Computer-generated vaccines

cm006 at FREENET.BUFFALO.EDU cm006 at FREENET.BUFFALO.EDU
Tue Nov 23 11:23:54 EST 1999


To adequately harness the power of computers in generating peptide vaccine
candidate sites, a physical chemical analysis of the interactions of
peptides and antibodies at a more basic, physical level than amino
acid combinatorics per se, needs to be addressed. 

For our, perhaps more atomic than molecular answer to this problem please
see:

Kokolus, et. al,  Does the Fountain Epitope Model's Rhythmic Hydropathy
Continuum Pattern Satisfy the Requirements of a Nucleic Acid Meta-code or
Protein Meta-form?,  Ann. N.Y. Acad. Sci. 870:423-427.

Happy Thanksgiving, everybody!

Yours,
William J. Kokolus, Ph.D.
President, Fountain's Rainbow Biomedicine,
Kenmore, New York

On Mon, 22 Nov 1999,
Tracy P. Hamilton wrote:

> 
> Pierre wrote in message <818dle$2jee$1 at news4.isdnet.net>...
> >What is the role of contingency/probability in protein folding ? If one
> >chain has many possible foldings, each affected with a given probability
> >amongst the population of molecules (like in evolution/population
> genetics),
> >is it possible to calculate all the variations ?
> 
> 
> [snip my previous post]
> 
> One would not be able to go thorough all possible protein conformations.
> I *believe* (I am no protein folding expert, but a theoretician in a more
> fundamental sense) that current approaches are more empirical.
> Predict secondary structure (alpha helix, beta sheet, random coil) from
> part of the amino acid sequence, tertiary structure (overall shape) is from
> a different database, but similarly empirical.  Both are correct about half
> the time now, last I heard.
> 
> A group was able to predict the sequence of a protein that would be
> the same shape as one of the zinc finger proteins, except without zinc!
> Makes one wonder why zinc fingers have zinc...
> 
> Theory does currently play a large role in constraining structures,
> particularly
> NMR ones (solution structures based on H-H distances).  I don't have a
> good feel for what would happen if you applied one of the good protein
> force fields to the superoxide dismutase enzyme (or the mutant that
> has been identified with inherited ALS which has a more exposed
> active site).
> 
> If I were to model the active site, I would probably put some geometric
> constraints on the active site to keep it in the neighborhood for at least
> some calculations.
> 
> Tracy P. Hamilton
> 
> 
> 
> 

William Joseph Kokolus, Ph. D.
President, Fountain's Rainbow Biomedicine
69 Ferndale Ave.
Kenmore, N. Y. 14217-1003
phone and fax: (716) 873-6940
e-mail: cm006 at freenet.buffalo.edu





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