How can I construct the structure of a protein which have multiple sub-units?

More Md Fahmid Hossain Bhuiyan's questions See All

Can anyone suggest me any dyes for observing plant cells under microscope?

I am preparing callus suspension culture of plants. So I am hoping to find dyes (not fluorophores) which are somewhat specific for plant cells.

06 July 2019 4,645 5 View

How to obtain the 5'-UTR region sequence of a particular eukaryotic gene (In silico)?

I need to obtain a long stretch (specific amount) of the sequence from the upstream (Upstream of the start codon) of a particular gene.

02 March 2019 2,904 5 View

How to design a gene specific primer which does not share any sequence identity with the genome sequence of any unintended organism?

I want to perform a transformation process where I want to transfer a plant gene into a another plant. I want to design a specific primer for that gene which will not share any sequence identity...

11 December 2018 853 13 View

How to find structures of ligands for proteins?

I am looking for some ligands which bind to particular parts of a protein. Here by ligands, I am pointing to a database of all known ligand structures. Is there anything available like that?...

08 September 2018 2,763 4 View

A certain protein shows 99% identity with E. coli and 100% identity with enterobacteriaceae. what does that mean?

i know that E. coli belongs to family enterobacteriaceae and the protein under consideration belongs to the E. coli K12 proteome.

05 June 2018 8,923 5 View

What do hyphens in between primer sequences for PCR mean?

I found a primer sequence for a particular gene from a publication. The sequence is- 5'-ATGGCAGTAGTAGCAG-CTCC-3' (forward) 5'-TCAGGTGTCT-AAGTTCAGAGATTC-3'(reverse) What does the hyphens...

04 May 2018 7,030 1 View

How good is HPLC for the purification of a particular secondary metabolite?

I want to enlist all the metabolites found in a particular plant. I have a very limited knowledge on chemical processes like chromatography. I wanted to know whether an HPLC can isolate particular...

01 February 2018 1,013 4 View

Why Austenite grains in steel show much more twinning than ferrite grains?

It is oftentimes said to be a distinctive metallographic trait that differentiates a fully austenitic and a fully felly ferritic steel without etching that might distinguish between two. Why...

02 March 2021 728 2 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

I have used an AllPrep DNA/RNA/Protein Mini Kit QIAGEN kit to extract RNA and protein from my samples. At the end of the protein purification, I resuspend my protein in 5% SDS. Will these samples...

28 February 2021 7,370 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View

Problem with ligating 2.8 kb insert into 8.5 kb plasmid?

I am trying to clone 2 copies of the same mammalian gene into the pSF-CMV-Ub-Puro Ascl (contains HindIII, KpnI and NheI cut sites) plasmid. This is what the final product is supposed to look like...

24 February 2021 6,310 3 View

What urea buffer can i use for biotagged protein extraction from streptavidin beads?

Hi all, I have been doing research on biotagged LDB1 proteins in Mel cells. I purify the proteins using M280 streptavidin beads. The yield is very low so I've been trying to optimize it by...

24 February 2021 5,749 3 View

Maria Kyriakidou

Do you have the the AA sequence of the protein you want to construct the structure? If yes, given an amino acid sequence, you can find which protein(s) of known 3-D structure are similar to it. Use BLAST against the PDB database to find templates. Then you choose a template based on the alignment, more similarities etc. It is important to have a good alignment. Then you create your model using a homology modelling software (i.e http://salilab.org/modeller/). Then you refine your model and finally you evaluate it (you can use http://swift.cmbi.ru.nl/servers/html/index.html, https://prosa.services.came.sbg.ac.at/prosa.php etc ).

Woonghee Lee

Assuming you already have two monomeric proteins, you can dock them using HADDOCK (automation) or Xplor-NIH (manual).