Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
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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 ...
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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 ...
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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 ...
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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-...
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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 ...
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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 ...
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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?
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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 ...
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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 ...
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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 ...
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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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