are horrendous. For example, it took me 10 hours on the fastest available desktop CPU to simulate 750 picoseconds (10 ** -12 seconds) of interaction between the VDR and Olmesartan.

I have also studied 25-D and 1,25-D but it is Olmesartan that the naysayers have focused upon, so today we will declare - game over - Olmesartan activates the VDR so that it can bind to the transcription coactivators, and transcribe genes from the DNA.

I have put online three versions of a short movie, representing about 18 picoseconds of time. The first, in Podcast format, can be downloaded by right-clicking on this link:
http://autoimmunityresearch.org/models/vdr-olme-podcast.mp4

There is a full resolution MP4 version (720x480) which can be downloaded by right-clicking on this link:
http://autoimmunityresearch.org/models/vdr-olme.mp4

and viewed by free software such as the excellent MPEG StreamClip, free from this URL
http://www.squared5.com/

And finally, a low resolution RealVideo version can be viewed on just about every computer, and it can be activated by left clicking on:
http://autoimmunityresearch.org/models/vdr-olme.ram

The Olmesartan molecule is just to the right of center of the image, in the background. Don't bother too much about the stick and ball amino acids at the lower front of the image - they are very important for reasons too complex to describe here:) The structure of the VDR is represented by the yellowy spiral backbones.

Enjoy!

wrotek
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:) Molecule "twitching" is a Brownian Motion, right ?
Very interesting, one can see how bonds twist and molecules behave in a real world.

Prof Trevor Marshall
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Brownian motion is a pseudo-random motion. These molecules are moving under inter-atomic forces, in a very regular manner. So 'Brownian' would not be a good description,in fact:):)

wrotek
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Ah yes of course, otherwise it would not be possible to simulate... if we did not know where molecule will go.

Molecule won't stop or turn if won't meet something on it's way just like car driver decides to stop near McDonald restaurant :)

Prof Trevor Marshall
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well, the molecule is in a box, to give a finite size to the simulation, and the box is filled with water molecules (about 5000 of them), so there is quite a lot of 'traffic' to stay clear of...

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So some 5,000 molecules banging around in some 750,000 femtoseconds, plus vanderwalls forces, covalent bonds; that sounds like a HUGE simulation.  What kind of machine did you run it on?

I watched the RAM version.  My engineer's heart loves it.  But when does the docking occur?  Is it already accomplished when the video starts?

john

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John, this is why i would like to quantum computer exist, so we did not have to worry about astronomical number of variables :)

Last edited on Fri Mar 2nd, 2007 09:39 by wrotek

Prof Trevor Marshall
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John,
The docking trajectory is problemmatic right now, as the entire field of biology is working with a VDR model (PDB:1DB1) which is genetically engineered to have amino acids missing from a critical region (residues 164-216) of the VDR. The region through which the ligand most likely enters the VDR:X I can get around this later by "growing" the VDR using MD, but first I have to learn to crawl, then walk:):):)

For this simulation, the benicar was tacked onto the VDR, so the software manipulates them as a single molecule (there's generalized software for you). It was placed into the optimum position obtained with Autodock. The 5004 water molecules were added, then the shebang was energy optimized, then the water was allowed to 'soak' into the receptor for a few picoseconds, and then the simulation begins. Actually, there are only an avg 2.5 hydrogen bonds at the very start, and the receptor/ligand complex bound themselves together over the first 600 picoseconds, or so, to a final average of about 7 hbonds, as the Olmesartan and VDR figured out the best orientation and position to nestle into. I have plotted the graphs of this trend, and will no doubt put them in some presentation, sooner or later:):)

I put together the computer system from a motherboard/CPU combination at FRY's, overclocked from 1800 MHz to 3000 MHz (the new E4300 is an overclocker's delight). I upgraded the motherboard when I found this was running twice as fast as my (2005 model) Opteron-based system:X

Operating system is Linux, Fedora core 6, everything is command-line driven (none of this silly GUI stuff)

This weekend I am going to finish off putting together a small 3-machine cluster, which should give me about 5 times the speed I am getting now (cut from 10 hour runs to 2 hours)..

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Command line driven?  There's a Marlboro man for you!

wrotek
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I can drive from command line DOS, and basic html only LOL :) And of course word processor.

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As per movement, I find it interesting that "in silico" is often described with "crystal structure" term which seems to imply a rigid form that is different from a plastic-pliable dance. Even "docking" sounds less organic or flowing.

But the structures move, and twist. I like that concept even when I've seen the videos when Dr Marshall has flipped them around to show different angles than the typical chemical compound 2-D structures you might find in a Wikipedia description. Made sense on the Science DVD label that way too, suggesting there was more than one way to see these. Clearly video is critical in describing the science.

I always see DNA as having to be a moving event else it wouldn't have the spiral shape. Even look at how they relate within the spiral structures. A logic for movement seems evident.--JRF

wrotek
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For less computer skilled :)

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Trevor, how about some music to the clip,for the cynics? Maybe Twisted Sister "We're not gonna take it,anymore" LOL:D

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My Doc won't look at this ...Maybe, if Dr.Sharma or the Americam Thoractic Society "gets it"  I'll get Beni Q6H as I requested... what I got today was -The Doctor says if your herxheimer reaction gets severe, you should give us a call and we'll see what we can do.:X bunk.

CONGRATS Trevor. Thank you for all your incredible work.

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Nice to see somebody from Wrozlaw be as fascinated as I am by Trevor's pathbreaking work!
Evelin
PS: My mother was born in Wrozlaw and in September I plan to visit it with my parents for the first time!:)

Last edited on Sat Mar 10th, 2007 13:26 by Evelin

wrotek
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Hi Evelin :)

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What is the underlying molecular basis behind the fact that olmesartan activates the VDR in a more controllable manner than vitamin D 1,25? Or is this based on clinical experience? What are the limits of molecular modelling in estimating an agonist's effect on a receptor?

Prof Trevor Marshall
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Inge,
The affinity for the VDR of Benicar is low. That's why we need to use a higher concentration.

Although Benicar closes off the Angiotensin II Receptor (AT2R) at below 20mg/day, we need a much higher dose to properly activate the VDR. Thus the displacement of ligands from the VDR is easier to control by dosage than its blockade of the AT2R.

A really high affinity VDR ligand, like the ANTAGONIST Telmisartan (which you don't want to take under any circumstances) only requires a fraction of a tablet to block the action of multiple Benicar tablets for 24 hours or so...

Does that help answer your question?
 

wrotek
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If someone takes telmisartan for hypertension, it is like he was taking steroids to suppresses his innate immune system ? :shock:




Last edited on Thu Aug 14th, 2008 16:18 by wrotek

Prof Trevor Marshall
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Much worse than suppressing the immune system, as the VDR also transcribes Cancer metastasis suppressing proteins, and other very important bodily functions as well :)
 
Luckily, it isn't a very popular ARB :) And they only take it once a day, which is not frequent enough to completely block VDR transcription.
 

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Trevor,

I am afraid it does not really answer my question directly. If you are saying that there is no difference in the way olmesartan activates the VDR as compared to vitamin 1,25 once docked in to the LBP, how can olmesartan activate the VDR in a more controllable manner? (Come to think of it, maybe you said in earlier  posts that olmesartan activates many other receptors than the VDR in a more controllable manner? Then I am sorry for the confusion) 

Inge  

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Inge,
The FDA has a mantra "It's all a matter of Dose."
The agonist effect of Olmesartan occurs at higher doses, and the degree of effect can be adjusted by adjusting the dose.

Whereas with a drug which is too high an affinity, like Telmisartan as an antagonist, you cannot adjust the dose to modulate the degree of the effect.

So Olmesartan is able to displace 1,25-D, or capnine, from the VDR LBP in a controlled manner, dependent on Olmesartan dose (and the concentration of capnine or 1,25-D).
 
This is called "homologous displacement" in most pharmacology texts. It follows a characteristic S-shaped curve.
 

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Trevor-

MP Th1 patients endeavor to restrict VitD intake, sunlight exposure and chlorogenic acid so as to not interfere with the Olmesartan blockade.  Capnine, however, appears to be a compound that cannot be controlled.  So I am wondering...

1) Is there a diagnostic test to check the blood level of this lipid? 

2) Does the level of Capnine indicate the degree of biofilm/microbacterial load?

3) Would knowing the Capnine level predict potential interference with the Olmesartan blockade?

4) Assuming of course there's a lab that can perform the test in the first place, would this data help patients and physicians better understand IP progression and/or fluctuations?

Always interested to hear what you have to say on such matters...

Regards,

TB

Last edited on Mon Jan 26th, 2009 14:39 by TikBitten

Prof Trevor Marshall
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Capnine is really just a "proof of concept." A substance from a common bacterium, Flavobacter, which has the ability to interfere with the immune system by blocking the VDR. I would be very surprised indeed if there was just one bacterial substance that had evolved to block the VDR. I certainly know that Caspase 3 attacks the VDR by proteolysis, and that substance is upregulated in infection. So there are many parallel pathways which all lead to the bacterial survival by closing down antimicrobial peptide production as much as possible.

Benicar displaces the ligands (it can't deal with the Caspase 3) in a concentration-dependent manner, like all receptor ligands.

More info in the discussion at
http://www.marshallprotocol.com/forum39/9348.html

The thing that is becoming really obvious right now is the sheer magnitude of the interactions between the 1 million (or so) bacterial genes and the 25,000 (or so) human genes. The potential total number of interactions is beyond quantification. That's why I say I would be surprised if only capnine was at issue in the pathogenesis, and I doubt that tests for any single metabolite would be much use.

I think it might be possible to use fluorescent markers to illuminate the "biofilm" matrix inside the cells, however, and we may be able to get that to a quantitative assay as the years go by. I spoke about this with respect to work being done on bacterial matrix as a byproduct of the prion research we heard at Karolinska in 2008.
The discussion and video about that is available (for members only) at
http://www.marshallprotocol.com/forum43/11932.html

I hope that helps,
Trevor

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About activating the VDR;

This paper about bone reseach, has some bold conclusions;
http://tinyurl.com/ab2eal

The researchers concluded: "Activation of VDR by PUFAs and curcumin may elicit unique, 1,25(OH)(2)D-3-independent signaling pathways to orchestrate the bioeffects of these lipids in intestine, bone, skin/hair follicle, and other VDR-containing tissues." 

So, my concern is the curcumin. It is suggested that it is activating the VDR! It looks like we really need to handle curcumin with care.

Curcumin is sold over the counter as a painrelif, a powerful supplement for arthritis, and it is also a big part of curry powder (which I happen to love). http://www.phytochemicals.info/phytochemicals/curcumin.php

The MP tells us already, that it is immunomodulating, that we can use it in cooking only not as a supplement;

Tumeric "Twelve scientific, peer-reviewed publications since 1999 suggest that curcumin, the major yellow pigment in tumeric, curry and mustard, may potentiate apoptosis or inhibit growth of selected cancer cells or function as a COX-2 inhibitor several in-vitro and animal models." http://tinyurl.com/nflgz

Curcumin, Tumeric, Curry and Mustard
Some spices, which are produced from plants, can have a chemical effect upon the immune system. Significant use of curcumin or its derivatives, for example, should be avoided while on the MP.
This article (pdf) said, "Twelve scientific, peer-reviewed publications since 1999 suggest that curcumin, the major yellow pigment in tumeric, curry and mustard, may potentiate apoptosis or inhibit growth of selected cancer cells or function as a COX-2 inhibitor several in-vitro and animal models."

-While writing up the summary of my sarcoidosis history, I was reminded that my hip pain occurred in Japan and waned outside of Japan. I have therefore experimented a bit with the food I am eating in Japan. I am rarely eating out, but prepare all by myself. I used a curry spice almost everyday, which I have left out for the past 10 days and the hip pain is almost gone, and this after persisting for many months. On http://en.wikipedia.org/wiki/Curcumin I read about curcumin and its effects. ~Evelin


Does anybody else here have experience or comments about using this?

Last edited on Thu Jan 29th, 2009 08:01 by Lottis

wrotek
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Perhaps Dr Marshall could run it in-silico for VDR. This chemical looks very flexible. I wonder how high affinity is.

Lottis, the website requires registration to view article.

Ps i use curry for zucchini :| Actually i have an appetite for zucchini right now :)

Pubmed version, full article is here http://tinyurl.com/ab2eal
Vitamin D receptor: key roles in bone mineral pathophysiology, molecular mechanism of action, and novel nutritional ligands. Jurutka PW, Bartik L, Whitfield GK, Mathern DR, Barthel TK, Gurevich M, Hsieh JC, Kaczmarska M, Haussler CA, Haussler MR. Department of Integrated Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona, USA. The vitamin D hormone, 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)], binds with high affinity to the nuclear vitamin D receptor (VDR), which recruits its retinoid X receptor (RXR) heterodimeric partner to recognize vitamin D responsive elements (VDREs) in target genes. 1,25(OH)(2)D(3) is known primarily as a regulator of calcium, but it also controls phosphate (re)absorption at the intestine and kidney. Fibroblast growth factor 23 (FGF23) is a phosphaturic hormone produced in osteoblasts that, like PTH, lowers serum phosphate by inhibiting renal reabsorption through Npt2a/Npt2c. Real-time PCR and reporter gene transfection assays were used to probe VDR-mediated transcriptional control by 1,25(OH)(2)D(3). Reporter gene and mammalian two-hybrid transfections, plus competitive receptor binding assays, were used to discover novel VDR ligands. 1,25(OH)(2)D(3) induces FGF23 78-fold in osteoblasts, and because FGF23 in turn represses 1,25(OH)(2)D(3) synthesis, a reciprocal relationship is established, with FGF23 indirectly curtailing 1,25(OH)(2)D(3)-mediated intestinal absorption and counterbalancing renal reabsorption of phosphate, thereby reversing hyperphosphatemia and preventing ectopic calcification. Therefore, a 1,25(OH)(2)D(3)-FGF23 axis regulating phosphate is comparable in importance to the 1,25(OH)(2)D(3)-PTH axis that regulates calcium. 1,25(OH)(2)D(3) also elicits regulation of LRP5, Runx2, PHEX, TRPV6, and Npt2c, all anabolic toward bone, and RANKL, which is catabolic. Regulation of mouse RANKL by 1,25(OH)(2)D(3) supports a cloverleaf model, whereby VDR-RXR heterodimers bound to multiple VDREs are juxtapositioned through chromatin looping to form a supercomplex, potentially allowing simultaneous interactions with multiple co-modulators and chromatin remodeling enzymes. VDR also selectively binds certain omega3/omega6 polyunsaturated fatty acids (PUFAs) with low affinity, leading to transcriptionally active VDR-RXR complexes. Moreover, the turmeric-derived polyphenol, curcumin, activates transcription of a VDRE reporter construct in human colon cancer cells. Activation of VDR by PUFAs and curcumin may elicit unique, 1,25(OH)(2)D(3)-independent signaling pathways to orchestrate the bioeffects of these lipids in intestine, bone, skin/hair follicle, and other VDR-containing tissues. PMID: 18290715 [PubMed - indexed for MEDLINE]
From what i can see the work was in-vitro, to assess curcumin VDR binding.

Last edited on Thu Jan 29th, 2009 05:22 by wrotek

Lottis
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Thank you, wrotek, I changed my link to your  http://tinyurl.com/ab2eal. :)

Yes, of course it is in vitro, but the good thing is that it is in human VDR.
I did not figure out if tumeric only activated the VDRe or the VDR, as the explanation for the immune modulating action.

Are you sure you are longing for zucchini? Maybe it is the curry powder you desire? ;)

wrotek
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Lottis, i think U may be right. I eat a lot of mustard :) I just hope curcumin won't happen to be an antagonist, after all.

Last edited on Sun Feb 1st, 2009 07:38 by wrotek

IngeD
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Hi Lottis. You may want to experiment with the garlic. I have avoided it since early on in the MP as it immediately increased my IP. Guess it is because garlic is a natural antibiotic.

Interesting about the cummin/curry. Why is it all the stuff we love is potentially so bad? Maybe with all its antibiotic/anti inflammatory tendencies it was palliative for us by helping to turn off the immune system. Or just comfort foods.

Wrotek: interesting about the Japanese foods. Pre MP I had Japanese nearly daily. Love the Wasabi. That too is a natural antibiotic (pure horse raddish). Haven't touched any Japanese since start of MP mainly because it was the seafood I went crazy over :). Just realising HOW MUCH of the hot stuff I used to eat. Curry Laksa was another favourite. Avoided since start of MP as it usualy contains some kind of seafood but ...also very spicy.

So much to look forward to :). All the best. IngeD:cool:

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Remember that just because something is 'an antibiotic' doesn't mean it will kill the Th1 nasties. In fact, some of the strongest antibiotics, the beta-Lactams, actually encourage pathogens to change into the persistent form, and some, eg Rocephin, turn off the immune system's ability to go after the Th1 microbiota. Brian Fallon's studies showed that IV Rocephin is purely palliative.

Not all antibiotics kill all bugs...
 

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Dr Trevor Marshall wrote: ...Brian Fallon's studies showed that IV Rocephin is purely palliative.

Not all antibiotics kill all bugs...
 

At this point in time, do you feel Dr. Fallon fully recognizes that or might he still tend dispute certain aspects of it?

TB

Last edited on Mon Feb 9th, 2009 08:13 by TikBitten

Prof Trevor Marshall
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I haven't personally spoken to Brian since 2004, when I attended one of the very  few presentations of his study results.

I still have photos of some of the slides, and there is no equivocation in that presentation - nearly all symptomatic improvement from IV Rocephin had disappeared within 3 months of cessation of treatment. Further - a large number suffered significant  infection due to the IV catheter, etc (offhand, I can't recall if it was 25% or 33%)

Brian has weathered a firestorm from people who (anecdotally) believe otherwise, including ILADS LLMDs, and IMO this is why his NIH-funded Columbia study has not been published in a peer-reviewed journal.
 

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Dr Trevor Marshall wrote: John,
The docking trajectory is problemmatic right now, as the entire field of biology is working with a VDR model (PDB:1DB1) which is genetically engineered to have amino acids missing from a critical region (residues 164-216) of the VDR. The region through which the ligand most likely enters the VDR:X I can get around this later by "growing" the VDR using MD, but first I have to learn to crawl, then walk:):):)



Dr Marshall,

Is this still the situation of the engineerd VDR? That quote is a litte old. And is this a human VDR?

My next question is answered before somewhere but I do not remember where;

Which of the ARBs and Statins have you found out to be agonist of the VDR?:?

Last edited on Sat Feb 14th, 2009 07:22 by Lottis

Prof Trevor Marshall
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Please move the off-topic discussion about Food allergies (etc) over to:

General Questions and Discussion


There are a lot of people who watch my Perspectives forum very closely for news of new science, and this is not a good place to discuss general stuff. I will try to move the comments that were posted while I was up at the Stanford conference (these last few days) to that correct forum.

Please continue the conversation at:

http://marshallprotocol.com/view_topic.php?id=13131&forum_id=11

I have transferred the posts over there to that general forum.

I messed up the transfer and lost some posts, sorry about that. I have no idea what happened. Please accept my apology if some of your contributions were accidentally deleted.

(Please send me a PM if you have copies of any of the missing material , I will add them to the header.)

 
 

Last edited on Sat Feb 14th, 2009 09:39 by Prof Trevor Marshall

Prof Trevor Marshall
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Is this still the situation of the engineered VDR? That quote is a litte old. And is this a human VDR?
My next question is answered before somewhere but I do not remember where;
Which of the ARBs and Statins have you found out to be agonist of the VDR?


Lottis,
Yes, the VDR in the PDB Crystal structures are engineered like PDB:1DB1, even the Rat VDR (PDB:1RK3). I can extend them with the new version of Modeller, I think. But it will take a quite a lot of work. Maybe a PhD student will be available to help me one day :)

Only Olmesatan is definitely a VDR agonist. I have some suspicion about Simvastatin being a very, very weak one. But that's all I have found :)
 

Prof Trevor Marshall
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At this point in time, do you feel Dr. Fallon fully recognizes that or might he still tend dispute certain aspects of it?

When I spoke with him in 2004 he was definitely aware that Rocephin was not acting as an antibiotic in his trial cohort :)
 



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