Bobhexa (Quark) 06-06-2007, 02:14 AM
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Capsid Geometry
I recently googled "AIDS" and "Cancer" and stumbled across a site that was dated 2005 which stated that a common ancestor billions of year ago allowed the DNA in viruses to evolve and that it uses the the same basic protein "fold" to construct the critical outer shell. I question this common ancestor theory insofar that billions of years ago the existing forces at that time are the same kind of forces we experience today.A sphere is formed because of these forces . Would it be more acceptable to saythat geometry is the language of these forces?
Location: Hawaii, Oahu, Manoa Valley
foodchain (Organism) 06-06-2007, 10:49 AM
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Much of ancestry in terms of biology can also simply be viewed via genetics and what not. As for you idea of geometry playing a role in some way or ways I don’t see why not. Life is based on the physiochemical like most anything else, be it a solar system of the geology of earth.
Join Date: Jan 2007 Posts: 1,126 Location: earth
bobhexa (Quark) 06-06-2007, 01:14 PM
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Thanks Foodchain for your response.My reason for asking the original question is that I have discovered a new flexible construction element which can be formed into a sphere which appears to look like a capsid kind of geometry.
Location: Hawaii, Oahu, Manoa Valley
foodchain (Organism) 06-06-2007, 02:27 PM
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I cant view the link. No big deal, I am somewhat interested in what you are talking about though. Reading stuff from say biophysics they are heavy on structure as its more readily able to accept being put in mathematical forms, such as the crystal lattice and what not.
Location: earth
CharonY (Biology Expert) 06-06-2007, 03:02 PM
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To be honest, I do not quite get what you mean. Viral capsules usually build themselves via self-assembly. This means that the information of how to assemble themselves is already provided by the proteins which constitute these capsules themselves. The authors you cite (Fokine et al; btw it is easier if you provide links btw ) have noted that tailed phages (in particular T4 and HK97) share a similar structure in the capsule, which they share with some eukaryotic viruses. So similar structures (and also assume conserved domains) hint that dsDNA containing phages might share a common ancestor.
It has long been recognized that 3D structure is conserved over much longer timespans than nucleotide or amino acid sequences (42). Thus, the large number of structural and functional similarities of tailed phage capsids makes it probable that these and the capsids of other related viruses have diverged from a common ancestral source. Considering the high abundance of phages on Earth (43), the HK97 capsid fold must be one of the most frequently occurring structures in the Earth's biomass.
Thus I do not understand your reasoning, as phage capsids are complex structures (as proteins go) and are not random molecules "pressed together" by some geometrical forces, as it might be interpreted from your post (at least I did). Change the amino acid sequence and you won't obtain a capsule.Judging from the link that you have given the patent is about the construction plans for a macroscopic construction unit. I fail to see the connection except for rough similarities. Like, say comparing golf balls to apples.
bobhexa (Quark) 08-12-2007, 04:32 PM
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Well I have been trying to put my ideas into a more logical order. I fully grasp the facts of viral self assembly. The question I have is what influenced the amino acid sequence? It appears that each variety of capsid geometry design has an equal matching twin in the material world of crystals. CharonY, you mention the phrase common ancestral source….Does the word “ancestral” preclude the crystal as having had any relevance in the design of proteins? If so, then what is the source of the geometry that they both share?What is the common source more likely to be? Do ambient forces acting upon matter dictate how things will form?. Couldn’t these forces that cause a crystal to grow in a certain manner also act upon proteins? They both start from “nothing” and expand into being. So what came first? Was it a photo finish? A strange freak of coincidence!Imagine blowing a steady stream of air through a narrow straw into a bowl of soapy water....blow enough bubbles to create three levels/layers/tiers.Observe middle layer .....what do you see??The link between this subject and my patent is that when I construct a double skinned sphere from this material it offers a brand new geometry for study that emulates certain capsids double skinned appearance.
bobhexa (Quark) 06-06-2007, 03:13 PM
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Ty ,Yes, I take your point FoodchainIf you register (takes 2 minutes) you will be able to view the link.Please give it a try. Good luck
Location: Hawaii, Oahu, Manoa Valley
bobhexa (Quark) 06-06-2007, 07:15 PM
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Thank you Charony for your well considered response.Yes, it’s all in the interpretation and you may have jumped to the wrong conclusion. No, I do not think that capsids are formed from random molecules “pressed together” by geometrical forces. The C60 molecule is a truncated icosahedron and it would appear that most capsids appear to take this geometry. Do you know the exact geometry of these family of capsids?If you do not then I am offering you a possible geometry to research. All in the name of knowledge. This maybe the last precept to form another concept.You fail to see the connection except for rough similarities. Like, say comparing golf balls to apples.So, like, say comparing C60's and capsids. Are they that far apart?
Location: Hawaii, Oahu, Manoa Valley
foodchain (Organism) 06-06-2007, 08:07 PM
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C60, that’s a buckyball right I don’t know the chemical composition of the item in question fully but I don’t think its based on C60. If you are more or less speaking in terms of the forces that give C60 its shape is the same in regards to what gives the item in question its shape, I don’t know to what extent that would be true as I have never giving it much thought/study. Its an interesting association, but on that note I don’t know how much the impact a structures geometry has in regards to interactions in the first place, such as a square making square waves when dropped in a liquid for instance, probably easier for circle I would imagine. I also do not understand fully of course the reality of chemical bonds in regards to molecular shape and fully what such derives from. Such as Carbon being able to exist in various configurations, such as diamond or graphite; More so in a case by case basis. I would think that reaction mechanisms have environmental variables involved, which could I guess play into it on some level, but overall I don’t really think I understand enough your question overall. If per say its just structure, well structure is important in biological systems, and is also conserved as I think was already pointed out.
Location: earth
CharonY (Biology Expert) 06-07-2007, 01:17 AM
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No, I do not think that capsids are formed from random molecules “pressed together” by geometrical forces.The C60 molecule is a truncated icosahedron and it would appear that most capsids appear to take this geometry. Do you know the exact geometry of these family of capsids?
I think you are completely on the wrong boat. See, a C60 simply consists of, well carbon. Capsids however are proteins, a far more complex composition. Check the original paper in which the crystal structure is resolved. The geometry of the phage heads is thus governed by the amino acid sequence. There are other viruses that have different architectures (e.g. retroviruses) which thus likely do not share the same common ancestors as T4 and related phages. Comparing an evolved protein structure with fullerens, even if they should share geometrical similarities is like assuming that there must be a common force between tennis balls and oranges.You are confusing very different things here.
Last edited by CharonY; 06-07-2007 at 06:00 AM.
bobhexa (Quark) 08-21-2007, 12:31 AM
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Moving on
Okay, I accept that, based upon the lack of replies from my posting of the image that it does not interest you bio-engineer guys. That is okay as I had originally posted that this exercise is for the sake of getting the concept out into the knowledge bank as I really do consider that this geometry has some important application somewhere in engineering. I tried you guys first! It must exist somewhere in nature ...perhaps it is a foolhardy belief of mine that if something is elegant and efficient that it will have already been utilised by Mother Nature. Perhaps I am naive.... Nanoworld next stop....medical stent perhaps.
Location: Hawaii, Oahu, Manoa Valley
pioneer (Molecule) 08-30-2007, 02:14 PM
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In crystals, the final geometry is not only impacted by the binding forces between atoms, but also due to external factors such as the solvant composition, foreign atoms, or even something simple like cooling profile. Typically one of the crystal shapes is minimum energy, while others may still be stable but contain some potential relative to the minimum potential shape. For example, if you took steel and hit it in one place with a hammer, this will affect the crystals at the point of impact and add potential. This will often be the first place to rust because of the potential that was added. Relative to C, diamond is the most stable crystal form of C. The capsid, by looking at it, looks cool, but it appears to indicate stored potential. This could be useful if one wished to build something stable, that contains a little extra potential so it can be used as a type of catalyst. Or it may allow stable electron states that are a little higher in energy than normal.Addressing viral self assembly, the potential in the water will put the squeeze on anything that tries to increase its potential. At the same time, the viral components have binding areas that allow these to minimize their own energy. Between the push of the water and the pull of the binding areas they self assemble. It does its best to minimize potential under the circumstances. But again, like the capsid, minimum potential is relative. Potential can be stored into a stable configuration. This makes it easier, later on, for the virus to shed its protein shell and release the DNA.
Location: Mandarin, Florida
bobhexa (Quark) 09-06-2007, 11:31 PM
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With capsid in hand............
A very interesting viewpoint Pioneer You say that “ Potential can be stored into a stable configuration. This makes it easier, later on, for the virus to shed its protein shell and release the DNA.” Consider then, could it be that the concertina geometry of this sphere is ‘stored potential’?When internal pushes come to a shove, the double skinned sphere will gradually expand outward into a single skinned angular truncated icosahedron.During this process of expansion the 12 pentagonal openings get larger in diameter. Could this be an unknown mechanism allowing it to ‘shed its protein shell and release the DNA’Do either of the views(last post), in any way or form, appear capsoidal? If it were so, it would need to be in an immature state of development, prior to shedding.
Location: Hawaii, Oahu, Manoa Valley
bobhexa (Quark) 06-07-2007, 05:59 PM
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I think we are getting hung up on the subject of forces.I am trying to draw your attention to the fact that there are exact similarities between space fillers and capsids. Suppose that I have discovered a new kind of geometry which goes a step beyond a truncated icosahedron by making it double skinned. This would be a geometry which has not as yet been discovered.Would it be of any interest at all to your profession?
http://www.sandforsk.se/articles/Whatmakesstructureandshapeofcapsidorcrystalaug2006.pdfRef page 11 of 14 Coxsackie virus based on the truncated icosahedron
Location: Hawaii, Oahu, Manoa Valley
foodchain (Organism) 06-07-2007, 07:07 PM
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I have to say that’s a really interesting reading for anybody interested. Secondly, what is your primary interest for the study of such? Is it more leaning towards evolution per say, or more towards structural geometry period? If its for evolution, there is a broad range of stuff that’s already known that I think would take sometime to integrate into that paper(you produced?).If its purely for structural purposes, well then I guess one would have to take into account on some level if the chemistry life typically uses, or that of what you study actually permits in some level of exactness what you are stating, as put forward as a possible tool in the paper for evolution for instance. Which structure of life is conserved such as having X limbs, or two eyes for instance. The problem I get is where the evolution thing ties into what works in the ecology overall in regards to any variables, such as needing to run, and how needing to run impacts the body. My guess is all that as you would have it structure and geometry play some role along with various forces and the chemical structures and so on, or available chemistries and I don’t know of any living things with some organic titanium joints for instance. Well anyways, please feel free to post more in reply, I find that very interesting.
Location: earth
CharonY (Biology Expert) 06-08-2007, 02:35 AM
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Hmm maybe I understand a bit better what you mean now (but then, maybe not ;P)I assume that may main problem with your reasoning and my focus in forces vs. structure is this from your OP:
which stated that a common ancestor billions of year ago allowed the DNA in viruses to evolve and that it uses the the same basic protein "fold" to construct the critical outer shell.I question this common ancestor theory insofar that billions of years ago the existing forces at that time are the same kind of forces we experience today.A sphere is formed because of these forces . Would it be more acceptable to saythat geometry is the language of these forces?
These sentences consists of a number of different assumptions that, at least to me do not sum up. Therefore I will try to ignore what I assume to be inconsistencies and try harder to get what you mean (yeh, I am probably thick-headed).Anyway, what I do not understand yet is what you mean with geometry? Do you mean structure? And do you mean identifying given structures in nature or about creating them, as e.g. in nanotechlogical applications? Or are you more interested mathematical modeling of said structures? Anyway, I still got to read the pdf first, when I got more time. Will get back to you then.
Last edited by CharonY; 06-08-2007 at 02:45 AM.
Bluenoise (Biology Expert) 06-08-2007, 03:43 PM
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He's basically making a comparison of the structural of viral capsids to various geometries. Like dodecahedrons etc... Along with this is the use of two different mathimatical methods to generate these geometries. Either the use of simple mathametics or a quantum harmonic ocillator.A fairly interesting read actually. Lot of great images.Though the math is definatley a little past what I've become accustomed to.
Location: Canada
bobhexa (Quark) 06-08-2007, 07:16 PM
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CharonY……Well, I must say that I admire your tenacity for staying with the thread, a subtle thread at that! Foodchain….your’e an angel sent to smooth rough edges (600 grit or more)Blue noise…. Ta very much for either the summing up of me or of the author of the link, I wasn’t quite sure to whom you were referring. However you do a fine summing up with a shrewd burst of objectivity.Okay I insist that you all really make an effort to log on to the original patent site link
http://www.freepatentsonline.com/20070015000.pdfand go to Figure 13 on page 7 of 14in the patent. There you will find a line drawing of a spherical structure .The line photograph was made from a halftone photograph of a sphere which I built using the construction element that I have discovered. I say ‘discovered’ because it is has always been there in the geometrical world but amazingly unnoticed by “Acadamia”. It is pure geometry without the interference of humans. I just followed the geometry.There is an undiscovered family of tiling units that can also take on this folding attribute in 3D geometry….namely… equilateral triangle, square and hexagon. I want you guys to take note of it and see if it has an application to your work! . The different surface areas they present seem akin to 3D geometry and a perfect fit in capsid structure. Perhaps we can look upon capsids as 3d geometrical structures and who really cares as to how they came to be, whether it was harmonics, mathematics, waves or geometry but just the fact that they ‘are’.
Location: Hawaii, Oahu, Manoa Valley
bobhexa (Quark) 06-08-2007, 09:05 PM
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This is a sweet site also
http://www.sandforsk.se/sandforsk-articles/index-article.htm I refer you to page 5 of 9I rather like the phrase "Mechanism of formation"
Location: Hawaii, Oahu, Manoa Valley
