Questions tagged [proteins]

For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.

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Mechanism of protein precipitation with TCA

In practice, TCA (trichloroacetic acid) is widely used for quantitative protein precipitation, but so far I have failed to discover the exact mechanism of TCA action. I highly doubt it's just the ...
23
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2answers
3k views

Why is the cyanide ion toxic?

As the title implies, what is the molecular basis of cyanide toxicity? I did some searching around at the CDC and it only states that it prevents cells from using oxygen. I also read how it could take ...
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1answer
704 views

why do we denature proteins before mass spectroscopy?

I'm learning about mass spectroscopy in particular the use of it in analyzing protein structure. they said we have to use trypsinolysis to cut the protein to segments, but why does the protein have to ...
3
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1answer
124 views

Why does no antitoxin for botulinum type H exist yet?

Antitoxins against the botulinum toxins type A–G produced by Clostridium botulinum are known. Why does none exist against the type H botulinum toxin yet?
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2answers
2k views

Why do unboiled eggs last longer than boiled eggs?

Just like the title says, I watched this video https://youtu.be/CHMY4G9gTPA and then became intrigued.
5
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1answer
3k views

Why does capping after each coupling in Solid phase peptide synthesis improve the results?

Why does capping after coupling improve results during solid phase peptide synthesis (SPPS)? The Case: I have conducted a lab experiment where we coupled three Fmoc-protected amino acids, and did a ...
4
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1answer
105 views

How to connect proteins via disulfide bonds computationally?

I want to connect proteins together to form a dimer. As seen in the picture, the monomers come close to each other along the edge of the higher-order structure (forget about the sulfate there). How ...
5
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1answer
99 views

Thermal stability of charged and uncharged alpha helices (the concept of alpha-helix capping)

I just learned that charged alpha helices are less thermally stable than uncharged ones. The only difference I see between them would be a larger dipole moment in the charged helix, but how would this ...
5
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1answer
388 views

Tandem mass spectrometry: a1 and immonium ions

In tandem mass spectrometry of proteins one will usually end up with a mix of $b$ and $y$ fragments but also $a$ fragments and immonium fragments. My problem is that wouldn't an $a_1$ ion be the exact ...
5
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1answer
90 views

Protein purification with Cobalt

Cobalt exhibits a more specific interaction with histidine tags, resulting in less nonspecific interaction than nickel. For this reason, cobalt is the preferred divalent cation for purifying His-...
2
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1answer
218 views

Hydrolysing large molecules to reveal amino acids

Consider Oxytocin: I am asked to hydrolyze Oxytocin and reveal 5 amino acids which are the result of this hydrolysis. I must admit I have no idea where to begin. I know that generally amino acids ...
3
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1answer
833 views

Denaturing of Proteins and Nucleic Acids - Effect of Temperature (Heating vs Cooling)

Heating a protein/nucleic acid will disrupt inter-molecular and intra-molecular forces in the tertiary structure. It will also interfere with the shape of the active site if the protein. Does this ...
0
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1answer
152 views

How does formylation of a nitrogen change the hydrophobicity of a target protein?

How does formylation, of the sort shown here: (from this Wikipedia page) affect the hydrophobicity of the target protein? Can we say anything general about adding a formyl group to a nitrogen?
6
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1answer
646 views

Is there a chemical test for gluten?

I am looking for a chemical test for the presence of gluten: however, having looked online for such a thing, all the results seem to be about 'home testing kits' (presumably for people with a gluten ...
3
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2answers
94 views

Explaining a biochemical reaction (protein labelling, e.g. with fluorescent probes)

I am an immunology master student without prior knowledge of biochemistry. Could someone explain to me the following 6 reactions? What I want to understand is why exactly the reactions happen at this ...
3
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1answer
11k views

Can acidic conditions break disulfide bonds

I am denaturing a protein using organic solvent and acid (49:49:2% water:methanol:acetic acid), but I want to maintain the disulfide bonds. My chemistry knowledge isn't good but disulfides are broken ...
25
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1answer
1k views

How can I determine if there are π-π interactions between an amide and an aromatic ring in a protein?

In a crystal structure I've determined, a triazole ring on my ligand appears to be stacking with a tyrosine (top in picture): However, there is also an amide, courtesy a glutamine, near it (bottom). ...

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