# Virus immunity

1. Apr 20, 2006

### Intuitive

Question?

Can Science make Antibodies smaller?

This way Antibodies can fit between the Major Capsid Protein of a virus with ease.

Wouldn't it be easier for the Antibody to invade the virus if the Antibody were normal but much smaller than the Average Antibody so it could get past the Major Capsid Protein to take a Viral DNA Sample so that the Antibodies could send out their Immune response more efficiently?

In order for the Antibodies to invade the Virus then it has to get past the Major Capsid Protein right?

2. Apr 20, 2006

### Intuitive

I sent out this question to all of the Major University Medical Groups and to the FDA, CDC and AMA, Universities included were Oxford, Harvard, Berkley.

If I get my replies back on the question posted about Antibodies I will post the E-mail letters for reading material on the possiblity.

Last edited: Apr 20, 2006
3. Apr 20, 2006

### Moonbear

Staff Emeritus
Antibodies don't need to get into the virus at all; they don't target DNA, they target proteins, usually, such as those in the virus coat.

I'll move this over to biology so you can get a more thorough response explaining how immunity works.

4. Apr 20, 2006

### Intuitive

Hi Moon Bear.
I like the Sniper Kitty, It's cool.

Back to the question?

The Antibodies take samples from the Major Capsid Protein or what you call the virus coat right? but in order for it to take the sample it has to fit itself between the Major Capsid Protein configuration like a puzzle correct?

I have heard that Antibodies can't fight off 'some' virus's because it is incapable of fitting between the Major Capsid Protein to collect protein samples, But if the Antibodies were smaller wouldn't the Antibodies pose more of a threat to a virus because the Antibodies could penetrate the Major Capsid Protein more efficiently with less obstruction from the Major Capsid Protein layer? and that the Major Capsid Protein acts as Armor for the virus

5. Apr 21, 2006

### Curious3141

What Moonbear said is mostly accurate, but some antibodies can indeed target nucleic acids. For example, an (autoimmune) antibody to double-stranded DNA is a common finding in systemic lupus erythematosus (SLE).

Antibodies can target pretty much any molecule of sufficient size/complexity. But (as Moonbear meant) antibodies produced by the body to target pathogens (like viruses and bacteria) are mainly directed against the epitopes (you should look this term up) on the exterior of the pathogen.

Antibodies come in various sizes dependent on their class. The "usual" antibody type people visualise when they talk about them is the IgG class (G-class immunoglobulin) which has 2 heavy chains and 2 light chains bonded together. IgM (M-class immunoglobulins) are the biggest and heaviest in their native state because they occur in a pentameric form with 5 units, each like an IgG molecule, giving a total of 10 heavy and 10 light chains.

You can make fragments of antibodies that retain the binding specificity but are lighter and smaller. These are called $$F_{ab}$$ fragments and they are sometimes used to bind and mop-up excess drug molecules to treat overdoses (like in digoxin toxicity).

VIral structure is more complex than you seem to think. They may have a lipid envelope that sheaths the nucleocapsid (in which case, the capsomeres or capsid proteins won't be exposed on the surface). Embedded in the lipid envelope may be lipoproteins or glycoprotein "spikes" which also can elicit an antibody response for e.g. when you talk about the flu (influenza), antibodies form against hemagglutinin and neuraminidase molecules which are prominent projections from the viral surface. Non-enveloped viruses will have their capsids on their outside but may also have these spikes on their surface, e.g. the glycoproteins poking out from the vertices of the icosahedral capsid of the adenovirus.

Another thing you must keep in mind is that not all antibodies are "neutralising" (blocking the virus' attachment and propagation through steric hindrance) - some work in other ways (like complement activation or "opsonisation" - making the virus particles "tasty" for macrophages which gobble them up). Still others serve no good function, they are simply ineffective products of the immune response, and some of these may actually be harmful to the body because of immunological cross reactions with healthy body tissue (the basis for one form of autoimmune disease).

Antibody mediated immunity is important to many viruses, but in some viruses it just doesn't work enough to prevent a reinfection. With nearly all viruses, some degree of "cell mediated immunity" is important. This has nothing to do with antibodies per se, but a lot to do with T-lymphocytes. This is a big topic, I suggest you do a search on this as well.

I hope I've answered some of your questions (even ones you haven't asked yet), and pointed you in some new directions. Immunology and Microbiology are fascinating subjects and the latter happens to be my bread and butter.

Last edited: Apr 21, 2006
6. Apr 21, 2006

### Intuitive

Hi Curious.

Do you know if there has been extensive research on the $$F_{ab}$$ efficiency on viral groups explicitly, I am mostly interested in the smallest Antibodies to see if any pattern effiencies exist in their smallness
property and if the $$F_{ab}$$ have more efficient binding strategies to viral protiens.

I would love to study this explicitly for the moment, Is there a good reference to such data?

7. Apr 21, 2006

### Curious3141

I'm afraid I don't know of any study of the sort you're looking for, but here's one on immunostaining (a diagnostic technique) : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2409131&dopt=Abstract

$$F_{ab}$$ fragments don't bind any more efficiently to their targets than whole antibodies, but they have some advantages - for example they're less immunogenic in vivo (elicit less of an immune response, so they're less dangerous), which is a good reason to prefer them in disposing of excess drugs, etc.

8. Apr 21, 2006

### Emieno

Intuitive, may I ask what type of virus are you searching on ?

Different viruses do possesses different structures and infection mechanisms. HIS's secreted antibodies are important in fighting against viruses but not the only ones under consideration for the viral elimination process. If you would like to use antibodies as therapeutic agents, I guess, you still might think of different problems existing such as inaccesibility, immunoglobulin hypersensitivity, side-effects to neighbor cells etc.

I think it is not about 'enough or not enough', it may be because (1) virus's high mutation rate which is not the main point for viral evolution as far as I know, and (2) it always takes some time for the recognition even when the former population of B-cells could already memorize the enemies.

I guess you might also find interesting to check out different IL levels due to different viral infections...

Last edited: Apr 21, 2006
9. Apr 21, 2006

### iansmith

Staff Emeritus
Just to add on making smaller antibodies. You can also make single chain Fv fragment(scFv) antibodies. These are about the same size of Fab if not smaller in some cases.

For a very brief intro
http://en.wikipedia.org/wiki/ScFv

10. Apr 21, 2006

### Intuitive

Here is what the F.D.A had to say about smaller Antibodies Question:

Nowadays scientist have be able to make fragments of antibodies or peptides that are shorter; also discovered "nanobodies" "incomplete" antibodies (lacking the light chain) which are able to grasp their targets just as firmly as normal antibodies do. Having said that, antibody fragments cannot recruit other components of the immune system, such as killer T cells, in the same way that full-size antibodies do, because they lack the protein stem that performs that task and also, even nanobodies, are not dimensionally more able to invade a membrane made up of proteins and lipids. What I'm implying here, is that the size of the molecules of an amino acid can not be made smaller. The membranes have evolved to evade invasion by virtually anything on the scale of an antibody combining site (perhaps 7-8 amino acids - each averages 100 daltons - so you can figure the minimum size.

Sincerely,

Andrei Perlloni
Consumer Safety Officer
Center for Biologics Evaluation and Research
Office of Communication, Training and Manufacturers Assistance
Division of Communication and Consumer Affairs
Phone: 301-827-2000

This communication is consistent with 21 CFR 10.85 (k) and constitutes an informal communication that represents my best judgment at this time but does not constitute an advisory opinion, does not necessarily represent the formal position of FDA, and does not bind or otherwise obligate or commit the agency to the views expressed.

11. Apr 21, 2006

### Curious3141

There are many reasons why an immune response fails to eradicate an infection or prevent a recurrence or reinfection. Mutation is just one. The pathogen may also seek "refuge" in an immunologically privileged site like the neuron (as happens in Herpes Simplex). Viruses may directly compromise the immune system, hijacking host defences to their advantage (as in HIV). And so forth.

Viral strategies for immune escape are protean. I was just keeping things simple for the OP - summing it up by saying that sometimes the immune response just isn't enough, which is true enough.

12. Apr 21, 2006

### Curious3141

He's referring here to the $$F_c$$ part of the immunoglobulin molecule. This stem serves as the membrane binding portion of the molecule. B cells carry antibodies anchored in their cell membranes (via $$F_c$$) that can contact antigenic epitopes via the variable regions and stimulate the B cell to produce more antibodies of that specificity (this is how you get a basic antibody response). Macrophages carry receptors for $$F_c$$ on their surface, so they can bind antibody-antigen complexes and internalise them (phagocytosis).

Lastly, remember the cell mediated immunity I was talking about, and how it was separate from antibody (humoral) immunity ? Well, that was a (conscious) simplification. There are points in the immune response where the two pathways interact - for e.g. Natural Killer (NK) cells bear $$F_c$$ receptors. When they encounter an antibody complexed to antigen (like a virus infected cell forced to express foreign proteins on its surface), they will release certain potent chemicals like perforins and granzymes that will kill the cell and reduce the viral load in the body. NK cells also play roles in immune surveillance against cancer, etc.

I haven't even gotten into the wondrous interleukin, cytokine and interferon pathways, nor have I touched on complement and other aspects of the immune system. Truly, it is an immensely complex subject, and you should do a lot of reading. I hope this has inspired you to.

13. Apr 21, 2006

### quantumcarl

Why doesn't a cell's P53 gene kick-in and destroy the cell in the event of a viral intrusion? Would this cause too much wide spread distruction?

Do some viruses have the ability to shut down P53 in a way that is similar to a cancerous mutation's ability to do the same?

14. Apr 22, 2006

### Intuitive

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15. Apr 23, 2006

### Intuitive

Custom immunoglobulin

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16. Apr 24, 2006

### Intuitive

Geometrical Simularities between a Ragweed Pollen and a Human Papilloma Virus.

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