Questions tagged [proteins]

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

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15
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1answer
3k views

What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?

Deoxymyoglobin ($\ce{Mb}$) is known to have iron in the +2 oxidation state; I believe this was deduced from its magnetic moment, which corresponds to four unpaired electrons in high-spin $\mathrm{d^6}$...
7
votes
3answers
2k views

Is it known for sure that bases feel slippery because of the production of soap/surfactant?

Discussion around the question Why does bleach feel slippery? has started me thinking about the saponification explanation for the slippery feeling of basic solutions. According to Wikipedia: ...
25
votes
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). ...
23
votes
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 ...
5
votes
1answer
141 views

Is the structure of a crystalized protein the native one?

When one finds the 3D structure of a protein by crystalizing it and then making a X-ray experiment, how does one know that the geometrical configuration of the crystal is the same (or even close) to ...
10
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2answers
1k views

Why do the physical properties of an egg shell change when the egg shell is exposed to vinegar for a week?

When an egg is kept in vinegar for one week, its hard calcium carbonate shell changes into a soft rubbery membrane. As vinegar is weak acetic acid, how does vinegar change calcium carbonate into a ...
5
votes
2answers
308 views

Peptide bond formation involving side chains of charged amino acids

Peptide bonds are formed as such: Aspartic acid, glutamic acid and lysine all contain either one extra $\ce{-COOH}$ or $\ce{-NH2}$ group in them. Why does that extra group not participate in peptide ...
1
vote
3answers
2k views

Buffer Capacity Calculation

I know buffer capacity is the following: $$β=\frac{Δ(\ce{H+})}{Δ(\mathrm{pH})}$$ specifically the amount of acid/base that needs to be added to change pH by 1 unit. If I have data about how pH of a ...
4
votes
0answers
102 views

Synthesis of tripeptide using Merrifield peptide synthesis procedure - Inclusion of asparagine

I am supposed to synthesize tripeptide, $\mathrm{Ala-Asn-Phe}$, using Merrifield peptide synthesis procedure. Accordingly, I have done followings: Attached protected $\mathrm{Phe}$ as the first ...
3
votes
0answers
67 views

Formating chemical equations for proteins binding in multiple configurations

I am working on problems involving protein-protein binding, particularly ones in which two proteins may bind in two or more configurations, and where some of the resultant structures may also bind ...
1
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1answer
96 views

How to unify all the subunits in a PDB file?

A PDB may contain a TER token. For example, hemoglobin has 4 subunits separated by a TER identifier. If we take hemoglobin's ...
0
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1answer
64 views

What do X-ray diffraction and NMR tell about the Proteins? [closed]

I have gone through a simple idea that proteins have different conformations; it is a dynamic system. Moreover, whenever we do ensemble experiments, so we get an average picture. There are some ...