Thursday, May 27, 2021

ProteoCool Pills#7:Small scale IMAC purification from Expi293 or Expi-CHO culture surnatant

 

The Expi293 (see ProteoCool n° ) and Expi-CHO Expression System (Thermo) provides high-yield recombinant protein production in mammalian cells     by combining high-density an optimized chemically defined media and transfection protocol.

Generally 'i'm performing the  small scale expression and solubility trials in 2ml scale culture (in 6 well plates)


The availability of a simple IMAC Small scale purification protocol is essential in the preliminary expression tests to detect those proteins that are poorly expressed and/or co-localize with other proteins secreted in the cell surnatant.

 

Here I report a simple and rapid protocol that can allow to you to perform small IMAC purification for up to 24 sample in parallel in short time (1-2h):

1.      The cells were Transferred in a 2ml Eppendorf or 24 deep well plates (depend from the number of sample tested);


2.      Centrifugation at 300g for 5;

        a)      Cell Pellet: resuspended in 2ml of binding buffer, diluted 1/3 and loaded in SDS page; 

       b)     Surnatant à go to step 3;

3.Centrifugation 10’ at maximum speed to completely remove cell debris (12000g in Eppendorf 2ml0

                              a)      Pellet  discharged;

b)     Surnatant were diluted 1:1 with the IMAC binding buffer (Tris 20mM, Nacl300mM, imidazole 10mM pH=8) and loaded in the purification column* (go to step5);


* Buffer exchange is not necessary to obtain good binding to the IMAC coloumn;


4.      Assembly of the purification column:

-   Biorad Bio-Spin (cod.7326008) loaded with 100ul of Ni-Sepharose FF (Ni-Sepharose FF - Cytiva cod.17531801*)

*The same protocol was also performed using Ni- Sepharose Excel resin (GE cod. E17371201) those theoretically was developer for purification of protein from the mammalian cell suratant but in our hands the standard Ni-sepharose seems to provide best results in terms of protein purity;

-   Column was washed (for gravity) with 2 ml of milliQ water to remove the ethanol.

-   Column was equilibrated with 2ml of IMAC Binding buffer;


    Using a simple 4 position tube rack (VWR cod. 525-0951) and a large volume adjustable spacer multipipette (e.g RAININ LA6-1200XLS) up to 32 protein sample can be easily loaded (step 5) and  washed in parallel (step 6)


5.      Protein sample were loaded into the equilibrated column and F.T discharged.

6.      Columns were washed with 6ml of IMAC binding buffer and buffer discharged

7.      Elution was performed with 300ul (3CV) of elution buffer (Tris 20mM, NaCL 300mM, imidazole 300mM pH=8) and the eluted fraction is collected in a 2 ml Eppendorf tube.

8.       To collect all the elute columns were centrifuged 2’ at 3000rpm.



Example of result obtained with this protocol:


where: 

C- are non transfected cells

 C+ are Expi293 transfected with a 10His-tagged protein cloned in pcdna3.4 with an N_terminal leader sequence for secretion in mammalian cells.

The culture volumes and the column size to be used in the scale up need to be carefully select on the basis of the expression level observed in the small-scale trials and of the amount of protein that we need to produce.

Eg:

<0,5mg of protein: 100 of Ni-sepharose resin in a Biorad Bio-Spin coloumn

0,5-1mg of protein: 200-300ul Ni-sepharose resin in a Biorad Poliprep (cod. #7311550)  Gravity flow ;

1-10 mg of protein:1-2ml di of Ni-Sepharose resin in a empty PD-10 gravity flow (a peristaltic pump could be used to perform sample loading, wash and elution)  

>10mg of protein   prepacked 5ml  His-trap FF Crude connected to a peristaltic pump or AKTA purification system

Differently from the expression test, when we would like to purify protein, all the fractions need to be collected and loaded in the SDS-page to follow the protein and washing steps with buffers contain intermediate imidazole concentration (e.g. 20mM for 6xHis-tagged protein or 30mM for 10xHis tagged proteins) are included  in order to improve  final protein purity.

The columns if correctly stored (must not go DRY and stored at 4°C in water or water/ethanol 20% for long time)  are reusable for several time. Metal stripping and regeneration could be performed as already shown in the ProteoCool n° 25: Simple IMAC regeneration 

 


Monday, May 17, 2021

ProteoCool Pills#6: Rapid protein Expression and solubility check using a 24 tip-horn sonicator

 

The use of high cell density media (e.g Enpresso reported in the ProteoCool n°7 or YGR reported in the ProteoCool n°32 ) for protein expression using E.coli allows to scale down culture volumes and easily express many clones in parallel.

Protein expression and solubility check can become a limiting step and the set-up of a simple and reliable protocol is essential.

Automation by using robotic platform is a possible solution for a real high-throughput approach, (e.g a screening projects that require to process  thousands samples for week) but in the most cases just the implementation of a optimized and rational protocol based on the use of multi-channel pipettes and 96-deep well plates can allow to manipulate in parallel up to hundreds samples/week with low cost and high protocol flexibility.

The lysis method used in the small scale test need to be similar to the ones that will be applied for the purification of the protein from rest of biomass in case of positive results, and therefore Sonication or is preferable respect than freeze-thaw cycles (work well in small scale but is not scalable) and chemical/enzymatic lysis ( expensive in scale-up)

Protocool

1) About 8OD of bacterial cells (for Enpresso correspond to 800ul not induced or 500ul induced 8h or 300 ul induced 24h) were transferred from culture into the 96 Deepwell plate following the scheme reported below (to fit the 24 tip sonicator horm)


2) Plate were centrifuged for 20' at 3700 rpm and 4°C


3) After centrifugation the surnatants were discharged 


4)   
The pellets were resuspended adding 960ul of cell Lysis/binding buffer ( eg: Tris 20mM, NaCl 300mM, imidazole 10mM pH=8 for His-tagged protein that will be purified by IMAC) and mixed 3-5 times with the multichannel to allow complete pellet re-suspension. 

2)    Cell Lysis by sonication using the 24-tip horn:

Sonication cicle: 30’’ ON/45’’ OFF , 20 cycles  50% power – Qsonica Q700 sonicator.

The plate need be placed in ICE during the sonication to avoid sample heating.

3)    From each well 60ul of sonicated solution (Total fraction) e transferred in PCR plate no skirted containing 20ul of Loading sample buffer 4X ( eg. Thermo scientific cod. NP0008 ) with reducing agent.

4)    The 96-deepwell plate were centrifuged at 20’ a 4000rpm 4°C;

5)    From each well 60ul of surnatant (Souble fraction) e transferred in PCR plate no skirted containing 20ul of Loading sample buffer 4X ( eg. Thermo scientific cod. NP0008 ) with reducing agent.

6)    The no skirted PCR plate is closed by aluminum foil and incubated 5’ a 95°C in a PCR machine.

7)   12ul of each samples were loaded in a 26well 4-12% SDS-page gel.

Example of results:




 

 

 


Sunday, May 9, 2021

ProteoCool Pills#5: Safe Comassie blue staining solutions (compatible with microwave coloration)

 


After SDS-polyacrylamide gel elettrophoresis proteins are "fixed" in the gel to prevent dispersion of the proteins and visualized by staining with a chromogenic dye.

Until some years ago the dyes like Coomassie Blue R-250, were usually dissolved in an acetic acid-methanol-water mixture where acetic acid and methanol provide an environment enhancing the interactions with dyes when you are using standard room temperature staining/destaining protocol.

https://pubmed.ncbi.nlm.nih.gov/30097924/

To speed up the procedure, heating the staining solution in the microwave oven for a short time is frequently used (see ProteoCool n° 6;

https://www.blogger.com/video.g?token=AD6v5dwhmY5GkO9_ezq3Va_Tfqi6u0ys99hBWy2OxXI0esS7px1EdB64LQXElfRjWFrifwHtPdDxUERBgln233r-2MAurJXhLDWcqkP1X5Gr1gSvjYZLKNS5fdeNossEHQrrnebrxiHw)

Staining/destaining which microwave is not feasible with the standard dye acetic acid-methanol-water formulation due to evaporation of hazardous Methanol coupled with the strong smell of acetic acid in the lab which should be avoided due to environmental and safety considerations.

In the last 10 years many different water methanol/acid free formulations (which in some cases contain a small % of ethanol) where developed for staining of SDS-page gel using microwave.

I had the opportunity to use some commercially available products:

1)    PRoBLue – Giotto biotech – https://www.giottobiotech.com/prodotto/problue-safe-stain-2/ 

Its my first choice!   Strong blue colour, medium cost; 50euro/liter

 

2)    SimplyBlue™ SafeStain - https://www.thermofisher.com/order/catalog/product/LC6065?SID=srch-srp-LC6065#/LC6065?SID=srch-srp-LC6065

 

Weaker blue colour  à staining time respect than Problue to reach a good coloration most expensive à >100euro/liter

Many other suppliers (eg BIorad) sell similar water based Comassie Blue stain, but I never add the opportunity to test in with microwave approach.

 

 

 

 

 

Sunday, May 2, 2021

ProteoCool Pills#4: Replacement of Ethidium bromide with a safe stain

 

Ethidium bromide thanks to its ability to show an intense fluorescence (ex 300nm/em 620nm) after binding with DNA.

 Ethidium bromide (EB) is inexpensive, sufficiently sensitive and very stable and thanks to this property has been the stain of choice for nucleic acid gel staining for decades.

 However on the other hands, EB is also a known powerful mutagen.

Recent years alternative reagents able to show an intense fluorescence after binding with DNA but not able to permeate cell membrane were developed:

 

My preferred one:

 

Gel REd - Biotium  (VWR cod. 41003) 

   https://biotium.com/product/gelred-nucleic-acid-gel-stain/

 

Safety assessment available at:

 

https://biotium.com/wp-content/uploads/2013/07/GelRed-and-GelGreen-Safety-Report.pdf

 

Cost: About 90€ for 500ul (stock 10000X) à  90€ for 5liter of agarose à 0,9€ for a mini gel (15x2well)

                                                                                                                                  2,5€ for a midi gel (up to 30x2 well)

                                                                                                                                     

Another alternative that I used in the past is the Sybr Safe (thermo cod. S33102) 

https://www.thermofisher.com/order/catalog/product/S33102?SID=srch-srp-S33102#/S33102?SID=srch-srp-S33102 

is another possible alternative. but in my experience, it shows limited stable under UV excitation.

 

More details are available in the following link

 

https://www.blogger.com/video.g?token=AD6v5dxB5wweSgHEks3TU3bm1QoGEYZU6GT8788soF0i7SEVvaQwM2AgHXmDY62fIzukFrMMDbFQEFOPMfSyV4GwvJHPY9U__KiUhmaCsx6NAwneL2yJYbaSu_DV-H4_to6BznMtlE59

usefull links #1

i would like with share the folliwng 3 links about usefull on line tool for the scientist working with recombinant monoclonal antibodies:   ...