Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Srivastava, Dhiraj 
Pyruvate kinase specially M2 isoform is one example which exists in tetramer 
and dimer/monomer state. Several ligands affect its shape and oligomeric state, 
thus affecting its activity.

Dhiraj

From: CCP4 bulletin board  on behalf of Gabriela GARCIA 
RODRIGUEZ 
Sent: Wednesday, October 9, 2019 6:14 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Changes in quaternary structure

Dear CCP4BB subscribers,

I am writing a discussion on extensive quaternary changes between two different 
homodimers of the same protein and I would like to ask you for any examples of 
your own work/that you know of to include in my analysis. Basically, any 
proteins known to exist in two different (or more) homodimerised states 
(suffering changes in domain organisation between states would be even more 
interesting).
I would greatly appreciate any examples! Thank you for your time and attention.

Warm regards,

Gabriela


Gabriela Garcia Rodriguez

gabriela.garcia.rodrig...@vub.be<mailto:gabriela.garcia.rodrig...@vub.be>

PhD candidate

Structural Biology Research Centre (SBRC)

Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel (VUB)

Pleinlaan 2- 1050 Brussels, Belgium








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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Eleanor Dodson 
Indeed!
Eleanor

On Wed, 9 Oct 2019 at 15:48, Tristan Croll  wrote:

> For that matter, the insulin *receptor* is a spectacular example of very
> large conformational changes in a homodimer.
>
> On 2019-10-09 15:27, Eleanor Dodson wrote:
> > There are many insulin structures with domain shifts.
> > 4ins and 1trz share sequence but have different conformations for one
> > of the molecules..
> > Eleanor Dodson
> >
> > On Wed, 9 Oct 2019 at 14:32, Tanner, John J. 
> > wrote:
> >
> >> The same enzyme adopting different quaternary structures is a form
> >> of allosteric regulation. Jaffe's group has described this
> >> phenomenon - the “morpheein" model of allosteric regulation.
> >>
> >> Reviews:
> >> https://www.ncbi.nlm.nih.gov/pubmed/22182754 [2]
> >> https://www.ncbi.nlm.nih.gov/pubmed/16023348 [3]
> >>
> >> John J. Tanner, PhD
> >> Professor of Biochemistry and Chemistry
> >> Associate Chair of Biochemistry
> >> University of Missouri
> >> 117 Schweitzer Hall
> >> 503 S. College Avenue
> >> Columbia, MO 65211
> >> Phone: 573-884-1280
> >> Email: tanne...@missouri.edu
> >> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html [4]
> >>
> >>> On Oct 9, 2019, at 6:14 AM, Gabriela GARCIA RODRIGUEZ
> >>>  wrote:
> >>>
> >>> Dear CCP4BB subscribers,
> >>>
> >>> I am writing a discussion on extensive quaternary changes between
> >>> two different homodimers of the same protein and I would like to
> >>> ask you for any examples of your own work/that you know of to
> >>> include in my analysis. Basically, any proteins known to exist in
> >>> two different (or more) homodimerised states (suffering changes in
> >>> domain organisation between states would be even more
> >>> interesting).
> >>> I would greatly appreciate any examples! Thank you for your time
> >>> and attention.
> >>>
> >>> Warm regards,
> >>>
> >>> Gabriela
> >>>
> >>> 
> >>>
> >>> GABRIELA GARCIA RODRIGUEZ
> >>>
> >>> _gabriela.garcia.rodriguez@vub.be_
> >>>
> >>> PhD candidate
> >>>
> >>> Structural Biology Research Centre (SBRC)
> >>>
> >>> Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit
> >>> Brussel (VUB)
> >>>
> >>> Pleinlaan 2- 1050 Brussels, Belgium
> >>>
> >>> -
> >>>
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 [1]
> >>
> >> -
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
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> >
> > -
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> >
> > Links:
> > --
> > [1] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BBA=1
> > [2] https://www.ncbi.nlm.nih.gov/pubmed/22182754
> > [3] https://www.ncbi.nlm.nih.gov/pubmed/16023348
> > [4] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> > [5] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Tristan Croll 
For that matter, the insulin *receptor* is a spectacular example of very 
large conformational changes in a homodimer.


On 2019-10-09 15:27, Eleanor Dodson wrote:

There are many insulin structures with domain shifts.
4ins and 1trz share sequence but have different conformations for one
of the molecules..
Eleanor Dodson

On Wed, 9 Oct 2019 at 14:32, Tanner, John J. 
wrote:


The same enzyme adopting different quaternary structures is a form
of allosteric regulation. Jaffe's group has described this
phenomenon - the “morpheein" model of allosteric regulation.

Reviews:
https://www.ncbi.nlm.nih.gov/pubmed/22182754 [2]
https://www.ncbi.nlm.nih.gov/pubmed/16023348 [3]

John J. Tanner, PhD
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html [4]


On Oct 9, 2019, at 6:14 AM, Gabriela GARCIA RODRIGUEZ
 wrote:

Dear CCP4BB subscribers,

I am writing a discussion on extensive quaternary changes between
two different homodimers of the same protein and I would like to
ask you for any examples of your own work/that you know of to
include in my analysis. Basically, any proteins known to exist in
two different (or more) homodimerised states (suffering changes in
domain organisation between states would be even more
interesting).
I would greatly appreciate any examples! Thank you for your time
and attention.

Warm regards,

Gabriela



GABRIELA GARCIA RODRIGUEZ

_gabriela.garcia.rodriguez@vub.be_

PhD candidate

Structural Biology Research Centre (SBRC)

Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit
Brussel (VUB)

Pleinlaan 2- 1050 Brussels, Belgium

-

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Links:
--
[1] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BBA=1
[2] https://www.ncbi.nlm.nih.gov/pubmed/22182754
[3] https://www.ncbi.nlm.nih.gov/pubmed/16023348
[4] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
[5] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Eleanor Dodson 
There are many insulin structures with domain shifts.
4ins and 1trz share sequence but have different conformations for one of
the molecules..
Eleanor Dodson


On Wed, 9 Oct 2019 at 14:32, Tanner, John J.  wrote:

> The same enzyme adopting different quaternary structures is a form of
> allosteric regulation. Jaffe's group has described this phenomenon - the
> “morpheein" model of allosteric regulation.
>
> Reviews:
> https://www.ncbi.nlm.nih.gov/pubmed/22182754
> https://www.ncbi.nlm.nih.gov/pubmed/16023348
>
>
>
> John J. Tanner, PhD
> Professor of Biochemistry and Chemistry
> Associate Chair of Biochemistry
> University of Missouri
> 117 Schweitzer Hall
> 503 S. College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Email: tanne...@missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
>
>
>
>
>
> On Oct 9, 2019, at 6:14 AM, Gabriela GARCIA RODRIGUEZ <
> gabriela.garcia.rodrig...@vub.be >
> wrote:
>
> Dear CCP4BB subscribers,
>
> I am writing a discussion on extensive quaternary changes between two
> different homodimers of the same protein and I would like to ask you for
> any examples of your own work/that you know of to include in my analysis.
> Basically, any proteins known to exist in two different (or more)
> homodimerised states (suffering changes in domain organisation between
> states would be even more interesting).
> I would greatly appreciate any examples! Thank you for your time and
> attention.
>
> Warm regards,
>
> Gabriela
> 
>
> *Gabriela Garcia Rodriguez*
>
> *gabriela.garcia.rodrig...@vub.be *
>
> PhD candidate
>
> Structural Biology Research Centre (SBRC)
>
> Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel
> (VUB)
>
> Pleinlaan 2- 1050 Brussels, Belgium
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Tanner, John J. 
The same enzyme adopting different quaternary structures is a form of 
allosteric regulation. Jaffe's group has described this phenomenon - the 
“morpheein" model of allosteric regulation.

Reviews:
https://www.ncbi.nlm.nih.gov/pubmed/22182754
https://www.ncbi.nlm.nih.gov/pubmed/16023348



John J. Tanner, PhD
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html





On Oct 9, 2019, at 6:14 AM, Gabriela GARCIA RODRIGUEZ 
mailto:gabriela.garcia.rodrig...@vub.be>> 
wrote:

Dear CCP4BB subscribers,

I am writing a discussion on extensive quaternary changes between two different 
homodimers of the same protein and I would like to ask you for any examples of 
your own work/that you know of to include in my analysis. Basically, any 
proteins known to exist in two different (or more) homodimerised states 
(suffering changes in domain organisation between states would be even more 
interesting).
I would greatly appreciate any examples! Thank you for your time and attention.

Warm regards,

Gabriela


Gabriela Garcia Rodriguez

gabriela.garcia.rodrig...@vub.be

PhD candidate

Structural Biology Research Centre (SBRC)

Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel (VUB)

Pleinlaan 2- 1050 Brussels, Belgium








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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Laure Yatime 
Dear Gabriela, 

We have encountered the example of the calcium-binding protein S100A6, which is 
known to form a canonical S100 homodimer whose quaternary structure is shared 
by all other members of the S100 protein family ( [ 
https://www.ncbi.nlm.nih.gov/pubmed/11937060 | 
https://www.ncbi.nlm.nih.gov/pubmed/11937060 ] ) but which displayed a distinct 
homodimerization mode when we crystallized it in complex with its cognate RAGE 
receptor ( [ https://www.ncbi.nlm.nih.gov/pubmed/27818100 | 
https://www.ncbi.nlm.nih.gov/pubmed/27818100 ] ). In this particular case, 
there was no domain reorganization within the monomers in between the 2 
homodimeric states. 

I don't know if this is what you're exactly looking for but I hope this helps. 

Laure 
 
Laure YATIME, PhD, HDR 
Inserm CRCN Researcher 

Laboratory of Pathogen-Host Interactions (LPHI) 
UMR 5235 - University of Montpellier 
Place E. Bataillon - Bât. 24 cc 107 
34095 - MONTPELLIER cedex 5 
FRANCE 

Tel: +33 (0)4 67 14 92 04 

E-mail: laure.yat...@umontpellier.fr 
laure.yat...@inserm.fr 

ORCID ID: [ http://orcid.org/-0002-3650-8012 | 
http://orcid.org/-0002-3650-8012 ] 
Web page: [ 
https://lphi.umontpellier.fr/en/le-laboratoire/trombinoscope/26-equipe-5/105-theme-2-danger-signals-and-chronic-inflammation
 | 
https://lphi.umontpellier.fr/en/le-laboratoire/trombinoscope/26-equipe-5/105-theme-2-danger-signals-and-chronic-inflammation
 ] 

> De: "EchelonIV ." 
> À: CCP4BB@JISCMAIL.AC.UK
> Envoyé: Mercredi 9 Octobre 2019 14:00:45
> Objet: Re: [ccp4bb] Changes in quaternary structure

> Dear Gabriela,
> while I don't have experience strictly on the same protein presenting multiple
> homodimerization modes, it might be useful to look into some conserved
> structure families (STAR domains, PDZ domains) which are known to form various
> different homodimerization modes. Perhaps some of the references below might 
> be
> useful:

> PDZ:
> [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022880/ |
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022880/ ]
> [ https://www.ncbi.nlm.nih.gov/pubmed/12954649/ |
> https://www.ncbi.nlm.nih.gov/pubmed/12954649/ ]
> [ https://www.ncbi.nlm.nih.gov/pubmed/12493751/ |
> https://www.ncbi.nlm.nih.gov/pubmed/12493751/ ]
> [ https://www.ncbi.nlm.nih.gov/pubmed/17928286/ |
> https://www.ncbi.nlm.nih.gov/pubmed/17928286/ ]

> STAR:
> [ https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26758068/ |
> https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26758068/ ]
> [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650229/ |
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650229/ ]
> [ https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4629-x |
> https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4629-x ]

> Hope this helps,
> Arne

> --
> Arne Raasakka
> PhD Biochemistry
> Department of Biomedicine, University of Bergen

> On Wed, Oct 9, 2019 at 1:25 PM Gabriela GARCIA RODRIGUEZ < [
> mailto:gabriela.garcia.rodrig...@vub.be | gabriela.garcia.rodrig...@vub.be ] >
> wrote:

>> Dear CCP4BB subscribers,

>> I am writing a discussion on extensive quaternary changes between two 
>> different
>> homodimers of the same protein and I would like to ask you for any examples 
>> of
>> your own work/that you know of to include in my analysis. Basically, any
>> proteins known to exist in two different (or more) homodimerised states
>> (suffering changes in domain organisation between states would be even more
>> interesting).
>> I would greatly appreciate any examples! Thank you for your time and 
>> attention.

>> Warm regards,

>> Gabriela
>> 

>> Gabriela Garcia Rodriguez

>> [ mailto:gabriela.garcia.rodrig...@vub.be | gabriela.garcia.rodrig...@vub.be 
>> ]

>> PhD candidate

>> Structural Biology Research Centre (SBRC)

>> Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel (VUB)

>> Pleinlaan 2- 1050 Brussels, Belgium

>> To unsubscribe from the CCP4BB list, click the following link:
>> [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 |
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ]
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread EchelonIV . 
Dear Gabriela,

while I don't have experience strictly on the *same protein* presenting
multiple homodimerization modes, it might be useful to look into some
conserved structure families (STAR domains, PDZ domains) which are known to
form various different homodimerization modes. Perhaps some of the
references below might be useful:

PDZ:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022880/
https://www.ncbi.nlm.nih.gov/pubmed/12954649/
https://www.ncbi.nlm.nih.gov/pubmed/12493751/
https://www.ncbi.nlm.nih.gov/pubmed/17928286/

STAR:
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26758068/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650229/
https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4629-x

Hope this helps,
Arne

--
Arne Raasakka
PhD Biochemistry
Department of Biomedicine, University of Bergen


On Wed, Oct 9, 2019 at 1:25 PM Gabriela GARCIA RODRIGUEZ <
gabriela.garcia.rodrig...@vub.be> wrote:

> Dear CCP4BB subscribers,
>
> I am writing a discussion on extensive quaternary changes between two
> different homodimers of the same protein and I would like to ask you for
> any examples of your own work/that you know of to include in my analysis.
> Basically, any proteins known to exist in two different (or more)
> homodimerised states (suffering changes in domain organisation between
> states would be even more interesting).
> I would greatly appreciate any examples! Thank you for your time and
> attention.
>
> Warm regards,
>
> Gabriela
> 
>
> *Gabriela Garcia Rodriguez*
>
> *gabriela.garcia.rodrig...@vub.be *
>
> PhD candidate
>
> Structural Biology Research Centre (SBRC)
>
> Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel
> (VUB)
>
> Pleinlaan 2- 1050 Brussels, Belgium
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Changes in quaternary structure

2019-10-09 Thread Gabriela GARCIA RODRIGUEZ 
Dear CCP4BB subscribers,

I am writing a discussion on extensive quaternary changes between two different 
homodimers of the same protein and I would like to ask you for any examples of 
your own work/that you know of to include in my analysis. Basically, any 
proteins known to exist in two different (or more) homodimerised states 
(suffering changes in domain organisation between states would be even more 
interesting).
I would greatly appreciate any examples! Thank you for your time and attention.

Warm regards,

Gabriela


Gabriela Garcia Rodriguez

gabriela.garcia.rodrig...@vub.be

PhD candidate

Structural Biology Research Centre (SBRC)

Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel (VUB)

Pleinlaan 2- 1050 Brussels, Belgium








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