Re: HIV-1 does not encode glutathione peroxidase. 13 January 2005
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James J Whitehead,
research/getting better
40A Josephine Avenue London SW2 2LA

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Re: Re: HIV-1 does not encode glutathione peroxidase.

On 23 October 2003 I asked

"On the subject of gp41 I would like the Perths groups and Christopher Nobles or any one elses informed opinion, view, interpretation on this. (37)HIV-1 Encodes a Sequence Overlappingenv gp41 With Highly Significant Similarity to Selenium-Dependent Glutathione Peroxidases Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 1997;15:393-394. " http://bmj.bmjjournals.com/cgi/eletters/326/7387/495#38558

On 24 October 2003 Christopher J Noble, postdoctoral fellow Bern Switzerland kindly replied.

"Dear James, The letter in JAIDS you cited is of interest because it provides a possible explanation for the correlation between selenium depletion and HIV infection. The same authors have subsequently published a full article (1)

It is important to note that the sequence similarity between the HIV sequence and mammalian glutathione peroxidases is very weak by "Perth Group" standards.

The sequence alignments are given in figure 1. Out of the ~89 amino acids in the HIV sequence only 28 are present in at least one of the mammalian glutathione peroxidase sequences. Hence there is less than 31% similarity. This does not take into account three major deletions which were necessary to align the sequences.

Nevertheless these researchers have shown that this HIV sequence can potentially code for a selenoprotein that has glutathione peroxidase activity. It performs the same function as mammalian glutathione peroxidases - it catalyses the reduction of hydroperoxides such as hydrogen peroxides.

The key criteria for the conservation of the function of glutathione peroxidases is three key residues containing respectively, selenocysteine, glutamine, and tryptophan at the active site. Substitutions in other parts of the sequence as long as they don't dramatically change the folding of the protein will not affect its activity. This can be seen in the variation in the mammalian glutathione peroxidase sequences.

This example effectively demonstrates the relationship between genetic sequence and protein function.

It should also be noted that these authors also claim that sequences coding for selenoproteins can also be found in other viruses including hepatitis B, Coxsackie virus B3 and MMTV (2).

(1) Lijun Zhao, Arthur G. Cox, Jan A. Ruzicka, Ajita A. Bhat, Weiqing Zhang, and Ethan Will Taylor. Molecular modeling and in vitro activity of an HIV-1-encoded glutathione peroxidase, PNAS 97, 2000, 6356-6361

(2) Taylor EW, Nadimpalli RG, Ramanathan CS, Genomic structures of viral agents in relation to the biosynthesis of selenoproteins. Biol Trace Elem Res 56, 1997, 63-91. "

In reply to :Brian T Foley

"HIV-1 does not encode a glutathione peroxidase. I don't quite understand why the very same "dissidents" who claim that HIV might not exist, are willing to accept that HIV causes AIDS as long as it does so by a "controversial" mechanism. "

The mechanism of oxidative stress and glutathione defiency being involved in cell death, wasting ,KS, Aids, cancer is not "contraversial" it is very well established and well documented in many fields of medicine. I could give you several hundred references for this fact published in peer revued journals by thousands of doctors and leading scientists including the discover of hiv prof Luc Montaignier who even wrote a book on the subject.

Oxidative Stress in Cancer, AIDS, and Neurodegenerative Diseases Marcel Dekker, 270 Madison Ave., New York, NY 10016-0602. 558p., illus., bibliog., index. (Oxidative Stress and Disease). ISBN 0-8247-9862-7. $195.00. edited by Luc Montagnier, Rene Olivier, Catherine Pasquier.

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"Oxidative stress is an underlying factor in health and disease. More and more evidence is accumulating that a proper balance between oxidants and antioxidants is involved in maintaining health and longevity, and that altering this balance in favor of oxidants may result in pathological responses causing functional disorders and disease." Some 50 chapters present different views of oxygen and nitrite-free radicals, from the chemical to the clinical standpoints, via biochemistry and cellular and molecular biology. It is highly technical and extensively referenced, making it a primary research publication on this topic. The 50 chapters are arranged under 7 broad headings: "Oxidative Stress in Cell Biology and Biochemistry," "Oxidative Stress and Cellular Signaling," "Oxidative Stress and Apoptosis," "Oxidative Stress and Antioxidants," "Oxidative Stress and Cancer," "Oxidative Stress and AIDS," and "Oxidative Stress in Neurodegenerative Diseases and Other Pathologies." There are 9 papers in the section concerning AIDS. This is a highly recommended book for all medical libraries. It will become background reading for those doing research in Oxidative Stress as it pertains to all areas of health. "

Oxidative Stress in Cancer, AIDS, and Neurodegenerative Diseases by Editor: Luc Montagnier

http://www.addall.com/detail/0824798627.html

oxidative stress ,glutathione, selenium, antioxidant, amino acid and micro nutrient defiencies roles in disease causation/progression are only "contraversial" to doctors who deny its existance , importance and ignore its clinical relevance and well documented biological effects ( prolonging,improving lives,stopping reversing aids/cancer wasting, slowing down progression) . One could even perhaps misuse again the word "denialists", but I will leave such silly terms to the school yard.

In my last post again I stated words to the effect of

"As regards causation Co-factors, hiv, or hiv plus co-factors I am keeping an open mind and can see and understand to a degree all "sides" ,points of view and beliefs. The only thing that I am certain of is that oxidative stress is pivatol in the causation of the diseases called aids, but understand that the causes/ causes of this oxidative stress is debatable and not proven beyond doubt at present. But I am certain that pro GSH agents, antioxidants,amino acids and micro nutritrients are powerfull weapons in treatning and preventing the diseases that can be called aids. "

Nicholas bennette replied (and I agree with him in parts) "What is interesting, and which Mr Whitehead brings to our attention, is that by treating this apparent "symptom" of the disease the outcomes can improve. There is considerable evidence that treating HIV directly can have an effect, but it is not permanent and can have costly side- effects. Further measures are clearly needed - and whether these are cytokine stimulation to clear the proviral reservoir, an effective vaccine, or improved immune function through better supplementation doesn't really matter: so long as it works"

I hope that answers your question.

In Reply to Brian T Foley : "First of all, HIV-1 does not encode a glutathione peroxidase. The paper trail in the Medical Hypotheses paper leads us back to a letter to the editor where Foster et al speculate that HIV-1 might possibly encode such an enzyme IF the ribosime slipped back on the env gene messenger RNA. That is a huge unproven IF"

I agree it is an unproven IF but as Mr Christopher Noble stated "it provides a possible explanation for the correlation between selenium depletion and HIV infection". If we where all honest we would admit that in hiv and aids science there are alot of big ifs past , present and future.

And heres some of the evidence that supports Foster HD. theory. Please note the word theory.

"Based on theoretical evidence, it has been proposed that HIV-1 may encode several selenoprotein modules, one of which (overlapping the env gp41-coding region) has highly significant sequence similarity to the mammalian selenoprotein glutathione peroxidase (GPx; EC 1.11.1.9). The similarity score of the putative HIV-1 viral GPx homolog relative to an aligned set of known GPx is 6.3 SD higher than expected for random sequences of similar composition. Based on that alignment, a molecular model of the HIV-1 GPx was constructed by homology modeling from the bovine GPx crystal structure. Despite extensive truncation relative to the cellular GPx gene, the structural core and the geometry of the catalytic triad of selenocysteine, glutamine, and tryptophan are well conserved in the viral GPx. All of the insertions and deletions predicted by the alignment proved to be structurally feasible. The model is energetically favorable, with a computed molecular mechanics strain energy close to that of the bovine GPx structure, when normalized on a per-residue basis. However, considering the remote homology, this model is intended only to provide a working hypothesis allowing for a similar active site and structural core. To validate the theoretical predictions, we cloned the hypothetical HIV-1 gene and found it to encode functional GPx activity when expressed as a selenoprotein in mammalian cells. In transfected canine kidney cells, the increase in GPx activity ranged from 21% to 43% relative to controls (average 30%, n = 9, P < 0.0001), whereas, in transfected MCF7 cells, which have low endogenous GPx activity, a near 100% increase was observed (average 99%, n = 3, P < 0.05). "(1)

"Most significantly, the existence of an HIV-encoded selenoprotein gene represents the basis for a novel pathogenic mechanism (involving in part competition with cellular selenoprotein synthesis as discussed above) that can help to explain why the effects of HIV-1 infection are exacerbated in individuals who are Se deficient (24-27). Our hypotheses regarding the potential roles of viral selenoproteins in HIV-1 pathogenesis have been discussed in more detail elsewhere and will not be repeated here because of space limitations (6, 7, 11, 24, 31). "(1)

"The proposed homology model is supported by the following factors:

(i) Despite several extensive deletions and truncations, the sequence encoded by HIV-1 includes the structural core and the complete catalytic center of the GPx enzyme.

(ii) The deletions are structurally feasible, because the deleted regions project away from the active site and in several cases consist of noncatalytic domains involved in dimer and tetramer formation.

(iii) The geometry of the GPx active site, e.g., distances between critical active-site atoms and residues, is not substantially changed in the model relative to the bovine GPx crystal structure.

(iv) There is no exceptional molecular mechanics strain energy associated with the HIV-1 GPx model, which appears to have an energetically favorable distribution of charged residues leading to the electronic stabilization of the structure.

Thus, overall, the molecular modeling results suggest that the proposed homology is structurally feasible and consistent with the known structural requirements for Se-dependent GPx catalysis (14), supporting the hypothesis that the hypothetical HIV-1 gene env-fs encodes a truncated but potentially functional Se-dependent GPx homolog. Using a standard enzyme assay, we have validated the theoretical results by cloning the putative viral peptide shown as env-fs in Fig. 1, and demonstrating that it encodes functional GPx activity when expressed as a selenoprotein in mammalian cells. " (1)

"The significance of these results can best be understood in the context of current knowledge regarding the biological roles of Se in the immune system and in the regulation of HIV-1 transcription. Se is an essential trace mineral that serves as a potent dietary antioxidant, in addition to other biological functions. Many of its cellular actions, mediated by selenoproteins such as GPx and thioredoxin reductase (TDR), are intimately linked to the redox status of the cell, and to the redox regulation of genes that are important for various immune cell functions (19). Significantly, oxidative stress has been widely documented in AIDS patients (20, 21), and is known to be an activator of HIV-1 replication in vitro (22, 23). In light of those observations, and the established redox- related roles of Se and selenoproteins, it is not surprising that Se has been found to be of critical importance in HIV-1 infection. Se status has consistently been correlated with various indicators of HIV-1 disease progression, and Se deficiency is highly correlated with HIV-related mortality (reviewed in refs. 7 and 24; 25-27). "(1)

"Most significantly, the existence of an HIV-encoded selenoprotein gene represents the basis for a novel pathogenic mechanism (involving in part competition with cellular selenoprotein synthesis as discussed above) that can help to explain why the effects of HIV-1 infection are exacerbated in individuals who are Se deficient (24-27). Our hypotheses regarding the potential roles of viral selenoproteins in HIV-1 pathogenesis have been discussed in more detail elsewhere and will not be repeated here because of space limitations (6, 7, 11, 24, 31). "(1)

"HIV-infected injection drug users (IDUs) often suffer from serious nutritional deficiencies. This is a concern because plasma levels of micronutrients such as vitamin B12, zinc, and selenium have been correlated with mortality risk in HIV-positive populations. Injection drug use also increases lipid peroxidation and other indicators of oxidative stress, which, combined with antioxidant deficiencies, can stimulate HIV-1 replication through activation of NF-kappaB transcription factors, while weakening immune defenses. As detailed herein, these prooxidant stimuli can also increase the pathogenic effects of HIV-1 by another mechanism, involving viral selenoproteins. Overlapping the envelope coding region, HIV-1 encodes a truncated glutathione peroxidase (GPx) gene (see #6 in reference list). Sequence analysis and molecular modeling show that this viral GPx (vGPx) module has highly significant structural similarity to known mammalian GPx, with conservation of the catalytic triad of selenocysteine (Sec), glutamine, and tryptophan. In addition to other functions, HIV-1 vGPx may serve as a negative regulator of proviral transcription"(2)

In reply to Nicholas Bennett: "In fact, glutathione peroxidase (GP) activity in AIDS patients is _lower_ than in uninfected controls (but higher than in HIV-infected but non-AIDS patients) [1, 2] "

Reference number 2 from Nicholas "Dworkin et al. Biol Trace Elem Res. 1988 Jan-Apr;15:167-77. "Abnormalities of blood selenium and glutathione peroxidase activity in patients with acquired immunodeficiency syndrome and aids-related complex." Does indeed make no sense.

However the same lead author DWorkin in 1994 (6 years later) writes in a paper:

" In a subsequent study blood selenium and glutathione peroxidase were diminished in 12 AIDS and 8 ARC patients compared with normals (all P < 0.001). For glutathione peroxidase the mean levels were decreased by 45% in AIDS and 27% in ARC versus controls (P < 0.001). Both plasma selenium and glutathione peroxidase significantly correlated with total lymphocyte counts (r = 0.65; P < 0.001; glutathione peroxidase and lymphocyte counts). "(3)

And

"To further assess mechanisms of nutrient and selenium deficiency in AIDS we studied dietary intake in outpatients and inpatients with various stages of HIV infection. Inadequate selenium intake based on a computer (Nutritionist 3) analysis of 72 h diet records was present in only 17% of clinically stable HIV positive outpatients and 71% of inpatients with AIDS.

Conclusions: Selenium deficiency is common in HIV positive patients as documented by low plasma and red blood cell levels of selenium, diminished activity of glutathione peroxidase, and low cardiac selenium levels in AIDS hearts.

Patients with AIDS tend to have more severe deficits than those with earlier stages of HIV infection.

The selenium deficit in blood does correlate with serum albumin levels and total lymphocyte counts. Poor dietary intake and malabsorption could lead to this condition which has important implications for both cardiac and immune functions in HIV positive patients. "(3)

And another paper states ".Serum selenium and GSH-Px activity in hospitalized AIDS patients was significantly lower as compared to asymptomatic patients and healthy subjects, whereas plasma SH and GSH concentrations were lower in both, asymptomatic -and AIDS-patients, than in the controls. CONCLUSION: The results show that stages I-III of HIV- disease are characterized by significant impairments of antioxidative defenses provided by selenium, GSH-Px, SH-groups and GSH." (4)

I must say again that I am certain that these defiencies exist, I am certain that they are linked to disease progression and I am certain that oxidative stress combined with low glutathione, selenium and antioxidant defence mechanisms is fno doubt pivatol in cell death. What causes this oxidative stress and associated defiencies is debateable.

Just a few questions to Brian Foley or Nicholas Bennette .

Do you deny/disagree oxidative stress and the associated antioxidant defiencies are involved in the causation of the diseases called aids ?

Do you deny/disagree that antioxidants have been shown to prolong life and slow down disease progression ?

Do you deny/disagree that hiv tat induces oxidative stress and depletes glutathione ?

I did not see the word "cured" in this paper did they really use the word "cured" ?

Last point, in regards to an earlier conversation regards radiation/UV I wondered what readers both "sides" may think of this specificaly no 2.

HIV-1 protein interactions Protein Interaction 1. Tat HIV-1 Tat causes a greater than 50% decrease in intracellular reduced glutathione (GSH), leading to the extracellular appearance of acidic FGF-1, an effect that is partially mediated through modulation of GSH biosynthetic enzymes PubMed

2. Expression of HIV-1 Tat in HeLa cells downregulates cytoplasmic glutathione peroxidase while upregulating phospholipid hydroperoxide glutathione peroxidase, thereby deregulating intracellular oxidant/antioxidant balance and amplifying UV sensitivity

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=2877

Best Wishes

James J Whitehead

Clinical trials volunteer memeber www.altheal.org and www.aidsmythexposed.com

References:

1.PNAS | June 6, 2000 | vol. 97 | no. 12 | 6356-6361

Biochemistry Molecular modeling and in vitro activity of an HIV-1-encoded glutathione peroxidase Lijun Zhao, Arthur G. Cox, Jan A. Ruzicka, Ajita A. Bhat, Weiqing Zhang, and Ethan Will Taylor Computational Center for Molecular Structure and Design, and Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602

Communicated by Norman L. Allinger, University of Georgia, Athens, GA, April 10, 2000 (received for review August 6, 1999)

Copyright 2000 by the National Academy of Sciences

http://www.pnas.org/cgi/content/full/97/12/6356

2.J Acquir Immune Defic Syndr. 2000 Oct 1;25 Suppl 1:S53-61.2 .Nutrition, HIV, and drug abuse: the molecular basis of a unique role for selenium.

Taylor EW, Cox AG, Zhao L, Ruzicka JA, Bhat AA, Zhang W, Nadimpalli RG, Dean RG.

Department of Pharmaceutical and Biomedical Sciences and Computational Center for Molecular Structure and Design, The University of Georgia, Athens 30602, USA. wtaylor@rx.uga.edu

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11126428

3 Chem Biol Interact. 1994 Jun;91(2-3):181-6.

Selenium deficiency in HIV infection and the acquired immunodeficiency syndrome (AIDS).

Dworkin BM.

Section of Nutrition, New York Medical College, Valhalla 10595.

4. Eur J Clin Nutr. 1997 Apr;51(4):266-72.

Serum selenium, plasma glutathione (GSH) and erythrocyte glutathione peroxidase (GSH-Px)-levels in asymptomatic versus symptomatic human immunodeficiency virus-1 (HIV-1)-infection.

Look MP, Rockstroh JK, Rao GS, Kreuzer KA, Barton S, Lemoch H, Sudhop T, Hoch J, Stockinger K, Spengler U, Sauerbruch T.

Department of General Internal Medicine, University of Bonn, Germany

Competing interests: Clinical trials volunteer member www.altheal.org