tRNA on Ribosome
tRNA on Ribosome 
Manager: Ottar Stensvold |
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Description: tRNA on Ribosome and how to wrap in and stop antigens with nucleic acids.
Proposed new drug paradigm: Are the classic ribosome-tRNA models wrong? - A chance.
(Regarding autoimmune MS and diabetes:
My idea is to take down the protein markers
which the T-cells home in on when they perform autoimmunity, and/or target the receptors /
surface proteins on the T-cells which they use in this task. At GenBank we can find some of
the needed gene/protein sequences.)
I try to explain my theory in this video:
http://www.youtube.com/watch?v=7834CXASQF8
(For clarity, the elongation factor binding to and shepherding aminoacyl-tRNA is omitted in the model.)
I found these articles supporting my theory about amino acids` binding to their cognate codons:
http://www.ncbi.nlm.nih.gov/pubmed/14561881?dopt=Abstract','NCBI','700','400')
http://www.ncbi.nlm.nih.gov/pubmed/16186130?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.
http://www.ncbi.nlm.nih.gov/pubmed/15952885?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
http://www.ncbi.nlm.nih.gov/pubmed/10354582?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
Idea in biochemistry part 1-4:
--------------------------------------------------------------------------------
PART 1
Quick websearches on the topic ribosome all show the same:
the amino acid-loaded tRNA arrives at the ribosome with its
anti-codon first. I think this could be an oversimplification, which
doesn`t take notice to the probable, intuitive fact that the gene is
a blueprint for the protein, a mirror-copy made through evolution.
Say the proteins initially instructed the genes and not vice versa.
Say the food came first, and then the means to carry it.
For such a coplex process as translation to proceed without many errors,
there have to be a second mechanism of proofreading. Maybe there is a
closer link between amino acids and the mRNA than previously thougth.
Maybe there is a transient key-lock binding between the amino acid and
the codon before the anticodon binds.
The bases seem to reach for the amino acids, and the first and the second
base seems to play the greatest role. For instance, the short one-cyclic U are
in the second (midst) position in codons binding hydrophobic amino acids,
indicating the hydrophobic aa`s R-groups (side chains) will turn downwards when binding.
And hydrophilic amino acids have the longer two-cyclic A in the midst position
in their codons, indicating the R-groups will turn upwards, away from the codon,
towards the water when encountering the codons.
My point is that it should be possible to make any short gene sequence
that could match any protein, almost as an antibody. The oligonucleotides
will be shrunk at point of binding, and they will probably work for only shorter
stretches. As far as I know it should not be too dangerous to appply in vivo,
but of course animal tests, research etc. are needed.
I read for instance in Discover Magazine and at Nature.com that eosinophilic cells
catapult mitochondrial DNA nets against parasites (malaria).
It should be possible to target any protein-markers in any disease,
and hence destroy the culprits. Say, put a virus in a PCR machine and make
cheap copies of tailored antibodies! Or use the new oligo synthesis factories!
I try to explain my theory in this video:
http://www.youtube.com/watch?v=7834CXASQF8
I found these articles supporting my theory about amino acids` binding to their cognate codons:
http://www.ncbi.nlm.nih.gov/pubmed/14561881?dopt=Abstract','NCBI','700','400')
http://www.ncbi.nlm.nih.gov/pubmed/16186130?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.
http://www.ncbi.nlm.nih.gov/pubmed/15952885?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
http://www.ncbi.nlm.nih.gov/pubmed/10354582?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
Sincerely,
Ottar Stensvold,
Reinhold Zieglers veg 14 B
6414 Molde
Norway
mobil: +47 95 177 433
epost: ottarstensvold@hotmail.com
web: http://ottarstensvold.spaces.live.com
born: February 7th 1971
------------------------------------------
PART 2
A drop of ordinary water-smear on a microscopy slide reveals a pattern:
the bacteria in the water lines up, symbolized like this: o.....o..o...o...o
These lines are best seen at 400x magnification.
My theory / idea is that DNA from ruptured bacteria binds and absorbs proteins
from its own species.
So what? If so, if a nucleic acid can bind to a protein in a coded manner,
then the aptamer technology is the tech of the future.
Say for instance the codon GUG, which codes for the amino acid valine, weakly
binds this amino acid. Symbolized like this: E -<
The codon-amino acid binding gives several combinatorial possibilities with
regard to polar interactions, mechanic fit and R-group placement.
If we can make aptamers tailored to bind specific proteins, then we can
take down any pathogen.
----
PART 3
The amino acid sequence of the HIV surface protein GP 120
can be found at GenBank:
http://www.ncbi.nlm.nih.gov/protein/7769644?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum
My plan is to try to make an array of different aptamers to hit this protein.
The approach I will use is basically to design aptamers that are based on
the amino acids` corresponding codons. In the DNA-aptamers, I will replace
U with T, and in the third wobble-position I will choose the assumed least
interfering base (T). RNA aptamers can also be used.
There is a chance that the aptamers will match directely.
The matches have to be at accessible parts of the protein`s surface.
The aptamers will be ordered (outsourced), for instance from:
http://www.biomers.net/upload/Image/Preislisten/DNA_En_EUR.pdf
or from Eurogentec in San Diego, California:
http://www.eurogentec.com/news/106-eurogentec-launches-new-oligo-synthesis-facility.html
The price of the aptamers will be maybe around one tenth of comparable drugs,
i.e. monoclonal antibodies.
The stock of different aptamers will be annotated at my portable computer.
Then, step 2, we have to beg institutions which store HIV viruses to test the aptamers in vitro.
The results can be viewed with electron microscopes.
(One can also test aptamers on oncoproteins in stored tissue samples,
e.g. the 17 aa CD44 protein which is overexpressed on membranes on glioma cancer brain cells.)
This project needs help from media. The headlines could be:
"Burn off money to test HIV drug"
"Find needle in haystack"
Press: "Will this be tested in humans? Will there be marketing? Sales?
Investing?"
Answer: "We will find a balanced solution, it`s fair that developed
countries pay for some of the venture."
The task will require all communication skills and business intelligence.
It is a bit like cloud computing: once the hidden codes are found,
they have to be administered.
It is my goal to reach this goal of my life!
------------------------------------------
PART 4
The aptamer:
GGTTGGTGTGGTTGG
(or ggttggtgtggttgg)
or GGT TGG TGT GGT TGG
or GGU UGG UGU GGU UGG (in RNA) corresponds to the amino acids:
gly trp cys gly trp abbreviations:
G W C G W
This aptamer binds to thrombin, the blood-clotting protein.
I found it at:
http://bloodjournal.hematologylibrary.org/cgi/content/abstract/83/3/677?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=aptamer&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT
To find the amino acid sequence in thrombin, I search GenBank at:
http://www.ncbi.nlm.nih.gov/nuccore/169808403?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum
The combination "GW" occurred once in the thrombin protein,
the combination "WG" occurred twice,
the combination "WC" occurred twice
the combination "GC" occurred twice
and the combination "CG" occurred three times
The latter combination, for instance, should then bind to the aptamer-codons UGU GGU.
I did not find similar matches in the comparable plasma proteins albumin or insulin,
and I think further research will find no other similar matches either.
It is striking that the aptamer comprises the range of codons encoding the protein (aa range) it binds!
This underscores my suggestion that proteins can bind specific to their codon combinatons in mRNA or (+)ssDNA.
The numbers of possibilities to get a twosome aa-combination of a pool of twenty different amino acids,
should plainly speaking be 1/20*1/20 = 1/400,
and this makes specific binding likely!
In the June 2009 Scientific American issue, there is an article about silent mutations (by Chamary and Hurst)
which highlights that different codons encoding the same amino acids give alterations in the proteins.
It`s thus feasible that this bias is caused by the codons` positioning of the amino acids (R-group placement in space).
Such a moulding will give a hand-glove fit which can be harnessed in aptamer-drug design.
I think this is an area that needs further investigation.
Sincerely,
Ottar Stensvold
Molde
Norway
(Photo at top, a sea water sample, from http://www.uib.no/rg/mm/artikler/2009/01/viruses-and-bacteria
For more photos of bacteria in water, see Alison Kelley`s blog at http://iceberg.dri.edu/blogs4.php)
Proposed new drug paradigm: Are the classic ribosome-tRNA models wrong? - A chance.
(Regarding autoimmune MS and diabetes:
My idea is to take down the protein markers
which the T-cells home in on when they perform autoimmunity, and/or target the receptors /
surface proteins on the T-cells which they use in this task. At GenBank we can find some of
the needed gene/protein sequences.)
I try to explain my theory in this video:
http://www.youtube.com/watch?v=7834CXASQF8
(For clarity, the elongation factor binding to and shepherding aminoacyl-tRNA is omitted in the model.)
I found these articles supporting my theory about amino acids` binding to their cognate codons:
http://www.ncbi.nlm.nih.gov/pubmed/14561881?dopt=Abstract','NCBI','700','400')
http://www.ncbi.nlm.nih.gov/pubmed/16186130?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.
http://www.ncbi.nlm.nih.gov/pubmed/15952885?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
http://www.ncbi.nlm.nih.gov/pubmed/10354582?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
Idea in biochemistry part 1-4:
--------------------------------------------------------------------------------
PART 1
Quick websearches on the topic ribosome all show the same:
the amino acid-loaded tRNA arrives at the ribosome with its
anti-codon first. I think this could be an oversimplification, which
doesn`t take notice to the probable, intuitive fact that the gene is
a blueprint for the protein, a mirror-copy made through evolution.
Say the proteins initially instructed the genes and not vice versa.
Say the food came first, and then the means to carry it.
For such a coplex process as translation to proceed without many errors,
there have to be a second mechanism of proofreading. Maybe there is a
closer link between amino acids and the mRNA than previously thougth.
Maybe there is a transient key-lock binding between the amino acid and
the codon before the anticodon binds.
The bases seem to reach for the amino acids, and the first and the second
base seems to play the greatest role. For instance, the short one-cyclic U are
in the second (midst) position in codons binding hydrophobic amino acids,
indicating the hydrophobic aa`s R-groups (side chains) will turn downwards when binding.
And hydrophilic amino acids have the longer two-cyclic A in the midst position
in their codons, indicating the R-groups will turn upwards, away from the codon,
towards the water when encountering the codons.
My point is that it should be possible to make any short gene sequence
that could match any protein, almost as an antibody. The oligonucleotides
will be shrunk at point of binding, and they will probably work for only shorter
stretches. As far as I know it should not be too dangerous to appply in vivo,
but of course animal tests, research etc. are needed.
I read for instance in Discover Magazine and at Nature.com that eosinophilic cells
catapult mitochondrial DNA nets against parasites (malaria).
It should be possible to target any protein-markers in any disease,
and hence destroy the culprits. Say, put a virus in a PCR machine and make
cheap copies of tailored antibodies! Or use the new oligo synthesis factories!
I try to explain my theory in this video:
http://www.youtube.com/watch?v=7834CXASQF8
I found these articles supporting my theory about amino acids` binding to their cognate codons:
http://www.ncbi.nlm.nih.gov/pubmed/14561881?dopt=Abstract','NCBI','700','400')
http://www.ncbi.nlm.nih.gov/pubmed/16186130?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.
http://www.ncbi.nlm.nih.gov/pubmed/15952885?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
http://www.ncbi.nlm.nih.gov/pubmed/10354582?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=4&log$=relatedreviews&logdbfrom=pubmed
Sincerely,
Ottar Stensvold,
Reinhold Zieglers veg 14 B
6414 Molde
Norway
mobil: +47 95 177 433
epost: ottarstensvold@hotmail.com
web: http://ottarstensvold.spaces.live.com
born: February 7th 1971
------------------------------------------
PART 2
A drop of ordinary water-smear on a microscopy slide reveals a pattern:
the bacteria in the water lines up, symbolized like this: o.....o..o...o...o
These lines are best seen at 400x magnification.
My theory / idea is that DNA from ruptured bacteria binds and absorbs proteins
from its own species.
So what? If so, if a nucleic acid can bind to a protein in a coded manner,
then the aptamer technology is the tech of the future.
Say for instance the codon GUG, which codes for the amino acid valine, weakly
binds this amino acid. Symbolized like this: E -<
The codon-amino acid binding gives several combinatorial possibilities with
regard to polar interactions, mechanic fit and R-group placement.
If we can make aptamers tailored to bind specific proteins, then we can
take down any pathogen.
----
PART 3
The amino acid sequence of the HIV surface protein GP 120
can be found at GenBank:
http://www.ncbi.nlm.nih.gov/protein/7769644?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum
My plan is to try to make an array of different aptamers to hit this protein.
The approach I will use is basically to design aptamers that are based on
the amino acids` corresponding codons. In the DNA-aptamers, I will replace
U with T, and in the third wobble-position I will choose the assumed least
interfering base (T). RNA aptamers can also be used.
There is a chance that the aptamers will match directely.
The matches have to be at accessible parts of the protein`s surface.
The aptamers will be ordered (outsourced), for instance from:
http://www.biomers.net/upload/Image/Preislisten/DNA_En_EUR.pdf
or from Eurogentec in San Diego, California:
http://www.eurogentec.com/news/106-eurogentec-launches-new-oligo-synthesis-facility.html
The price of the aptamers will be maybe around one tenth of comparable drugs,
i.e. monoclonal antibodies.
The stock of different aptamers will be annotated at my portable computer.
Then, step 2, we have to beg institutions which store HIV viruses to test the aptamers in vitro.
The results can be viewed with electron microscopes.
(One can also test aptamers on oncoproteins in stored tissue samples,
e.g. the 17 aa CD44 protein which is overexpressed on membranes on glioma cancer brain cells.)
This project needs help from media. The headlines could be:
"Burn off money to test HIV drug"
"Find needle in haystack"
Press: "Will this be tested in humans? Will there be marketing? Sales?
Investing?"
Answer: "We will find a balanced solution, it`s fair that developed
countries pay for some of the venture."
The task will require all communication skills and business intelligence.
It is a bit like cloud computing: once the hidden codes are found,
they have to be administered.
It is my goal to reach this goal of my life!
------------------------------------------
PART 4
The aptamer:
GGTTGGTGTGGTTGG
(or ggttggtgtggttgg)
or GGT TGG TGT GGT TGG
or GGU UGG UGU GGU UGG (in RNA) corresponds to the amino acids:
gly trp cys gly trp abbreviations:
G W C G W
This aptamer binds to thrombin, the blood-clotting protein.
I found it at:
http://bloodjournal.hematologylibrary.org/cgi/content/abstract/83/3/677?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=aptamer&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT
To find the amino acid sequence in thrombin, I search GenBank at:
http://www.ncbi.nlm.nih.gov/nuccore/169808403?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum
The combination "GW" occurred once in the thrombin protein,
the combination "WG" occurred twice,
the combination "WC" occurred twice
the combination "GC" occurred twice
and the combination "CG" occurred three times
The latter combination, for instance, should then bind to the aptamer-codons UGU GGU.
I did not find similar matches in the comparable plasma proteins albumin or insulin,
and I think further research will find no other similar matches either.
It is striking that the aptamer comprises the range of codons encoding the protein (aa range) it binds!
This underscores my suggestion that proteins can bind specific to their codon combinatons in mRNA or (+)ssDNA.
The numbers of possibilities to get a twosome aa-combination of a pool of twenty different amino acids,
should plainly speaking be 1/20*1/20 = 1/400,
and this makes specific binding likely!
In the June 2009 Scientific American issue, there is an article about silent mutations (by Chamary and Hurst)
which highlights that different codons encoding the same amino acids give alterations in the proteins.
It`s thus feasible that this bias is caused by the codons` positioning of the amino acids (R-group placement in space).
Such a moulding will give a hand-glove fit which can be harnessed in aptamer-drug design.
I think this is an area that needs further investigation.
Sincerely,
Ottar Stensvold
Molde
Norway
(Photo at top, a sea water sample, from http://www.uib.no/rg/mm/artikler/2009/01/viruses-and-bacteria
For more photos of bacteria in water, see Alison Kelley`s blog at http://iceberg.dri.edu/blogs4.php)
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