Re: [ccp4bb] Off-topic question related to ITC binding studies

Hi Gergő, Thank you for discussing it in detail. It is a great help. Based on the curve fit, we also believe that the two proteins bind independently to the DNA duplex with the same affinity. The DNA indeed contains 2 sites for protein binding. As far as the dimerization of protein is concerned,

[ccp4bb] RES: [ccp4bb] Off-topic question related to ITC binding studies

16 de agosto de 2022 14:41 Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Assunto: [ccp4bb] Off-topic question related to ITC binding studies Hello everyone! Hope this email finds you well. I have an off-topic question regarding ITC binding studies, which was asked by a reviewer

[ccp4bb] Off-topic question related to ITC binding studies

Hello everyone! Hope this email finds you well. I have an off-topic question regarding ITC binding studies, which was asked by a reviewer. We performed an ITC binding study (using Affinity ITC, TA Instruments) to evaluate protein-DNA interaction which resulted in a perfect sigmoidal curve.

Re: [ccp4bb] OFF TOPIC question

nt: Thursday, November 26, 2020 8:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] OFF TOPIC question Hi all, I have two constructs having different ori, p15ori and M13 ori, different promoters araC and LacI, and different antibiotic resistance chloramphenicol and Ampicillin respectively. I would

Re: [ccp4bb] OFF TOPIC question

, November 26, 2020 2:48:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: [ccp4bb] OFF TOPIC question Bl21Pro j Von: CCP4 bulletin board Im Auftrag von Anamika Singh Gesendet: Donnerstag, 26. November 2020 11:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] OFF TOPIC question One

[ccp4bb] AW: [ccp4bb] OFF TOPIC question

Bl21Pro j Von: CCP4 bulletin board Im Auftrag von Anamika Singh Gesendet: Donnerstag, 26. November 2020 11:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] OFF TOPIC question One correction to the previous question: I have two constructs having different ori, p15ori and M13 ori, different

Re: [ccp4bb] OFF TOPIC question

*One correction to the previous question:* I have two constructs having different ori, p15ori and M13 ori, different promoters *araBAD promoter* and LacI, and different antibiotic resistance chloramphenicol and Ampicillin respectively. I would like to know which E. coli host cells will be good for

[ccp4bb] OFF TOPIC question

Hi all, I have two constructs having different ori, p15ori and M13 ori, different promoters araC and LacI, and different antibiotic resistance chloramphenicol and Ampicillin respectively. I would like to know which *expressing E. coli host cells* will be good for the co-transformation of these

Re: [ccp4bb] Off-topic question

Hi, there is a guide here, but you should get the proper script for Pymol from the Consurf server. http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/consurf.php Jan On 6/22/19 10:24 PM, khaja faisal tarique wrote: > Hi everyone, > > I was wondering can anyone suggest

[ccp4bb] Off-topic question

Hi everyone, I was wondering can anyone suggest me how to project the primary sequence conservation calculated through the Consurf server. Any help or suggestion will be appreciated. I have pasted a figure from an article just for reference. Best Khaja [image: image.png]

[ccp4bb] OFF topic Question Nucleotide exchange of RAS protein?

Hi All, Does anyone know what is the actual difference between CIP and EDTA method for exchanging the GppNHp (non-hydrolysable GTP) or GDP with the purified RAS protein? I have a protocol according to which I need to incubate the purified RAS with GppNHp having 20U of alkaline phosphatase, 10uM

Re: [ccp4bb] Off topic question

Dear Reza, CD hit will do exactly that. Cheers, Georg Sent from my iPhone On Jan 3, 2019, at 2:41 PM, Reza Khayat mailto:rkha...@ccny.cuny.edu>> wrote: ​Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n"

Re: [ccp4bb] Off topic question

Hi Reza, happy new year! The choice would depend on your alignment (aminoacid or nucleotides? are the sequences closely or distantly related? is it a large alignment? are there many gaps?)... Anyway, I think the safest, unbiased way to determine a group of outliers might be to compute a

Re: [ccp4bb] Off topic question

On Thursday, January 3, 2019 12:40:05 PM PST Reza Khayat wrote: > ?Hi, > > > Happy new year to all! A bit of an off topic question. Does anyone know of > a method/program to extract the most distinct "n" (n>2) sequences from a > sequence alignment? Thanks. If these putative "most distinct"

Re: [ccp4bb] Off topic question

PCA? On Jan 3, 2019, at 3:41 PM, Reza Khayat mailto:rkha...@ccny.cuny.edu>> wrote: ​Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n" (n>2) sequences from a sequence alignment? Thanks. Best wishes, Reza

[ccp4bb] Off topic question

?Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n" (n>2) sequences from a sequence alignment? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry

Re: [ccp4bb] Off-topic question

.pharmacie.univ-paris5.fr/spip.php?article18 > > > > De : Jobichen Chacko <jobich...@gmail.com> > À : CCP4BB@JISCMAIL.AC.UK > Envoyé le : Mardi 6 mars 2018 5h11 > Objet : [ccp4bb] Off-topic question > > Dear All, > We are trying to identify/sequence a D

Re: [ccp4bb] Off-topic question

6 mars 2018 5h11 Objet : [ccp4bb] Off-topic question Dear All, We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which was co-purified along with our protein. The expression was done in E.coli. Any suggestions on how to do this. Thank you. Jobi

[ccp4bb] Off-topic question

Dear All, We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which was co-purified along with our protein. The expression was done in E.coli. Any suggestions on how to do this. Thank you. Jobi

Re: [ccp4bb] Off-topic question about SEC

> on behalf of Reza > Khayat <rkha...@ccny.cuny.edu> > Reply-To: Reza Khayat <rkha...@ccny.cuny.edu> > Date: Wednesday, January 11, 2017 6:42 PM > To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> > Subject: Re: [ccp4bb] Off-topic question about SEC > > ​All

Re: [ccp4bb] Off-topic question about SEC

t;> Reply-To: Reza Khayat <rkha...@ccny.cuny.edu <mailto:rkha...@ccny.cuny.edu>> Date: Wednesday, January 11, 2017 6:42 PM To: "CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [cc

Re: [ccp4bb] Off-topic question about SEC

t <rkha...@ccny.cuny.edu<mailto:rkha...@ccny.cuny.edu>> Date: Wednesday, January 11, 2017 6:42 PM To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Off-topic question about SEC ​

Re: [ccp4bb] Off-topic question about SEC

Whoa! Big change! Any possible physiological relevance? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza Khayat Sent: Wednesday, January 11, 2017 7:43 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic question about SEC ​All these make sense. Protein

Re: [ccp4bb] Off-topic question about SEC

Yes if it either A) oligomerizes B) significantly changes shape C) aggregates reversibly On option B: Lower NaCl could make the protein “appear” bigger by unfolding it a bit; hydrophobic interactions should be weaker in lower NaCl. JPK Artem www.harkerbio.com

Re: [ccp4bb] Off-topic question about SEC

Yes if it either A) oligomerizes B) significantly changes shape C) aggregates reversibly Artem www.harkerbio.com "where wild SEC columns roam free" On Jan 11, 2017 7:22 PM, "Reza Khayat" wrote: > Hi, > > > Sorry for the off-topic question. Can a protein in lower [NaC]

[ccp4bb] Off-topic question about SEC

Hi, Sorry for the off-topic question. Can a protein in lower [NaC] run faster on a SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The protein elutes well within the resolution limits of the SEC with a symmetric gaussian A280 profile. I know that at lower [NaCl] the protein can

[ccp4bb] off topic question about amount measurements of Membrane protein

Dear all, I am a new starter in the membrane protein field and working with the cell free expression system. As the really small amount of protein I could get in hand, I got somehow stuck in the quantification of the protein yield. so Is there any suggestion of any methods or reagents suitable

[ccp4bb] off topic question regarding SPR

Dear all i have a basic question regarding SPR experiment and that is: What is the recommended glycerol concentration in the protein sample for doing SPR experiment and getting the best possible result.? i have kept 10% Glycerol in my protein preparation..is it O.K ? Thanx in advance --

Re: [ccp4bb] off topic question regarding SPR

Hi Faisal, whatever makes your protein happy is good. What type of experiment were you thinking of ? Protein-protein interaction or protein-small molecule interaction ? In the latter case add some Tween20 or Brij-35 into the mix. A decent overview can be found under this webpage for what to

[ccp4bb] off topic question BIAcore problem

Dear all, Recently I have measure a set of kinetic data of a receptor ligand interaction using BIAcore 3000. To my surprise, the dissociation rate is very low (~ 10e-6). During the measurement, I use a long dissociation time (2 hours) .I repeat several time which give very similar results. So I

Re: [ccp4bb] off topic question BIAcore problem

I assume you use CM5 chips ? I further assume you run at pH 7.5 perhaps ? What's the pI of your analyte ? 7.5 ? Do you get significant binding to your reference cell under the conditions you are running ? You might get rebinding to your negatively charged surface and the dissociation you are

Re: [ccp4bb] off topic question BIAcore problem

Dear Xianchi, unfortunately, dissociation rate constant kd 10^-6 s^-1 was just beyond the limit of Biacore in 1999 (e.g. see Fig. 1 in http://www.ncbi.nlm.nih.gov/pubmed/10556876). I am not sure about these days. As Juergen noted, you may have a problem with rebinding (you could try to reduce

Re: [ccp4bb] off topic question BIAcore problem

means. HTH, Zhijie From: xianchi dong Sent: Wednesday, February 20, 2013 12:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off topic question BIAcore problem Dear all, Recently I have measure a set of kinetic data of a receptor ligand interaction using BIAcore 3000. To my surprise

Re: [ccp4bb] off topic question BIAcore problem

Thanks a lot for the kind reply. I used CM5 chip at pH 7.4. I am not quite sure about the PI of my protein but I have different truncations of my protein which behaved similarly. I can fit my data quite good with the Chi2 around 1 and Rmax 150. The kon is about 10e4 and the KD is around 0.2 nM.

Re: [ccp4bb] off topic question BIAcore problem

Well that looks pretty real then. You might have wrong concentrations in one or the other experiment perhaps hence the difference. Jürgen On Feb 20, 2013, at 5:45 PM, xianchi dong wrote: Thanks a lot for the kind reply. I used CM5 chip at pH 7.4. I am not quite sure about the PI of my protein

Re: [ccp4bb] off topic question BIAcore problem

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off topic question BIAcore problem Thanks a lot for the kind reply. I used CM5 chip at pH 7.4. I am not quite sure about the PI of my protein but I have different truncations of my protein which behaved similarly. I can fit my data quite good

Re: [ccp4bb] Off topic question. NACCESS

Dear Armando, don't know about NACCESS, but I guess it is superseded by AREAIMOL in CCP4 (also in CCP4i); it outputs the accessible volume per atom in the pdb file and per residue and per chain and some other statistics in the log-file. Mark Quoting Armando Albert: Does anyone has got some

Re: [ccp4bb] Off topic question. NACCESS

Hi Armando, The information can be found here: http://www.bioinf.manchester.ac.uk/naccess/ It looks like you'll need to compile it from source code. I can help you with this, if you're unsure. It also plugs in nicely to the excellent LIGPLOT, which I have found incredibly useful (and, by

Re: [ccp4bb] Off topic question. NACCESS

I think one of the options of PISA is to calculate accessibilities -- I recall when I was learning how to use pisa that I saw this option. Also DSSP outputs accessibilities per residue Areaimol in ccp4 does too. I have seen many programs in the internet, google accessibilities, accessible

Re: [ccp4bb] Off topic question. NACCESS

On 06/17/2011 05:25 PM, Armando Albert wrote: Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando Maybe this server can do the job:

[ccp4bb] off topic question

Hi, A nuclear receptor is purified only in the presence of strong affinity bound ligand. Is there some method to study and quantitate binding affinities of this protein with other ligands (it is bound to the high affinity ligand after purification)? Attempts to purify in presence of low affinity

[ccp4bb] Off topic: Question about CD spectrum

Hi all, I've limited experience interpreting CD spectra, so I might be missing something, but I've collected CD data for a hydrophobic 15-mer peptide that forms a putative alpha-helix. I get a region of strong negative ellipticity, bottoming out at ~222nm; however, I also get a strong

[ccp4bb] Off topic question

Hi CCP4ers Apologies for the off topic... I have been trying to get hold of L-ribulose-5-phosphate (D- is readily available). Does anyone know where I can get such a compound? Thanks in advance for any suggestions and Merry Xmas! Gina