Re: [ccp4bb] Nucleophilic attack by the side-chain carboxyl group of Asp?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: off topic Thermal shift assay
From: Artem Evdokimov artem {- dot -} evdokimov {- at -} GMAIL {- dot -} COM
Date: 2012-07-21

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Subject: Re: Nucleophilic attack by the side-chain carboxyl group of Asp?
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2012-07-21

Subject: Re: Nucleophilic attack by the side-chain carboxyl group of Asp?
From: Justin Jones jej428 {- at -} GMAIL {- dot -} COM
Date: 2012-07-21

Unfortunately, their isn't a "general rule" for good versus bad
nucleophiles. However, their are some key classical examples, which are
reviewed extensively in enzymology textbooks. Remember, that a nucleophile
is dependent on it's pKa value, which depends on the surrounding residues.
Thus, two different enzymes that possess the same type of nucleophile but
perform different reactions can have different pKa values, and therefore
different rates. It is also dependent on the leaving group potential of
the electrophile and the stability of the covalent intermediate. Some
examples of nucleophiles in no particular order include, serine, cysteine,
aspartate, lysine, histidine, and tyrosine. Hope this help.

Justin

On 7/21/12 1:03 AM, "Peter Hsu" wrote:

>I too am also studying the reaction mechanism of an enzyme, but my
>chemistry/enzymatic biochemistry is rather weak after many years of
>non-use and no review. Does anyone know just as a general rule which
>residues are the best to worst nucleophiles?
>
>Sorry if this seems rather presumptuous, just not sure where to look in
>literature for a summary of these things.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: off topic Thermal shift assay
From: Artem Evdokimov artem {- dot -} evdokimov {- at -} GMAIL {- dot -} COM
Date: 2012-07-21

Next message:
Subject: Re: Nucleophilic attack by the side-chain carboxyl group of Asp?
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2012-07-21