Re: [Fis] Molecular recognition: Similarity rule and complementarity rule (PG or reader must be over 20)

Dear Pedro,

You listed many pair-wise recognition examples. Thanks! Pedro, can you
complete the list and maintain the list? Actually in many cases
the involved parts are more than 2. The enzymatic system
enzymes/substrates/cofactors/solvent molecules is an example.

Regarding complementarity rule for pairs, the hydrophobic molecular docking
should be included which is very much like sex between male and female.
It is just a non-bonding convex -concave
process. After the satisfactory "recognition", the combined body of the two partners
may become very symmetric and the desire satisfied. (Molecules also have sex).

(Warning: To go on, FISers must remove the filter for their incoming e-mails because
some words in many spam e-mails might be used).

Shu-Kun

"Pedro C. Marijuán" wrote:

> Thanks, Shu-Kun, for the well posed questions.
>
> In a paper, posted at the fis site, I have put together a brute taxonomy of biomolecular recognition events (inspired in Meggs, 1998):
>
> enzymes/substrates,
> enzymes/effectors,
> enzymes/cofactors
> antibodies/antigens,
> receptors/transmitters,
> receptors/hormones,
> channels/ions,
> channels/ligands
> nucleotides/DNA-RNA chains,
> RNA/RNA pairing,
> RNA/DNA pairing,
> DNA/DNA pairing,
> DNA/promoters,
> DNA/histones,
> RNA/ribosomes,
> amino acids/protein chains,
> proteins/chaperons,
> proteins/proteasomes,
> proteins/protein multimers,
> proteins/protein complexes,
> proteins/protein kinases-phosphatases,
> tubulins/microtubules,
> actins/microfilaments
> carbohidrates/glycoproteins,
> lipids/lipoproteins,
> phospholipids/membranes
>
>
>
>> There seem to be only similarity rule and complementarity rule
>> for molecular recognition. Are there any other rules?
>
>
> Intriguing question in front of the above taxonomy. Should we open a third category related to systematic detection of 'transition states' (at
> least, thinking on enzymic active sites and perhaps antibodies ---or are they somehow covered by 'complementarity')?
>
>
>> Xerman related molecular recognition to chemical bond. Is the
>> molecular recognition simply a special case of
>> chemical bonding?
>
>
> In general I agree (although hydrophobic forces do not neatly fall into that line).
>
>
>> Let us do it step-by step. We must first define it. Then try to
>> find a plausible theory about it.
>
>
> OK!
>
> Pedro

--
Dr. Shu-Kun Lin
Molecular Diversity Preservation International (MDPI)
Matthaeusstrasse 11, CH-4057 Basel, Switzerland
Tel. +41 79 322 3379, Fax +41 61 302 8918
e-mail: lin@mdpi.org
http://www.mdpi.org/lin
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