Re: [ccp4bb] Are there reliable methods for Selenomet incorporation in Pichia ?
> > hi > you can find details in this manuscript on how to label recombinant proteins > produced by P. pastoris > Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals > insights into its translocation into plant cells and recognition by > resistance proteins. <https://www.ncbi.nlm.nih.gov/pubmed/26082394> > Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, > Lazar N, Daverdin G, Balesdent MH, Choi DH, Tyler BM, Rouxel T, van Tilbeurgh > H, Fudal I. > > Plant J. 2015 Aug;83(4):610-24. doi: 10./tpj.12913. Epub 2015 Jul 14. > > it is not easy to obtain a homogenous labeled sample, but if there are enough > methionines in you protein it might work > all the best > > > Herman van Tilbeurgh > Professor structural biology > Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à > l'appliqué > > Institut de Biologie Intégrative de la Cellule - I2BC > UMR 9198 CNRS- Université Paris Sud > Team: Fonction et Architecture des Assemblages MacroMoléculaires > http://www.i2bc.paris-saclay.fr/spip.php?article256 > <http://www.i2bc.paris-saclay.fr/spip.php?article256> > > Batiment 430 > 91405 Orsay > France > > Tel: 33 1 69 82 61 16 > herman.van-tilbeu...@u-psud.fr <mailto:herman.van-tilbeu...@u-psud.fr> > > > > > >> Le 29 mars 2018 à 00:32, Anirban Banerjee <ani...@gmail.com >> <mailto:ani...@gmail.com>> a écrit : >> >> Dear all, >> >> There is not much by way of published literature on this. Are there >> unpublished methods that people have used and have found to work reliably ? >> >> Any help will be very much appreciated. >> >> Warm regards, >> >> Anirban >
Re: [ccp4bb] Van der waals force
jiri, VDW forces are always acting and between any pair of atoms the optimal distance (most favourable interaction energy) depends on the pair of atoms involved in the interaction, but is a big bitter than the sum of atomic radii all the best herman Herman van Tilbeurgh Professor structural biology Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à l'appliqué Institut de Biologie Intégrative de la Cellule - I2BC UMR 9198 CNRS- Université Paris Sud Team: Fonction et Architecture des Assemblages MacroMoléculaires http://www.i2bc.paris-saclay.fr/spip.php?article256 Batiment 430 91405 Orsay France Tel: 33 1 69 15 31 55 fax: 33 1 69 85 37 15 herman.van-tilbeu...@u-psud.fr > Le 8 déc. 2017 à 08:52, KLAHOLZ bruno <klah...@igbmc.fr> a écrit : > > > Hello, > > van der Waals interactions are very weak, this is why we usually speak about > van der Waals contacts rather than interactions. > These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate > a close contact or steric clash of an atomic model under refinement), > corresponding to the packing of the van der Waals spheres of the individual > atoms. > In hydrogen bond interactions, the term “interaction” normally implies > sharing a hydrogen atom between two polar residues, for example between the > hydroxyl group of a threonine side chain with a carbonyl group of the main > chain peptide backbone; in there one should take into account the geometry as > well (e.g. ~120°-180° is favorable, 90° is not). Note that some positions > such as Calpha-H can be slightly polarized (these contribute to bifurcated > H-bonds in beta sheets for example, see e.g. > https://www.ncbi.nlm.nih.gov/pubmed/12220491 > <https://www.ncbi.nlm.nih.gov/pubmed/12220491> ). > In the context of series of van der Waals contacts between hydrophobic > residues there can be additive effects of the weak interactions with then sum > up, but in this context one should also consider entropic effects such as > de-solvatation which becomes favorable energetically. > > Hope this helps. > > Best regards, > > Bruno > > > ### > Bruno P. Klaholz > Centre for Integrative Biology > Institute of Genetics and of Molecular and Cellular Biology > 67404 ILLKIRCH > FRANCE > http://igbmc.fr/Klaholz <http://igbmc.fr/Klaholz> > > > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of chemocev marker > Sent: 08 December 2017 07:55 > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Van der waals force > > Hi > I just have a basic question if the Van der waals interaction will exist > between the hydrophobic residues or it can also be contributed by the polar > residues as well. What distance is required for the Van der waals > interaction. > > best > > Jiri
Re: [ccp4bb] ITC data clarification.
hi dharma your ITC data suggest at least that your complex also exists in solution ITC never will answer to the question whether this is a “biological” interface one way getting around this, would be to check the response of your mutant versus WT in biological assay ALA substitutions soemtimes are not drastic enough to interrupt protein protein interactions introduction of a charged residue facing a hydrophobic pocket often is more efficient good luck Herman van Tilbeurgh Professor structural biology Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à l'appliqué Institut de Biologie Intégrative de la Cellule - I2BC UMR 9198 CNRS- Université Paris Sud Team: Fonction et Architecture des Assemblages MacroMoléculaires http://www.i2bc.paris-saclay.fr/spip.php?article256 Batiment 430 91405 Orsay France Tel: 33 1 69 15 31 55 fax: 33 1 69 85 37 15 herman.van-tilbeu...@u-psud.fr > Le 8 déc. 2017 à 02:15, Dharma <genedha...@gmail.com> a écrit : > > Hello CCP4 users, > Based on the crystal structure of a two molecule protein complex, I have > mutated (alanine substitutions) one of the putative binding interface. The > mutant binds with much higher affinity than the wild type. > However, the signature plot of ITC data reveals a decrease in the enthalpy > but increase on the entropy (deltaS). Thus overall increase in deltaG. > I want to know if it’s relevant biological interface or a crystal artifact. > Suggestions please. > > Thanks > Regards > Dharma > Sent from my iPhone
