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You are not doing a myriad of things with protein folding.
It is a very narrow part of the whole.
you are only testing their theories on how the proteins fold.
here is a link to the scince page.

folding.stanford.edu...

Originally posted by bodebliss
You are not doing a myriad of things with protein folding. ...you are only testing their theories on how the proteins fold.

folding.stanford.edu...

Sorry bodebliss - I don't understand your response. ...I personally don't do anything with proteins or protein folding. ...My interest originally developed because I have an incurable disease that causes fibrosis and now is progressed to be untreatable.

...I researched the disease trying to find self-help pointers - and ended up in a pit of cover-ups and doublespeak. I now know my disease results from a protein mis-folding problem - and that while this administration wants to call it genetic, it's not.



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Soficrow,
I'm sorry to hear of your condition.

This doesn't change the nature of protein folding , follow the link and learn.

They have published some papers, but as you will see while reading them , they have a narrow focus.

The fact that protein folding can be done at all is a miracle, but they don't yet know if the info they get represents the real world and if it does how that fits in w/ a possible cure.

Originally posted by bodebliss

follow the link and learn. ...They have published some papers, but as you will see while reading them , they have a narrow focus.

The article above introduces the World Community Grid - which has a much larger focus than folding@home - and which just started up. Please feel free to read the actual article, and learn.

This doesn't change the nature of protein folding , ...The fact that protein folding can be done at all is a miracle,

Protein folding is a fact of life and nature, not a 'miracle.' Most incurable untreatable modern diseases result from mis-folded proteins, ...which in turn result from infectious prions. ...The "prion conterovesy" is entirely synthetic, designed to protect industry from liability and the costs of clean-up.

Despite the constraints on the sharing of scientific information that Bush imposed in his "anti-terrorist" orders, specifically with respect to prions, there is a great deal of information about protein mis-folding available on the Net. ...You must have missed it.

As I recall, some of the links provided may offer backgrounders on mis-folded proteins. If you let me know your levels of interest and expertise, I'm sure I have something in my own files that is appropriate for you.


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Soficrow are you ok man?

It's protein-folding simulation that is the miracle,ok.

I am already involved in the top protein folding program . You don't know the people involved in the world community grid or how they will use their findings.

The nimber 1 and 2 killers of humans do not have anything to do w/ prions.

You are probably talking about alzheimer's which the CDC ranks as the 7th most deadly disease it kills 49,600/yr , but 49,000 are over 65 years old.

I assure you I've missed nothing.

Thanks for the offer soficrow ,but I am sure you don't understand that protein-folding simulation is in such infancy that they are only testing to see if their methods of simulation are correct.

There is a ton of info on the methods , aims, and products of protein-folding simulation on the Stanford site.

folding.stanford.edu...

Here are the stats for bodebliss .

I am 39,677th out of 398,132 folding agents.

[edit on 11/30/2004 by bodebliss]

I respect your commitment to folding@home, but suggest that your information base is narrow and consequently, limiting.

Originally posted by bodebliss

The nimber 1 and 2 killers of humans do not have anything to do w/ prions.

You're making unfounded assumptions, and supporting spin generated to protect industry from liability charges and clean-up costs.

www.kup.at...

Atherothrombosis is the underlying condition that results in events leading to myocardial infarction, ischemic stroke, and vascular death. As such, the leading cause of death of the estimated 55,694,000 people worldwide who died in 2000 was atherothrombosis, manifested as cardiovascular disease, ischemic heart disease and stroke (52% of deaths). Other main causes of death were: AIDS (5%) violent death (12%) pulmonary disease (14%) infectious diseases (19%) cancer (24%).

FYI - fibrosis commonly underlies atherothrombosis and also, precedes cancer (therefor 76% of deaths worldwide). Fibrosis results from mis-folded proteins that cause connective tissue stem cells to mutate into "myofibroblasts."

More on fibrosis at:
www.pharma.tno.nl/Common/PDF/LE136A_Fibrosis.pdf

...There is no argument that mis-folded proteins underly most modern diseases - and IMHO the "controversy" as to whether or not prions cause proteins to mis-fold is largely synthetic.

Here is a quick and random selection of research to indicate the range of information available on prions and protein misfolding or "conformational" disorders:

1. * �Protein misfolding and disease: the case of prion disorders.� Cell Mol Life Sci. 2003 Jan;60(1):133-43. Hetz C, Soto C. Serono Pharmaceutical Research Institute, 14 Chemin des Aulx, 1228 Plan les Ouates, Switzerland. PMID: 12613663

* �Cyclic amplification of protein misfolding: application to prion-related disorders and beyond.� Trends Neurosci. 2002 Aug;25(8):390-4. Soto C, Saborio GP, Anderes L. Serono International SA, Geneva, Switzerland. PMID: 12127750

2. * �Primary myopathy and accumulation of PrPSc-like molecules in peripheral tissues...� Neurobiol Dis. 2001 Apr;8(2):279-88. Chiesa R, Pestronk A, Schmidt RE, Tourtellotte WG, Ghetti B, Piccardo P, Harris DA. Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA. PMID: 11300723 QUOTE: �mutant PrP in the brain and spinal cord, intermediate levels in skeletal muscle, heart, and testis and low levels in kidney, lung, spleen, intestine, and stomach. Up to 70% of the PG14 PrP expressed in peripheral tissues�

* �Prions in skeletal muscle.� Brazier MW, Cappai R, Collins SJ. Aust Vet J. 2002 Aug;80(8):484-5. PMID: 12224617

* �Deposition of disease-associated prion protein involves the peripheral nervous system in experimental scrapie.� Acta Neuropathol (Berl). 1999 Nov;98(5):453-7. Groschup MH, Beekes M, McBride PA, Hardt M, Hainfellner JA, Budka H. Bundesforschungsanstalt fur Viruskrankheiten der Tiere, Institut fur Impfstoffe, Tubingen, Germany. PMID: 10541866

* �A protease-resistant prion protein isoform is present in urine of animals and humans affected with prion diseases.� Shaked GM, Shaked Y, Kariv-Inbal Z, Halimi M, Avraham I, Gabizon R. Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah University Hospital, Jerusalem 91120, Israel. J Biol Chem. 2001 Aug 24;276(34):31479-82. Epub 2001 Jun 21. PMID: 11423531

* �Chronic Subclinical Prion Disease Induced by Low-Dose Inoculum� Received September 24, 2001; J Virol. 2002 March; 76 (5): 2510�2517 Alana M. Thackray,1 Michael A. Klein,2 Adriano Aguzzi,3 and Raymond Bujdoso www.pubmedcentral.nih.gov...

* �Peripheral Tissue Involvement in Sporadic, Iatrogenic, and Variant Creutzfeldt-Jakob Disease: An Immunohistochemical, Quantitative, and Biochemical Study.� Am J Pathol. 2004 Jan;164(1):143-153. Head MW, Ritchie D, Smith N, McLoughlin V, Nailon W, Samad S, Masson S, Bishop M, McCardle L, Ironside JW. National Creutzfeldt-Jakob Disease Surveillance Unit and Division of Pathology, School of Molecular and Clinical Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom. PMID: 14695328 QUOTE: �the biochemical isoform of PrP(Sc) found is influenced by the cell type in which it accumulates.�

* �Prion plaques: molecular tumors. A hypothesis on the etiopathogenesis of prion diseases.� Ossa JE, Machado G, Giraldo MA, McEwen JG. Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia. Med Hypotheses. 1995 Feb;44(2):124-6. PMID: 7596306 QUOTE: ��this hypothesis would shed some light on other diseases not presently classified as prion diseases and in the process of ageing.�

* �Subclinical scrapie infection in a resistant species: persistence, replication, and adaptation of infectivity during four passages.� Race R, Meade-White K, Raines A, Raymond GJ, Caughey B, Chesebro B. Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, 903 S. Fourth Street, Hamilton, MT 59840, USA. J Infect Dis. 2002 Dec 1;186 Suppl 2:S166-70. PMID: 12424693 QUOTE: �Cross-species infection with transmissible spongiform encephalopathy agents may lead to subclinical infection and to adaptation of the infection to new species.�

* �New marker for human prion protein (CD230)� QUOTE: �... of diseased individuals forming lesions, vacuoles and ... New marker for human prion protein CD230 ... been reported on neurons, astrocytes, smooth muscle cells and on ...� www.serotec.co.uk/supplement%20pdfs/June2001.pdf

* �Anchor-dependent and -independent Prion Protein Association� JBC -- Abstracts: Mahfoud et al. 277 (13): 11292 QUOTE: �... effect of A[beta] peptides on vascular smooth muscle cells and ...� www.jbc.org/cgi/content/abstract/277/13/11292

* �Cholesterol is necessary both for the toxic effect of A[beta] peptides on vascular smooth muscle cells and for A[beta] binding to vascular smooth muscle cell membranes� J. Neurochem., February 1, 2003; 84(3): 471 - 479. S. Subasinghe, S. Unabia, C. J. Barrow, S. S. Mok, M.-I. Aguilar, and D. H. Small

�PrPc expression influences the establishment of herpes simplex virus type 1 latency.� J. Virol. 76, 2498-2509. Thackray, A. M. and Bujdoso, R. (2002) also Joint Funders Conference (BBSRC, DoH, MRC, MAFF), Durham, UK. PMID: 11836428

jvi.asm.org...

* �Subclinical prion infection in humans and animals.� Br Med Bull. 2003;66:161-70. Hill AF, Collinge J. MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, London, UK. PMID: 14522857

* �Why fibrous proteins are romantic.� J Struct Biol. 1998;122(1-2):3-16. Cohen C. Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, 02254-9110, USA. PMID: 9724602

* �A new kind of prion: a modified protein necessary for its own modification.� Cell Cycle. 2004 Mar-Apr;3(2):100-3. Roberts BT, Wickner RB. National Institute of Diabetes, National Institutes of Health, Bethesda, Maryland USA. PMID: 14712063
www.landesbioscience.com...

8. * �Role of islet amyloid in type 2 diabetes mellitus: consequence or cause?� Mol Cell Endocrinol. 2002 Nov 29;197(1-2):205-12. Hoppener JW, Nieuwenhuis MG, Vroom TM, Ahren B, Lips CJ. Department of Clinical Endocrinology, University Medical Center Utrecht, Location University Hospital, G02.228, P.O. Box 85500, 3508 GA Utrecht, The Netherlands. PMID: 12431814

9. * �Cell biology: The strain of being a prion,� Nature, 428:265, March 18, 2004. M.F. Tuite. www.nature.com...

* �Conformational variations in an infectious protein determine prion strain differences� Nature, 428:323-328, March 18, 2004. Tanaka et al. www.nature.com...

* �Prion folding produces strains� www.biomedcentral.com...



[edit on 30-11-2004 by soficrow]

Originally posted by bodebliss

You don't know the people involved in the world community grid or how they will use their findings.

This is quite true - I do know IBM and the UN as well as other "international organizations" are involved. ...But I don't know the players, or how the information will finally be used - by folding@home OR the World Community Grid.

I don't think the two organizations are competing - and do judge that it's necessary to trust, both folding projects.

Anyone have any hard information to say either of these organizations is not trustworthy?



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I'm just saying they haven't even scratched the surface on protein folding simulation and it is going to be a while till they are sure their models are correct. I remember reading on the stanford site that stanford's project is one of 2 that actually seen a protein's simulated folding. all the rest were not able to get a simulated folding of even the most simple proteins.

This whole field is baby stepping right now.

[edit on 12/1/2004 by bodebliss]

Originally posted by bodebliss
I remember reading on the stanford site that stanford's project is one of 2 that actually seen a protein's simulated folding. all the rest were not able to get a simulated folding of even the most simple proteins.

This whole field is baby stepping right now.

...I need to go back to my research - my sense is that the whole thing is going forward leaps and bounds - and that it's now possible to 'watch' dynamic molecular processes (as opposed to look at inactive dead cells and proteins under a microscope). ...This ability has opened up whole new vistas in scientific/medical/biological research...

But - the truth is probably somewhere between your and my 'take' on it. lol. ...Thanks for the dialogue - keep me udated on your end and I'll do the same, okay?


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You are probably thinking of xray chromatography which is the taking of snap shots of atomic processes.

here is the science page of Stanford folding .

you will see few completed prjects and why that is so.

folding.stanford.edu...

Originally posted by bodebliss
You are probably thinking of xray chromatography which is the taking of snap shots of atomic processes.

The Stanford project is doing very important work - but I think they simplify their copy for non-scientists, maybe too much (and maybe don't update it that often).

...I am thinking more of the multi-disciplinary and multi-technology marriages that are now taking place, towards 'complex adaptive systems analysis' of biological and atomic processes. ,,,ie., atomic, molecular optical and plasma physics. ...the key technologies are more spectroscopy and the like, while the various chromatographies are more limited (but are often used in conjunction).

My interpretation of the stuff I've been reading about: an atomic MRI, with digital movie capacity.

Did a quick search - found the following blurbs, which weren't what I was looking for, but are fairly informative...

Ultrafast Spectroscopy and Dynamics of Biomolecules
www4.nationalacademies.org...

Proteins and other biomolecules are often thought of in terms of the exquisitely detailed atomic pictures revealed by x-ray crystal structures. However, x-ray crystallography only provides a representation of the average structure, or a snapshot of a single configuration. In reality, proteins are constantly fluctuating between conformers that may represent large displacements from the atomic positions shown in the crystalline form. These motions impact fundamental biochemical processes such as allostery, interactions with binding partners, susceptibilities to proteolytic cleavage, and hydrogen exchange kinetics. Therefore, a molecular-level description of biology requires an understanding of protein dynamics.

...The dynamics of biological macromolecules span an enormous range of time scales, ranging from femtoseconds (10-15 sec) to seconds. The characterization of these motions represents a formidable experimental challenge. ...We are interested in measuring the spectra of bimolecular motions, understanding the structural nature of these motions, and relating the dynamics to biological function. The laboratory employs ultrafast laser spectroscopies for measuring the femtosecond through nanosecond time scale dynamics, which underlie the slower motions. ...We will also develop a quantitative understanding of the role of femtosecond-nanosecond dynamics in the entropy changes which occur during ligand binding, folding, and other conformational transitions.


www4.nas.edu...

Unlike simple chemical reactions, protein folding is a very heterogeneous process with a large distribution of microscopic pathways connecting folded and unfolded states. Experimental determination of the distribution of these pathways requires measurements on single molecules, as ensemble measurements yield only average properties. Since it is rapidly becoming possible to fold proteins by molecular dynamics calculations, which consist of single molecule trajectories, experimental distributions are becoming essential as tests of the validity of these simulations. Up to now, single molecule folding studies have been confined almost entirely to fluorescence resonance energy transfer from intensity measurements on free diffusing molecules. The next step will be to develop methods to isolate single molecules for observation of multiple folding and unfolding events, as has already been accomplished with RNA. Expertise and advanced instrumentation exists at NIST for optical and physical studies of single molecules, such as force techniques including optical tweezers and cantilever-based molecular pullers that can be used in conjunction with optical measurements to study structural changes under an applied load. Conventional single molecule and ensemble instrumentation (for kinetic studies at nanoseconds and longer) exist at NIH, as well as expertise in theoretical and computational aspects of protein folding.


www4.nationalacademies.org...

The structure and dynamics of these proteins and polypeptides will be qualitatively assessed in microfluidic channels with spectroscopic techniques. Fluorescence resonant energy transfer (FRET) and surface enhanced Raman spectroscopy (SERS) each offer unique capabilities and insight into the difficult task of assigning protein structure. With FRET, each partner of a binding pair is labeled with a different fluorophore--one, the "donor" is bluer than the other, the "acceptor". The donor molecule is excited with a laser and begins to fluoresce; the acceptor molecule will only fluoresce if the distance between the two molecules is less than ~50 Angstroms. Therefore, it is possible to observe the tagged positions on the protein as they come in out of contact during folding or unfolding. Through the use of metallic nanoparticles fabricated in situ in the microfluidic channel, SERS provides the frequency of the vibrational bands of specific chemical groups within the protein. This inelastic photon scattering process offers a mechanism to monitor the proximity and environment of specific chemical groups, such as the carbonyl stretch, or so-called amid I band at ~1600 cm-1, which is a signature for protein conformation. Furthermore, unlike with infrared spectroscopy, it is possible to gather this vibrational data proteins in H20 media.

...All of these blurbs are from publicly funded NIH labs and projects - labs in private facilities are likely way ahead of this game.

I'll keep an eye out for the other stuff I've found, but I can't make it a priority to search it right now.

Anyway - keep up the good work.