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Is My Protein Pure or Not?


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#1 rpjkmust916

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Posted 11 February 2011 - 12:46 AM

Hi Everyone,

This is my second post in this section.
Attached herewith is the pic of my SDS-Page of protein purification that I've done.
The 8,9 and 10 column were the protein that I need to purify.
Based from the bands that appear, I would like to confirm whether it is pure or not. Any advice,suggestion and ideas are welcome.
Thank you.

Attached Thumbnails

  • 140111-ppar-pu-sdspage(1-7)2.jpg


#2 mdfenko

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Posted 11 February 2011 - 12:34 PM

that depends on the subunit structure of your protein and what you will do with the protein.

there appears to be some minor (possibly insignificant) high molecular weight contamination.

the band just below the protein of interest (i assume) is significant. is it a subunit? degraded protein of interest? will it interfere with the usage of the protein?

you can express purity as a percentage of the total if you evaluate the lanes.

you can also load a large amount of protein and see what else shows up.
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#3 rpjkmust916

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Posted 11 February 2011 - 07:47 PM

Thanks mdfenko :),

that depends on the subunit structure of your protein and what you will do with the protein.

I need to purify the protein 95% pure at least.

there appears to be some minor (possibly insignificant) high molecular weight contamination.
the band just below the protein of interest (i assume) is significant.

When you mentioned it, I noticed too, that it has high molecular weight contamination which is shown by the band below of the protein of interest (yes, the darker band at 43KDa)

is it a subunit? degraded protein of interest? will it interfere with the usage of the protein?

Actually my knowledge in protein expression and purification is so little.
May I ask what do you mean by 'subunit, degraded protein of interest'?
I'm not sure whether the contaminate will interfere with the usage of the protein. It might cause an interference , I think. That's why my supervisor really angry with me when I showed him this gel. He also asked me why there were two bands.

you can express purity as a percentage of the total if you evaluate the lanes.
you can also load a large amount of protein and see what else shows up.

Could you elaborate more about this, please. Do I have to measure the protein concentration before I load it to the gel? How I can evaluate the lanes?
I'm sorry for asking a lot of question.
Thank you for spending time to answer my questions.

#4 proteaMatt

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Posted 15 February 2011 - 12:04 PM


is it a subunit? degraded protein of interest? will it interfere with the usage of the protein?

Actually my knowledge in protein expression and purification is so little.
May I ask what do you mean by 'subunit, degraded protein of interest'?
I'm not sure whether the contaminate will interfere with the usage of the protein. It might cause an interference , I think. That's why my supervisor really angry with me when I showed him this gel. He also asked me why there were two bands.


I think his point is that, your protein could possibly be pure, but if there are some degradation products those would show up as different bands in your gel because they are only fragments of the protein of interest. Another possibility could be formation of dimers, trimers, etc. that would form higher molecular weight bands.

Edited by proteaMatt, 15 February 2011 - 12:06 PM.

Lab Technician at Protea Biosciences

#5 mdfenko

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Posted 15 February 2011 - 01:11 PM


is it a subunit? degraded protein of interest? will it interfere with the usage of the protein?

Actually my knowledge in protein expression and purification is so little.
May I ask what do you mean by 'subunit, degraded protein of interest'?
I'm not sure whether the contaminate will interfere with the usage of the protein. It might cause an interference , I think. That's why my supervisor really angry with me when I showed him this gel. He also asked me why there were two bands.

(your supervisor shouldn't get angry) many proteins are made up of multiple protein chains, called subunits. sometimes they are the same (eg- hemoglobin), sometimes they are different (eg-igg heavy and light chains). the two bands you see could be subunits of the protein. are they in the same ratio for each sample? do you know the native molecular weight of the protein? how do these bands compare? do they both stain in a western blot? if so, are you using polyclonal or monoclonal antibodies?

the lower band could be a fragment of your protein of interest.


you can express purity as a percentage of the total if you evaluate the lanes.
you can also load a large amount of protein and see what else shows up.

Could you elaborate more about this, please. Do I have to measure the protein concentration before I load it to the gel? How I can evaluate the lanes?


you should always have an idea of how much protein you load in each lane but that is not really necessary to determine percent purity.

you can evaluate the lanes by either scanning them or by imaging them (take a picture) and determine the relative amount of each band in each lane (you can use a program like imagej to evaluate the image).
talent does what it can
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i do what i get paid to do

#6 rpjkmust916

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Posted 16 February 2011 - 06:22 PM

Thanks proteaMatt and mdfenko,

Now my knowledge in protein is increasing, may I ask more :)


the two bands you see could be subunits of the protein. are they in the same ratio for each sample? do you know the native molecular weight of the protein? how do these bands compare? do they both stain in a western blot? if so, are you using polyclonal or monoclonal antibodies?

the lower band could be a fragment of your protein of interest.

May I know, what do you mean 'in the same ratio for each sample'?
I have not learn to do the western blot yet :(
Is it possible to identify it as a fragment if I run western blot?

About the native molecular weight of the protein, let me give the details
It is a nuclear receptor protein with 280-486 aa, cloned into PET 32a Rosetta.
My senior told me the molecular weight of this protein is 43KDa.
The calculation she showed me was like this,
- 206 aa x 110 Da = 22660 so ~23KDa
- 23KDa + 20 = 43KDa

Actually, I don't understand :( But I'm afraid to ask for more because we do have language barrier and she seems like not in good condition lately.


you should always have an idea of how much protein you load in each lane but that is not really necessary to determine percent purity.

you can evaluate the lanes by either scanning them or by imaging them (take a picture) and determine the relative amount of each band in each lane (you can use a program like imagej to evaluate the image).

Thanks for the explanation.
There is no scanning machine for the gel in the lab. I only scanned the gel with scanner that attached with the computer.

Thank you again and again.....

#7 Adrian K

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Posted 16 February 2011 - 09:29 PM

Thanks proteaMatt and mdfenko,

Now my knowledge in protein is increasing, may I ask more :)



the two bands you see could be subunits of the protein. are they in the same ratio for each sample? do you know the native molecular weight of the protein? how do these bands compare? do they both stain in a western blot? if so, are you using polyclonal or monoclonal antibodies?

the lower band could be a fragment of your protein of interest.

May I know, what do you mean 'in the same ratio for each sample'?
I have not learn to do the western blot yet :(
Is it possible to identify it as a fragment if I run western blot?

About the native molecular weight of the protein, let me give the details
It is a nuclear receptor protein with 280-486 aa, cloned into PET 32a Rosetta.
My senior told me the molecular weight of this protein is 43KDa.
The calculation she showed me was like this,
- 206 aa x 110 Da = 22660 so ~23KDa
- 23KDa + 20 = 43KDa

Actually, I don't understand :( But I'm afraid to ask for more because we do have language barrier and she seems like not in good condition lately.


you should always have an idea of how much protein you load in each lane but that is not really necessary to determine percent purity.

you can evaluate the lanes by either scanning them or by imaging them (take a picture) and determine the relative amount of each band in each lane (you can use a program like imagej to evaluate the image).

Thanks for the explanation.
There is no scanning machine for the gel in the lab. I only scanned the gel with scanner that attached with the computer.

Thank you again and again.....


On referring to your pet32a vector, Is your protein Tagged (Trx, S, His)?
CAn you explain into detail about your work flow? Do you pre-treat your protein

Based on your calculation from your senior, I assume that you did not pre-treat your protein with thrombin/enterokinase before purify your protein through the column.

The Trx tag, s tag and His tag together forms roughly 158aa before your protein.
So 158 x 110 = 17380 ~17kDa
You probably use HindIII or SalI RE to cut the vector for your cloning which adds around ~18aa (~2kDa)(rough calculation) so the total would be around 20kDa (17+2=19, ~20) contributed from your vector.

Your cloned in protein was 206aa, which you suggested to be ~23kDa. So in total, you should get 23 + 20 =~ 43kDa protein.

P/S: Slightly off track from your topic, I really not sure whether is it a good idea to have so many "tag" before your protein, as your "tag" was almost the same size with your protein, and wouldn't it affect your protein functions?
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#8 rpjkmust916

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Posted 16 February 2011 - 10:22 PM

Thanks Adrian :) ,

On referring to your pet32a vector, Is your protein Tagged (Trx, S, His)?
CAn you explain into detail about your work flow? Do you pre-treat your protein


It was His-Tag.

About my work flow, do you mean by the expression process?
I've never done the cloning part.
I only do the culture by starting with small culture (culture 1 colony in 10 ml LB with antibiotics) and incubate it for overnight at 370C.
After that transfer it to 1L of LB (with antibiotics) and incubate again untill it reach the OD600 = 0.6-1.0.
Then, I add 0.1mM IPTG and incubate at 18o C for 20hrs.
Next, I harvest the cell and discard the supernatant.
Lysis the pellet with sonicator and filter it (I did not treat the lysate with any protease inhibitor).
Centrifuge and pool all the supernatant (now I know it also known as 'soluble protein' :) ).

And finally, run the purification with the supernatant.

I'm using HiTrap Chelating HP (5ml)affinity column.

The buffers that I used for the column as listed below:
Running/Lysis buffer: 50mM Tris, 5mM 2-Me
Elution buffer : 50mM Tris, 5mM 2-Me, 500mM Imidazole


P/S: Slightly off track from your topic, I really not sure whether is it a good idea to have so many "tag" before your protein, as your "tag" was almost the same size with your protein, and wouldn't it affect your protein functions?


Actually, I'm not fully understand. Could you explain,please?


Anyway, thank you very much Adrian :D


P/S: It looks like more explanation given, I ask more and more. Apologize for any inconvenience :(
I'm a newbie in molecular biology :( .

Edited by rpjkmust916, 16 February 2011 - 10:41 PM.


#9 Adrian K

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Posted 17 February 2011 - 02:14 AM

Thanks Adrian :) ,


On referring to your pet32a vector, Is your protein Tagged (Trx, S, His)?
CAn you explain into detail about your work flow? Do you pre-treat your protein


It was His-Tag.

About my work flow, do you mean by the expression process?
I've never done the cloning part.
I only do the culture by starting with small culture (culture 1 colony in 10 ml LB with antibiotics) and incubate it for overnight at 370C.
After that transfer it to 1L of LB (with antibiotics) and incubate again untill it reach the OD600 = 0.6-1.0.
Then, I add 0.1mM IPTG and incubate at 18o C for 20hrs.
Next, I harvest the cell and discard the supernatant.
Lysis the pellet with sonicator and filter it (I did not treat the lysate with any protease inhibitor).
Centrifuge and pool all the supernatant (now I know it also known as 'soluble protein' :) ).

And finally, run the purification with the supernatant.

I'm using HiTrap Chelating HP (5ml)affinity column.

The buffers that I used for the column as listed below:
Running/Lysis buffer: 50mM Tris, 5mM 2-Me
Elution buffer : 50mM Tris, 5mM 2-Me, 500mM Imidazole


P/S: Slightly off track from your topic, I really not sure whether is it a good idea to have so many "tag" before your protein, as your "tag" was almost the same size with your protein, and wouldn't it affect your protein functions?


Actually, I'm not fully understand. Could you explain,please?


Anyway, thank you very much Adrian :D


P/S: It looks like more explanation given, I ask more and more. Apologize for any inconvenience :(
I'm a newbie in molecular biology :( .



Hmn, exactly what I want to ask about your cloning strategy (did you removed any of the "tag" or modify them), but then you said you did not do the cloning work...
Forget about what I had asked in previous since you might not know exactly the construct.... lets see, what is your purpose of using this recombinant protein? If you do not need a native protein, you can always excise the band and do electro elution to get a pure band. How is that?

Edited by adrian kohsf, 17 February 2011 - 02:16 AM.

Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#10 rpjkmust916

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Posted 17 February 2011 - 06:17 AM

Thanks for the reply Adrian,

My senior told me that she did not remove the His-tag. I have to purify the protein for my colleague at concentration 1mg/ml. I'm not really sure of her works/experiment.
According to my senior, the his-tag should not be a problem for the experiment.
If I excise the band and electro elution it, how about the concentration?
The main concern here is to get 95% purity of the protein at mass 1mg/ml.....*sigh*

Anyway, thanks Adrian for the suggestion. I've gained a lot about protein purification here :)
Still need to read a lot.
Just a silly question...is there any book like "Protein Purification for Dummies" like me :lol:

Any suggestions, advices, opinions are mostly welcome :D

Thank you.....Kamsahamnida....Ariatou gozaimasu...last but not least....Terima Kasih!!!!

#11 Adrian K

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Posted 17 February 2011 - 08:45 AM

Try to talk to your colleague about his/her application. If your colleague do not require a native protein, you can just use your current column purified products and do SDS-PAGE, followed by excise the band and do electro elution. After the electro elution, you can concentrate the protein by using vivaspin protein concentrator (column with membrane). Do a protein quantification (BCA, Bradford etc...), and dilute to the concentration you want.

LOLx, I'm also a dummies as well...
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#12 mdfenko

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Posted 17 February 2011 - 01:39 PM

Thanks proteaMatt and mdfenko,

Now my knowledge in protein is increasing, may I ask more :)



the two bands you see could be subunits of the protein. are they in the same ratio for each sample? do you know the native molecular weight of the protein? how do these bands compare? do they both stain in a western blot? if so, are you using polyclonal or monoclonal antibodies?

the lower band could be a fragment of your protein of interest.

May I know, what do you mean 'in the same ratio for each sample'?
I have not learn to do the western blot yet :(
Is it possible to identify it as a fragment if I run western blot?

About the native molecular weight of the protein, let me give the details
It is a nuclear receptor protein with 280-486 aa, cloned into PET 32a Rosetta.
My senior told me the molecular weight of this protein is 43KDa.
The calculation she showed me was like this,
- 206 aa x 110 Da = 22660 so ~23KDa
- 23KDa + 20 = 43KDa

Actually, I don't understand :( But I'm afraid to ask for more because we do have language barrier and she seems like not in good condition lately.


you should always have an idea of how much protein you load in each lane but that is not really necessary to determine percent purity.

you can evaluate the lanes by either scanning them or by imaging them (take a picture) and determine the relative amount of each band in each lane (you can use a program like imagej to evaluate the image).

Thanks for the explanation.
There is no scanning machine for the gel in the lab. I only scanned the gel with scanner that attached with the computer.

Thank you again and again.....


the scanned image of the gel can be brought into a program like imagej and the lanes can be evaluated like they were scanned. each band can be integrated and given a value relative to the amount of stain incorporated (you can, if you know how much protein was loaded, determine the actual mass for each band). you can then determine the percent purity based on the whole lane and the ratio of the two bands of interest.

the ratio would be important to determine if the two bands are subunits of the same protein, if they maintain the same ratio for all samples then they may be. from what you say in the post about the formula weight of your protein, they are probably not subunits.

you can determine if the lower band is a fragment of the upper band by western blot if the remaining protein contains the epitope(s) recognized by the antibody.

Edited by mdfenko, 17 February 2011 - 01:39 PM.

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#13 rpjkmust916

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Posted 17 February 2011 - 09:39 PM

the scanned image of the gel can be brought into a program like imagej and the lanes can be evaluated like they were scanned. each band can be integrated and given a value relative to the amount of stain incorporated (you can, if you know how much protein was loaded, determine the actual mass for each band). you can then determine the percent purity based on the whole lane and the ratio of the two bands of interest.

the ratio would be important to determine if the two bands are subunits of the same protein, if they maintain the same ratio for all samples then they may be. from what you say in the post about the formula weight of your protein, they are probably not subunits.

you can determine if the lower band is a fragment of the upper band by western blot if the remaining protein contains the epitope(s) recognized by the antibody.


Thanks mdfenko,
I will learn how to use the ImageJ :)


Adrian,

Thank you for ur advice....:D

Edited by rpjkmust916, 17 February 2011 - 09:41 PM.


#14 Adrian K

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Posted 17 February 2011 - 09:58 PM

Welcome, hope this helps.
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#15 Inmost sun

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Posted 19 February 2011 - 07:03 AM

some might be satisfied with CCB-stained gels to state purity however staining with silver or nanogramm-sensitive dyes is the correct method to state purity on the gel level...

Hi Everyone,

This is my second post in this section.
Attached herewith is the pic of my SDS-Page of protein purification that I've done.
The 8,9 and 10 column were the protein that I need to purify.
Based from the bands that appear, I would like to confirm whether it is pure or not. Any advice,suggestion and ideas are welcome.
Thank you.






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