Re: [ccp4bb] Suggestions on Dynamic Light Scattering instruments

__ Debasish Kumar Ghosh CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho

Re: [ccp4bb] domain prediction of a membrane protein

Hi Firdous, The question, if I am understanding correctly, is to find the topology of the regions of a membrane protein, that is cytoplasmic, membranous or extra-cellular. You can do it by site directed cystine mutagenesis nearby to the the preferred region/domain followed by MAL-PEG analysis.

Re: [ccp4bb] Predict effects of mutations on protein stability and protein-protein interaction

Hi Wenhe , You can mutate the desired residue in 'pymol' (save the new pdb structures) and run them for molecular dynamic simulations (in Gromacs, Desmond etc.) to see the stability of your protein [for the full length protein or its segments] (by checking RMSD and RMSF values). You can analyz

Re: [ccp4bb] Precipitation issue during refolding

Dear Dipankar, Your problem is quite tricky to solve. I have two opinions which worked for me for a very high aggregation prone protein (Huntingtin, which always used to go in inclusion bodies and precipitate even in elution buffer). 1. First have 4-5M Guanidinum Hydrochloride in the lysis buf

Re: [ccp4bb] Hydrophobic hotspots

Hi Hugh, Waltz is an excellent web-server to give very good results on amyloidogenic regions based on sequence stretches (correlate the regions with hydrophobic patches by hydropathy plot obtained from Expassy-Protscale). Aggrescan and PASTA are two other reliable servers for the same kind of p

Re: [ccp4bb] Primer design

"Debasish Kumar Ghosh" , CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 6:48:25 PM Subject: RE: Primer design Or sequence the whole exome for what, $500-1000? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh S

Re: [ccp4bb] Primer design

Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specif

Re: [ccp4bb] Separating Monomers and Dimers

monomer and higher oligomers. Best regards, Debasish Kumar Ghosh CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone

[ccp4bb] Spam : Re: [ccp4bb] Off-topic: Attach His-tagged Protein to Coverslip

Assuming the protein is in solution, drop cast 2ul of solution onto a glass surface and spread evenly with a sharp needle. Air dry in dust free chamber and blow the surface with gentle stream of nitrogen gas. Proteins stick to surface quite well to be analyzed for various microscopy (AFM, SEM et

[ccp4bb] Spam : Re: [ccp4bb] Protein Ligand interaction using SPR technique

Dear Praveen, We have very good experience with protein ligand interaction with Biacore 3000 using CM5 chip. The NTA chip is prone to nonspecific interactions and give erroneous results. However the gold standard is ITC since it is more sensitive than Biacore 3000. One quick note for using Bia

[ccp4bb] Spam : Re: [ccp4bb] Protein Ligand interaction using SPR technique

Debasish Kumar Ghosh CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab

Re: [ccp4bb] How to determine the concentration of biotinylated peptide?

Hi Alex, In addition to Mirella's suggestion I would like to make an addition which might be specifically useful for you. Since your peptide has biotin tag, You may use HABA dye assay for the exact quatifiation of biotin (and thus biotinylated peptide). As far I recall, Thermo scientific provid

Re: [ccp4bb] For stabilizing protein-protein complex

degree/ rotation) might give at least formation of some complex. Hope this helps. Best!! Debasish Kumar Ghosh CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s

Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

Thank you all for your valuable suggestions. They have really worked well for me :) Regards, Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s

[ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091

[ccp4bb] Crystallization of aggregation prone protein

for me if I can get advises so as to troubleshot this problem. All advises are deeply appreciated. Thank you, Best regards, Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and

[ccp4bb] Crystallization condition for trimeric protein

n (if there is any empirical rule/idea). Any suggestion will be highly appreciated. Thanks and regards, Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Em