Search found 5 matches

by CoffeeIsTheColour
Thu Nov 04, 2010 11:10 am
Forum: Cell Biology
Topic: GDP_pKa_Query
Replies: 1
Views: 2054

GDP_pKa_Query

Hi all, Generally, I was wondering what the pka of GDP is? In particular, I'm interested in the state of it in the cell, i.e pH ~7.4. I found this...pKa - <1 2.9 6.3 9.6 I would assume that these are the corresponding pKa's while progressively deprotonating the molecule, so <1 corresponds to all 3 O...
by CoffeeIsTheColour
Fri Sep 10, 2010 3:15 pm
Forum: Bioinformatics
Topic: Capping termini - protein modeling
Replies: 2
Views: 4868

Re: Capping termini - protein modeling

Thanks for the reply... I'm referring to capping protein residues with NME and ACE residues. I know they are used in when simulating short alpha helices, to introduce an level of stability and to prevent helix fraying... Perhaps a better way to phrase the question...what is the best way to treat ter...
by CoffeeIsTheColour
Wed Sep 08, 2010 11:06 pm
Forum: Bioinformatics
Topic: Capping termini - protein modeling
Replies: 2
Views: 4868

Capping termini - protein modeling

Hi,

My question regards peptide caps. I have a few proteins (~25kDa) in which the first and last few residues are truncated. In what circumstances should I cap the protein termini, and apart from stability in small alpha helices, why should we cap protein termini?

Thanx,
by CoffeeIsTheColour
Mon Jun 21, 2010 10:10 am
Forum: Molecular Biology
Topic: GDP protonation state for QM
Replies: 0
Views: 1409

GDP protonation state for QM

Hi folks, I planned to set up a QM system of GDP and Mg2+. The Mg2+ will be octahedrally coordinated with 4 H2O, the GDP BO- and a side chain OH residue. I would like some information on the best way in which to treat the GDP, in particular the protonation state of the B phosphate oxygen. Any advice...
by CoffeeIsTheColour
Fri May 14, 2010 12:06 pm
Forum: Molecular Biology
Topic: RanGDP and importin alpha
Replies: 0
Views: 970

RanGDP and importin alpha

Hi All, I have a quick question, which I hope someone can help with. Does RanGDP and Importin-alpha interact (form any contacts) in any way during the nuclear import process? I know Importin-B interacts largely with Ran GDP prior and during import and that Importin alpha is an adaptor for importin-B...