Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0

Re: [ccp4bb] [Proteopedia] announcement: course on Proteopedia with JSmol

Dear Angel, Jaime and Joel, Proteopedia is great work, but I am unlucky as I won't be able to visit you at Alcalà. This makes me think it would be great to have a web seminar on the topic. Thanks, Jaime! Enjoy your meeting in Madrid and around. Best regards, Nadir Pr. Nadir T. Mrabet

Re: [ccp4bb] Guard columns from FPLC

most aggregates if not all. HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33

Re: [ccp4bb] areaimol and hydrogens

Jose, Your are most probably right. Atoms used for ASA calculations are unified atoms as their vdW radii incorporate light atoms (hydrogens) which, by and large, crystallographers don't see. Adding extra H atoms is likely to end up in miscalculations. Nadir Mrabet Pr. Nadir T. Mrabet

Re: [ccp4bb] metal chelation

will probably need several washes but it works! Also be aware that EDTA binds well to several proteins. HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de la

Re: [ccp4bb] repulsive effects of arginine

Resonance was to be understood exactly as meaning all the bonds are averaged between both types (single and double bonds). Furthermore, fluctuations in the immediate environment will affect electron distribution with time, as proteins exist in a dynamic state. Nadir Mrabet Pr. Nadir T. Mrabet

Re: [ccp4bb] AW: [ccp4bb] repulsive effects of arginine

Dear Jan, Is there a possibility for bifurcated salt bridges/H-bonds where the Asp would be entrapped between the two arginines, in which case, repulsive effects would not take place ? Cheers, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954

Re: [ccp4bb] repulsive effects of arginine

Yes, indeed Andrey. And this results from resonance (tautomerization) of the guanidinium group. Regards, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de

Re: [ccp4bb] repulsive effects of arginine

all the guanidinium group so that it is not punctual as is the case for lys NZ. H-bonds also solvate charges. Are you stating that asp can in no way be entrapped between the arginines? Recall arg-asp interactions in proteins are hot spots. Cheers, Nadir Pr. Nadir T. Mrabet Structural

Re: [ccp4bb] Modelling Software for beta turn design

://dunbrack.fccc.edu/molide/) and do the exercise in local mode. Best of luck, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505

[ccp4bb] Recent IUPAC definition of the hydrogen bond

, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)* Thanks for your input and interest. Greetings, Nadir Mrabet -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences

Re: [ccp4bb] Off Topic- Cystine Detection

(2009) 147–158. HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0

Re: [ccp4bb] X-PLOR

Thanks Francisco. Nicolas, thanks also for your feedback. In fact, I had already downloaded the X-PLOR manual, but I needed some more details on the H-atoms optimization procedure. That was for the purpose of a teaching work on a 1995 paper. Best regards, Nadir Pr. Nadir T. Mrabet

[ccp4bb] X-PLOR

Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry

Re: [ccp4bb] protein structure for high schoolers

I would suggest MolProbity along with KiNG (on Firefox!) would be most appropriate (http://kinemage.biochem.duke.edu/). HTH, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505

Re: [ccp4bb] Metal won't strip from IMAC

. If you reduce the pH, say to 5.2-5.5, not only you make adsorption less stronger (hence, column capacity may drop down), but you will at the same time prevent cysteine oxidation. You can also increase [imidazole] in the equilibration buffer to reduce adsorption. HTH, Nadir Pr. Nadir T. Mrabet

Re: [ccp4bb] How to assess geometry in a model?

Along you can consider also using MolProbity online. Best, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax

Re: [ccp4bb] Description of a newly solved structure

I would also suggest using MolProbity to assess structure quality. Best, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0

[ccp4bb]

Hi, We have been receiving several spam mail from this person. Any way to stop that quickly? Thanks, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy

Re: [ccp4bb] projecting SC value on protein surface

Hi Pavlina, I suggest you have a look at http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP2. Runs on Windows. HTH Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye

Re: [ccp4bb] off-topic: 2 peaks on Cation

In your original mail (2011-02-18; 18:45 GMT), you wrote: Possibly deamidation of the protein, in particluar one or more lysines Hence, my comment was based on your own writing, that is deamiDation. Wishing you a better week. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry

Re: [ccp4bb] off-topic: 2 peaks on Cation

Given no info on the protein, it can be anything. Is it recombinant? Which host? etc. Oxydation (cys, met) is also a possibility By the way, deamination concerns asn and gln, not lys. Best, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University

Re: [ccp4bb] off-topic: 2 peaks on Cation

Typo! I actually meant deamidation. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E

Re: [ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?

It can go both ways: If you increase atom radii by adding that of the probe (e.g. 1.4 A° for a water probe) and calculate the molecular surface using a zero probe with atom radii as previously defined (Ri +1.4 A°), the area you get is that of the accessible surface. Pr. Nadir T. Mrabet

Re: [ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?

first. How could I get the Varshney code? Best regards, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33

Re: [ccp4bb] Removing a tight binding ligand

Hi, It could help if you said what your ligand is. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0

Re: [ccp4bb] Query - inhibitor screening by fluorescence based assay.

system. Note however that binding (1) might be non specific and (2) need not correlate with enzyme inhibition. Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex

Re: [ccp4bb] Native Gel Theory and Practice

actually need both data to infer stoechiometry and subunit composition. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax

Re: [ccp4bb] Native Gel Theory and Practice

, ABB, AAB). Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat

Re: [ccp4bb] Ion exchange protein lost

Human gcsf has a pI ~ 6. As Ursula suggests you might be better off with anion exchange. There are protocols that show you can both refold and purify onto such column type. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School

Re: [ccp4bb] How could I Extract Iron from Protein?

I would go for DTPA and acid pH. Better than dialysis, I would use IEX and flush le bound protein with a buffer with as low a pH as possible with 10-100 mM DTPA, then wash with no DTPA, and elute le protein with clean (e.g. treated with Chelex) salt. HTH, Pr. Nadir T. Mrabet Structural

Re: [ccp4bb] pdb-l: [mockeldri...@yahoo.com: Retraction of 12 Structures]

) by both crystallographers and modelers, but also by curators at the rcsb.. Regards, Nadir Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France

Re: [ccp4bb] structure - function

Ok, now we can perhaps debate of another problem. With a multiple choice question that has more than one acceptably good answer, is it convergent, or rather independent, evolution? This multiple choice question is open for discussion. Greetings, Nadir Pr. Nadir T. Mrabet Cellular

Re: [ccp4bb] Glycerol as metal chelator?

I wouldn't use a pH of 9 when dealing with metal cations in solution. By and large, metal hydroxides precipitate at alkaline pH. HTH Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505

Re: [ccp4bb] Van der Waals Interaction Distances

* *20.298* *-0.006* *1.90* *0.042* *23.776* *-0.005* *1.95* *0.036* *27.742* *-0.005* *2.00* *0.031* *32.252* *-0.004* -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry

Re: [ccp4bb] PDB protein strucutrues as screen saver

Hi, You may want to have a look at http://www.luminorum.com/html/luminorum_ltd___extras.html. hth Nadir -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy

Re: [ccp4bb] protocol for harvesting proteins from bacterial periplasmic space

will be depleted of Me2+ (easily seen with Cu2+). Moreover, it is always possible to add some Me2+ to your extract prior to IMAC. All this was published long ago (Biochemistry. 31: 2690-2702, 1992). Nadir -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

by coordination bond formation to a metal-chelate. Coordination bond lentghs decrease (and binding improves) as ionic strength increases, so a 1-2 M salt concentration in you buffer may turn out to be appropriate. HTH, Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry

Re: [ccp4bb] Definition of salt bridge

-- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: [EMAIL PROTECTED

Re: [ccp4bb] Definition of salt bridge

Mrabet Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: [EMAIL PROTECTED

Re: [ccp4bb] off-topic: Enzymology textbook recommendations?

Alan Fersht: Enzyme structure and mechanism. Definitely! Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0

Re: [ccp4bb] Na Acetate Buffer

-- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: [EMAIL PROTECTED

Re: [ccp4bb] Na Acetate Buffer

such a repeatability using a pH-meter. HTH, Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax

Re: [ccp4bb] Imidazole's ability to chelate metal ions

(pKa 7.0) or else results from competitive elution from an IMAC column. What should be done depends on your exact conditions. hth, Nadir -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184

Re: [ccp4bb] Imidazole's ability to chelate metal ions

Well, I happen to lecture on this... The bible is Data for biochemical research, Dawson et al., Oxford University Press. Should be available in most biochemistry labs, if not in the library. Cheers, Nadir -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy

Re: [ccp4bb] pH gradient in Mono Q

is required and sufficient volumes of buffer A. Again, I ask the question: Did Matthew ever mentioned before he intended to perform a CHROMATOFOCUSING experiment? Nadir -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de

Re: [ccp4bb] pH gradient in Mono Q

). An equimolar (50mM) mixture of these with Buffer A titrated to 8.0 and Buffer titrated to 4.0 has been shown (in my hands) to yield a very linear gradient (must not be too steep, though). Matthew's question does not seem to concern chromatofocusing. Hth, Nadir -- Pr. Nadir T. Mrabet

Re: [ccp4bb] 3D model building without CRT monitor

to be the one and only crt from Viewsonic (but only 19). Cheers, Nadir -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0

Re: [ccp4bb] crashing-out protein eluted from Nickel column

. 6.5 or even 6.0 (try and see) so that you dont need to go beyond 100 mM imidazole in your elution buffer (as mentioned earlier, you must ajust the pH of the latter as required with extra HCl). Best, Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724

Re: [ccp4bb] questions about hydrophobic core

hand, taking away even residues that display very little ASA ( 5%) would certainly leave you with genuine core residues. Hope this helps. Greetings, Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine Avenue de la Foret de Haye, BP 184

Re: [ccp4bb] Nature policy update regarding source code

Hi, I believe such requirements concern only Nature Methods rather than Nature by and large. Regards, Nadir Mrabet Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy