EcoliWiki - User contributions [en]

File:1PFK.pdb

2009-05-20T18:56:17Z

Gdrlab: uploaded a new version of "Image:1PFK.pdb"

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Category:Reinhart Lab reading list

2009-05-19T17:13:59Z

Gdrlab:

These are papers you should read if you want to stay in the Reinhart lab.

== References ==

* PMID:1445885<ref name='PMID:1445885'/>
* PMID:15518560<ref name='PMID:15518560'/>

<references/>

Category:Reinhart Lab reading list

2009-05-19T17:13:23Z

Gdrlab:

These are papers you should read if you want to stay in the Reinhart lab.

* PMID:1445885<ref name='PMID:1445885'/>
* PMID:15518560<ref name='PMID:15518560'/>

<references/>

PMID:15518560

2009-05-19T17:11:42Z

Gdrlab: /* References */

{{RightTOC}}

<span style = 'font-size: large'> '''Fenton, AW, Paricharttanakul, NM and Reinhart, GD''' (2004) Disentangling the web of allosteric communication in a homotetramer: heterotropic activation in phosphofructokinase from Escherichia coli.''Biochemistry'' '''43''':14104-10</span>

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Phosphofructokinase from Escherichia coli (EcPFK) is a homotetramer with four active sites and four allosteric sites. Understanding the allosteric activation of EcPFK by MgADP has been complicated by the complex web of possible interactions, including active site homotropic interactions, allosteric site homotropic interactions, and heterotropic interactions between active and allosteric sites. The current work has simplified this web of possible interactions to a series of single heterotropic interactions by forming and isolating hybrid tetramers. Each of the four unique heterotropic interactions have independently been isolated and compared to a control that has all four of the unique heterotropic interactions. If the interactions are labeled with the distances between interacting ligands, the 45-A interaction contributes 20% +/- 1%, the 33-A interaction contributes 34% +/- 1%, the 30-A interaction contributes 21% +/- 1%, and the 23-A interaction contributes 25% +/- 1% with respect to the total free energy of MgADP/fructose 6-phosphate (Fru-6-P) activation in the control. The free energies of the isolated interactions sum to 100% +/- 2% of the total. Therefore, the four unique interactions are all contributors to activation, are nonequivalent, and are additive.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15518560 PubMed]
|}

==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==


{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==References==
{{RefHelp}}
<references/>
[[category:Reinhart Lab reading list]]

Category:Reinhart Lab reading list

2009-05-19T17:09:09Z

Gdrlab: New page: These are papers you should read if you want to stay in the Reinhart lab.

These are papers you should read if you want to stay in the Reinhart lab.

PMID:1445885

2009-05-19T17:08:08Z

Gdrlab: /* References */

{{RightTOC}}

<span style = 'font-size: large'> '''Johnson, JL and Reinhart, GD''' (1992) MgATP and fructose 6-phosphate interactions with phosphofructokinase from Escherichia coli.''Biochemistry'' '''31''':11510-8</span>

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>A thermodynamic linked-function analysis is presented of the interactions of MgATP and fructose 6-phosphate (Fru-6-P) with phosphofructokinase (PFK) from Escherichia coli in the absence of allosteric effectors. MgATP and Fru-6-P are shown to bind in random fashion by product inhibition of the back-reaction as well as by the kinetically competent binding of each ligand individually as monitored by the consequent changes in the intrinsic fluorescence of E. coli PFK. When Fru-6-P is saturating, the dissociation of MgATP is sufficiently slow that it cannot achieve a binding equilibrium in the steady state, causing the observed Km (49 microM) to significantly exceed the Kd (1.7 microM) deduced from a thermodynamic linkage analysis. The following features distinguish the interactions of MgATP and Fru-6-P with E. coli PFK: MgATP and Fru-6-P antagonize each other's binding to the enzyme in a saturable manner with an overall apparent coupling free energy equal to +2.5 kcal/mol at 25 degrees C; MgATP induces positive cooperativity in the Fru-6-P binding profile, with the Hill coefficient calculated from the Fru-6-P binding curves reaching a maximum of 3.6 when MgATP is saturating; and MgATP exhibits substrate inhibition at low concentrations of Fru-6-P. Simulations based upon the rate equation pertaining to a two-active-site, two-substrate dimer indicate that these features can all result from two independent couplings: an antagonistic MgATP-Fru-6-P coupling extending at least in part between active sites and a MgATP-induced Fru-6-P-Fru-6-P coupling.(ABSTRACT TRUNCATED AT 250 WORDS)</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1445885 PubMed]<br/>
|}

==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|
PfkA (Phosphofructokinase)
|

|
GO:0000287
|
magnesium ion binding
|
IDA: Inferred from Direct Assay
|

|
F
|
Purified PfkA was shown in bind MgATP, as shown by an increase in intrinsic fluorescence (monitored at 320 nm) as shown in Figure 1B.
|
complete

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</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[category:Reinhart Lab reading list]]

File:1PFK.pdb

2009-05-19T17:03:04Z

Gdrlab: uploaded a new version of "Image:1PFK.pdb"

File:1PFK.pdb

2009-05-19T17:00:25Z

Gdrlab:

File:1PFK.pdb

2009-05-19T16:59:48Z

Gdrlab:

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File:1PFK.pdb

2009-05-19T16:58:58Z

Gdrlab:

RL257

2007-09-28T22:01:26Z

Gdrlab: /* References */

==Alternate Names {{HelpIcon|Help:Strains}}==

==Sources {{HelpIcon|Help:Strains}}==
This is available from the [http://cgsc2.biology.yale.edu/Strain.php?ID=9973 E.coli Stock Center]

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==
MQ Δ''pfkB''::FRT Δ''pfkA''::FRT (MQ is a ''lac''<sup>+</sup> ''lacI''<sup>q</sup> derivative of MC4100

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]
PMID:16289704

RL257

2007-09-28T22:01:03Z

Gdrlab: /* References */

RL257

2007-09-28T21:40:28Z

Gdrlab: /* Chromosomal Genotype {{HelpIcon|Help:Strains}} */

RL257

2007-09-28T21:39:55Z

Gdrlab: /* Chromosomal Genotype {{HelpIcon|Help:Strains}} */

==Alternate Names {{HelpIcon|Help:Strains}}==

==Sources {{HelpIcon|Help:Strains}}==
This is available from the [http://cgsc2.biology.yale.edu/Strain.php?ID=9973 E.coli Stock Center]

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==
MQ Δ''pfkB''::FRT Δ''pfkA''::FRT (MQ is a lac<sup>+</sup> lacI<sup>q</sup> derivative of MC4100

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]

RL257

2007-09-28T21:39:03Z

Gdrlab: /* Chromosomal Genotype {{HelpIcon|Help:Strains}} */

==Alternate Names {{HelpIcon|Help:Strains}}==

==Sources {{HelpIcon|Help:Strains}}==
This is available from the [http://cgsc2.biology.yale.edu/Strain.php?ID=9973 E.coli Stock Center]

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==
MQ ΔpfkB::FRT ΔpfkA::FRT (MQ is a lac<sup>+</sup> lacI<sup>q</sup> derivative of MC4100

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]

RL257

2007-09-28T21:26:50Z

Gdrlab: /* Sources {{HelpIcon|Help:Strains}} */

==Alternate Names {{HelpIcon|Help:Strains}}==

==Sources {{HelpIcon|Help:Strains}}==
This is available from the [http://cgsc2.biology.yale.edu/Strain.php?ID=9973 E.coli Stock Center]

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]

RL257

2007-09-28T21:25:44Z

Gdrlab: /* Sources {{HelpIcon|Help:Strains}} */

==Alternate Names {{HelpIcon|Help:Strains}}==

==Sources {{HelpIcon|Help:Strains}}==
E. coli Genetic Stock Center

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]

RL257

2007-09-28T21:24:40Z

Gdrlab: New page: ==Alternate Names {{HelpIcon|Help:Strains}}== ==Sources {{HelpIcon|Help:Strains}}== ==Chromosomal Genotype {{HelpIcon|Help:Strains}}== ==Plasmids {{HelpIcon|Help:Strains}}== ==Phage {{...

==Alternate Names {{HelpIcon|Help:Strains}}==

==Sources {{HelpIcon|Help:Strains}}==

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]