Re: [ccp4bb] Na-Binding Protein?

[Diana Tomchick]

The human branched-chain alpha-ketoacid dehydrogenase requires a K+ ion to 
stabilize the binding of the cofactor thiamine diphosphate and to achieve 
maximum catalytic efficiency. See

https://www.ncbi.nlm.nih.gov/pubmed/10745006

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas 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)

On Jan 9, 2018, at 8:42 AM, Keller, Jacob 
> wrote:

Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale conformation +/- 
Na+, and is specific for Na+ per se, or at least ignores K+ and Ca++? E.g., Rb+ 
or Li+ might be okay. Structural info would be a plus, but not a sine qua non.

Similarly, what about with K+ or Cl- specificities, but oblivious to similar 
common ions?

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

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Re: [ccp4bb] Na-Binding Protein?

[Patrick Shaw Stewart]

That's very interesting.  I guess it's an unusual manifestation of the
Hofmeister series.

It might give guidance to developers of screens for both crystallization
and cryoEM.

Thx, Patrick


On 9 January 2018 at 15:44, Andrew Mesecar  wrote:

> Dear Jacob,
>
>
>
> One of my favorite examples of monovalent cation discrimination is by the
> enzyme Pyruvate Kinase.  It prefers K(+), NH4(+), Rb(+) and Tl+ for maximum
> catalysis and then activity falls off as the monovalent cation sizes get
> larger, Cs(+) or smaller Na(+) >> Li (+).  The conformations of pyruvate
> kinase are known to be altered by binding of monovalent cations and it has
> been studied for over 50 years by a variety of approaches.  A number of the
> X-ray structures are with K(+).  I spent a few years of my life studying
> this enzyme a couple of decades ago.  It will hopefully provide some
> information for your project.
>
>
>
> Best of luck,
>
>
>
> Andy Mesecar
>
> On Tue, Jan 9, 2018 at 9:42 AM, Keller, Jacob 
> wrote:
>
>> Dear Crystallographers,
>>
>>
>>
>> Is anyone aware of a soluble protein which changes large-scale
>> conformation +/- Na+, and is specific for Na+ per se, or at least ignores
>> K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info would be a
>> plus, but not a sine qua non.
>>
>>
>>
>> Similarly, what about with K+ or Cl- specificities, but oblivious to
>> similar common ions?
>>
>>
>>
>> All the best,
>>
>>
>>
>> Jacob Keller
>>
>>
>>
>> +
>>
>> Jacob Pearson Keller
>>
>> Research Scientist / Looger Lab
>>
>> HHMI Janelia Research Campus
>>
>> 19700 Helix Dr, Ashburn, VA 20147
>> 
>>
>> (571)209-4000 x3159 <(571)%20209-4000>
>>
>> +
>>
>>
>>
>> The content of this email is confidential and intended for the recipient
>> specified in message only. It is strictly forbidden to share any part of
>> this message with any third party, without a written consent of the sender.
>> If you received this message by mistake, please reply to this message and
>> follow with its deletion, so that we can ensure such a mistake does not
>> occur in the future.
>>
>>
>>
>
>
>
> --
> *Andrew D. Mesecar*
> Head, Department of Biochemistry
> Walther Professor of Cancer Structural Biology
> Deputy Director, Purdue Center for Cancer Research
> E-Mail: amese...@purdue.edu
> _
> *Department of Biochemistry Contact Information:*
> 175 S. University Street
> 
> W. Lafayette, IN 47907
> 
> -2063
> 765-494-1607
> --
> *Research Lab Contact Information:*
> Hockmeyer Hall of Structural Biology
> Room 311
> 
> 240 S. Martin Jischke Drive
> 
> West Lafayette, IN 47907
> 
> -1971
> 765-494-1924
> _
>
>



-- 
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 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

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Re: [ccp4bb] Na-Binding Protein?

[Bernhard Lechtenberg]

Dear Jacob,

The protease thrombin is another example. Thrombin is activated by Na+ (but not 
Li+ or K+). We have shown using NMR that Na+ binding allosterically stabilizes 
active conformations of thrombin. Additionally, numerous crystal structures of 
Na+-free (“slow” thrombin) and Na+-bound (“fast” thrombin) have been published.

These publications should give you a good overview:
https://www.ncbi.nlm.nih.gov/pubmed/20660315
https://www.ncbi.nlm.nih.gov/pubmed/22944689
http://www.pnas.org/content/100/24/13785/T1.expansion.html

Best,
Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Associate
Riedl Lab
Cancer Metabolism and Signaling Networks Program
NCI-Designated Cancer Center

[cid:24A04CE0-5418-4257-A8D1-8084CA766BC9@burnham.org]

10901 N. Torrey Pines Road, La Jolla, CA 92037
T  858.646.3100 ext. 4216  E 
blechtenb...@sbpdiscovery.org
Science Benefiting Patients®

On Jan 9, 2018, at 6:42 AM, Keller, Jacob 
> wrote:

Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale conformation +/- 
Na+, and is specific for Na+ per se, or at least ignores K+ and Ca++? E.g., Rb+ 
or Li+ might be okay. Structural info would be a plus, but not a sine qua non.

Similarly, what about with K+ or Cl- specificities, but oblivious to similar 
common ions?

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

Re: [ccp4bb] Na-Binding Protein?

[Andrew Mesecar]

Dear Jacob,



One of my favorite examples of monovalent cation discrimination is by the
enzyme Pyruvate Kinase.  It prefers K(+), NH4(+), Rb(+) and Tl+ for maximum
catalysis and then activity falls off as the monovalent cation sizes get
larger, Cs(+) or smaller Na(+) >> Li (+).  The conformations of pyruvate
kinase are known to be altered by binding of monovalent cations and it has
been studied for over 50 years by a variety of approaches.  A number of the
X-ray structures are with K(+).  I spent a few years of my life studying
this enzyme a couple of decades ago.  It will hopefully provide some
information for your project.



Best of luck,



Andy Mesecar

On Tue, Jan 9, 2018 at 9:42 AM, Keller, Jacob 
wrote:

> Dear Crystallographers,
>
>
>
> Is anyone aware of a soluble protein which changes large-scale
> conformation +/- Na+, and is specific for Na+ per se, or at least ignores
> K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info would be a
> plus, but not a sine qua non.
>
>
>
> Similarly, what about with K+ or Cl- specificities, but oblivious to
> similar common ions?
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
> 
>
> (571)209-4000 x3159 <(571)%20209-4000>
>
> +
>
>
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.
>
>
>



-- 
*Andrew D. Mesecar*
Head, Department of Biochemistry
Walther Professor of Cancer Structural Biology
Deputy Director, Purdue Center for Cancer Research
E-Mail: amese...@purdue.edu
_
*Department of Biochemistry Contact Information:*
175 S. University Street
W. Lafayette, IN 47907-2063
765-494-1607
--
*Research Lab Contact Information:*
Hockmeyer Hall of Structural Biology
Room 311
240 S. Martin Jischke Drive
West Lafayette, IN 47907-1971
765-494-1924
_

Re: [ccp4bb] Na-Binding Protein?

[Conn Mallett]

Hi Jacob,

Ion-channel and receptor folks have been working on these types of 
questions... see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629458/


if you are looking for a model system, perhaps engineer a version of 
calmodulin that is specific for Na+ rather than Ca++?  Perhaps someone 
has already done that.


-Conn

Conn Mallett, PhD
Carlsbad, CA
conn.mallettgmail.com
skype: conn.mallett

On 9Jan2018 06:42, Keller, Jacob wrote:


Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale 
conformation +/- Na+, and is specific for Na+ per se, or at least 
ignores K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info 
would be a plus, but not a sine qua non.


Similarly, what about with K+ or Cl- specificities, but oblivious to 
similar common ions?


All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the 
recipient specified in message only. It is strictly forbidden to share 
any part of this message with any third party, without a written 
consent of the sender. If you received this message by mistake, please 
reply to this message and follow with its deletion, so that we can 
ensure such a mistake does not occur in the future.

[ccp4bb] Na-Binding Protein?

[Keller, Jacob]

Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale conformation +/- 
Na+, and is specific for Na+ per se, or at least ignores K+ and Ca++? E.g., Rb+ 
or Li+ might be okay. Structural info would be a plus, but not a sine qua non.

Similarly, what about with K+ or Cl- specificities, but oblivious to similar 
common ions?

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.