Re: [ccp4bb] How to make GDP.BeF3 solution ?

2024-01-07 Thread Marian Oliva 
Dear Firdous,

As Matt refers BeF3 mimics the GTP/ATP bound states. For the transition state 
we have used mixtures of AlCl3 and HKF2 in combination with GDP (or ADP) and 
MgCl2 within the buffer. Be aware that depending on the concentrations used of 
each component you get different proportions of AlF3 and AlF4 (Goldstein G. 
1964. Equilibrium distribution of Metal-Fluoride complexes. Analytical 
Chemistry 36:243–244. DOI: https://doi.org/10.1021/ac60207a074). Also, if you 
are thinking on doing some biochemistry (binding affinity or similar), you must 
know about Al3+ contamination in glass material and nucleotide solutions 
(Sternweis PC, Gilman AG. 1982. Aluminum: a requirement for activation of the 
regulatory component of adenylate cyclase by fluoride. PNAS 79:4888–4891. DOI: 
https://doi.org/10.1073/pnas.79.16.4888).

Best,
Marian


> El 4 ene 2024, a las 11:19, Matthew BOWLER  escribió:
> 
> Dear Firdous,
> 
> beryllium fluoride is actually a ground state analogue of GTP as 
> trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
> either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
> advantage of metal fluoride transition state analogue and ground state 
> analogue complexes is the fact that all components are present in solution 
> and readily self-assemble in the active site forming stable enzyme complexes 
> that are relevant to the catalytic cycle. The inorganic metal fluoride salts 
> (AlF3, and MgF2) are too insoluble to use; therefore, the fluoride anion and 
> metal cation components must be added from separate stock solutions. Both 
> ammonium fluoride and sodium fluoride are suitable as the source of fluoride 
> and are readily soluble in water. Metal chlorides can be easily dissolved in 
> water at high concentration (0.5 M) and the solutions conserved at -20°C. One 
> of the critical aspects in preparing metal fluoride enzyme complexes is the 
> pH of the resulting solution. In particular, solutions of AlCl3 and BeCl2 are 
> highly acidic (pH 2) samples should be prepared in 100 mM unbuffered Tris 
> base. The optimized sequence of component addition is to add fluoride to the 
> prepared buffer first, then the metal chloride stock.
> 
> Hope this helps, Matt
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 02/01/2024 18:53, Firdous Tarique wrote:
>> Hi
>> 
>> I would appreciate it if someone could share with me a step by step protocol 
>> for making a stable GDP.BeF3 solution which is often used as a transition 
>> state analogue for structural studies of a protein complex ? 
>> 
>> Or a vendor from where it can be purchased directly.
>> 
>> Regards
>> 
>> Firdous
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> -- 
> Matthew Bowler
> Project Leader MASSIF1@ESRF
> European Molecular Biology Laboratory
> 71 avenue des Martyrs 
> CS 90181 F-38042 Grenoble
> France
> ===
> Tel: +33 (0) 4.76.20.76.37
> Fax: +33 (0) 4.76.20.71.99
> 
> http://www.embl.fr/
> http://www.esrf.eu/MASSIF1
> https://twitter.com/id30_massif1 
> https://www.embl.org/people/person/mbowler/
> ===
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Re: [ccp4bb] How to make GDP.BeF3 solution ?

2024-01-05 Thread Bernhard Rupp 
Some blast from the past: Facility management came in full hazmat suits to 
decommission the old multiwire detectors with the large Be windows.

https://www.ruppweb.org/Garland/gallery/Ch8/pages/Biomolecular_Crystallography_Fig_8-07.htm

 

Anyhow, got one on the DOE Beryllium worker’s list. Free lung X-rays

 

--

Bernhard Rupp, Psilosopher

 <https://psilosophy.org/> https://psilosophy.org/

 <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Don’t lick it and don’t breathe it. 

--

 

From: CCP4 bulletin board  On Behalf Of Diana Tomchick
Sent: Friday, January 5, 2024 13:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

 

Be aware that beryllium is also quite toxic.

 

https://en.wikipedia.org/wiki/Acute_beryllium_poisoning

 

Diana

 

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu <mailto:diana.tomch...@utsouthwestern.edu> 
(214) 645-6383 (phone)
(214) 645-6353 (fax)

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Dr. Kevin M Jude mailto:kj...@stanford.edu> 
>
Sent: Friday, January 5, 2024 1:51 PM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ? 

 

EXTERNAL MAIL

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.

 

Best wishes

Kevin

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Matthew BOWLER mailto:mbow...@embl.fr> >
Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt

 

 

 

 

 

On 02/01/2024 18:53, Firdous Tarique wrote:

Hi 

 

I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ? 

 

Or a vendor from where it can be purchased directly.

 

Regards

 

Firdous

 


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-- 
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Project Leader MASSIF1@ESRF
European Molecular Biology Laboratory
71 avenue des Martyrs 
CS 90181 F-38042 Grenoble
France
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Re: [ccp4bb] How to make GDP.BeF3 solution ?

2024-01-05 Thread Pius Padayatti 
Hi Firdous
Can you ask Trilink biotechnologies
if they can make it
for you
very good experience many speciality materials made
Disclaim: i do not work with them or have any financial connections with
them
I think jena discontinued this item but they used to sell this as well
When you get an answer can everyone know here as well
best

*Pius Padayatti*




On Tue, Jan 2, 2024 at 9:54 AM Firdous Tarique 
wrote:

> Hi
>
> I would appreciate it if someone could share with me a step by step
> protocol for making a stable GDP.BeF3 solution which is often used as a
> transition state analogue for structural studies of a protein complex ?
>
> Or a vendor from where it can be purchased directly.
>
> Regards
>
> Firdous
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] How to make GDP.BeF3 solution ?

2024-01-05 Thread Diana Tomchick 
Be aware that beryllium is also quite toxic.

https://en.wikipedia.org/wiki/Acute_beryllium_poisoning

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Dr. Kevin M Jude 

Sent: Friday, January 5, 2024 1:51 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?


EXTERNAL MAIL

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.



Best wishes

Kevin



From: CCP4 bulletin board  on behalf of Matthew BOWLER 

Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt











On 02/01/2024 18:53, Firdous Tarique wrote:

Hi



I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ?



Or a vendor from where it can be purchased directly.



Regards



Firdous





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--

Matthew Bowler

Project Leader MASSIF1@ESRF

European Molecular Biology Laboratory

71 avenue des Martyrs

CS 90181 F-38042 Grenoble

France

===

Tel: +33 (0) 4.76.20.76.37

Fax: +33 (0) 4.76.20.71.99



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Re: [ccp4bb] How to make GDP.BeF3 solution ?

2024-01-05 Thread Dr. Kevin M Jude 
Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.

Best wishes
Kevin

From: CCP4 bulletin board  on behalf of Matthew BOWLER 

Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt










On 02/01/2024 18:53, Firdous Tarique wrote:
Hi

I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ?

Or a vendor from where it can be purchased directly.

Regards

Firdous



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

--

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Project Leader MASSIF1@ESRF

European Molecular Biology Laboratory

71 avenue des Martyrs

CS 90181 F-38042 Grenoble

France

===

Tel: +33 (0) 4.76.20.76.37

Fax: +33 (0) 4.76.20.71.99



http://www.embl.fr/

http://www.esrf.eu/MASSIF1

https://twitter.com/id30_massif1

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Re: [ccp4bb] How to make GDP.BeF3 solution ?

2024-01-04 Thread Matthew BOWLER 

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you 
need either AlF4- or MgF3-. Preparation of these complexes is very easy. 
The great advantage of metal fluoride transition state analogue and 
ground state analogue complexes is the fact that all components are 
present in solution and readily self-assemble in the active site forming 
stable enzyme complexes that are relevant to the catalytic cycle. The 
inorganic metal fluoride salts (AlF3, and MgF2) are too insoluble to 
use; therefore, the fluoride anion and metal cation components must be 
added from separate stock solutions. Both ammonium fluoride and sodium 
fluoride are suitable as the source of fluoride and are readily soluble 
in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the 
critical aspects in preparing metal fluoride enzyme complexes is the pH 
of the resulting solution. In particular, solutions of AlCl3 and BeCl2 
are highly acidic (pH 2) samples should be prepared in 100 mM unbuffered 
Tris base. The optimized sequence of component addition is to add 
fluoride to the prepared buffer first, then the metal chloride stock.


Hope this helps, Matt






On 02/01/2024 18:53, Firdous Tarique wrote:

Hi

I would appreciate it if someone could share with me a step by step 
protocol for making a stable GDP.BeF3 solution which is often used as 
a transition state analogue for structural studies of a protein complex ?


Or a vendor from where it can be purchased directly.

Regards

Firdous



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 




--
Matthew Bowler
Project Leader MASSIF1@ESRF
European Molecular Biology Laboratory
71 avenue des Martyrs
CS 90181 F-38042 Grenoble
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.20.71.99

http://www.embl.fr/
http://www.esrf.eu/MASSIF1
https://twitter.com/id30_massif1  
https://www.embl.org/people/person/mbowler/

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[ccp4bb] How to make GDP.BeF3 solution ?

2024-01-02 Thread Firdous Tarique 
Hi

I would appreciate it if someone could share with me a step by step
protocol for making a stable GDP.BeF3 solution which is often used as a
transition state analogue for structural studies of a protein complex ?

Or a vendor from where it can be purchased directly.

Regards

Firdous



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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