The REFINE Project asks you

Hi all,

Bubbles affects the absorbance reading from my assay. How can avoid bubbles when pipetting with multichannel pipette.

Thank you

how many decimals for rmsd between alpha carbons in two protein structures? One or two?

Hello,

we are running sds-page electrophoresis gel of two purified protein. Both proteins have the same theoretical size but in the gels they migrated differently. Both have different Pi, one is 6 and the other one is 7. Do you think that this could affect the migration?

Thanks.

Dear PIs,

If you have any projects in the field of molecular biology and/or epigenetics, please let me know

Thanks in advance ☺

I'm a non-scientist fascinated by structural biology and trying to understand how structural biologists do molecular replacement, and I would love your help.

I understand that the general rule of thumb for molecular replacement is that you need a search model that shares >20% sequence similarity as your target protein. However, sequence similarity does not always translate into structural similarity, and a search model with low sequence similarity may turn out to be a good model if its 3D structure shares enough similarity with the target protein.

My question is: how do you find such search models with low-sequence identity but high structural similarity for molecular replacement? We do not yet know the structure of the target protein, so I'm having a hard time understanding how you can identify a search model that may share high structural similarity.

For instance, based on the sequence of the target protein, do you use databases like InterPro that predicts which protein family the target protein might fall in and find potential search models from that predicted family?

Thank you!

Hello,

I want to combine my 1692 bp chitinase gene region with the pBlueScript II SK(+) cloning vector. I added BamHI and HindIII cut sites to the ends of my primers to amplify my gene region. I cut and purify my pcr product. Likewise, I cut and purify my vector. I then perform a 3:1 ligation and transform into E.coli Dh5alpha competent cells. I inoculate on LB medium containing 100 uq/ml amp. I also add X-gal and IPTG to my medium for blue-white colony selection. After 1 day, I choose from white colonies and do both colony PCR and plasmid DNA isolation. Faint bands appear in the gel as a result of colony PCR. In the spectrophotometer measurements, my plasmid DNA isolation results look good, but I cannot see my plasmid in the gel. Apart from this, I also performed the operations using Thermo CloneJET PCR Cloning Kit, but I cannot obtain my recombinant vector.

What could be the problem?

After production of recombinant protein using the Pichia pastoris system, I always get two bands (figA and B) of my target protein. This time I got three bands figC) after purification using His-tag column. why are there two bands? Glycosylation?

Dear colleagues,

I am developing devices for non-destructive sorting of forest seeds, as well as seeding, including aerial seeding.

Some basic values are necessary for the design of air seeding devices.

Please share the following parameters:

1) The weight of the seed (whether the seed is pelletized or not, group seeding or one at a time).

2) The depth of seed embedding in the soil.

3) The distance between adjacent wells for sowing the seed.

4) Elastic-viscous properties of the soil.

5) The minimum and maximum flight altitude of the UAV for aerial seeding.

6) Overall dimensions and weight of the seeding apparatus.

Take care,

Arthur Novikov.