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Questions tagged [proteins]

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

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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 $\mathrm{d^6}$...
orthocresol's user avatar
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8 votes
3 answers
3k 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: ...
uhoh's user avatar
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25 votes
1 answer
2k 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). ...
Nick T's user avatar
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23 votes
2 answers
4k 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 ...
Aubrey Champagne's user avatar
2 votes
3 answers
4k 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 ...
user2657817's user avatar
2 votes
2 answers
138 views

How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
Gunther Schadow's user avatar
10 votes
2 answers
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 ...
DARYL JOSEPH.G's user avatar
7 votes
2 answers
2k 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 ...
Aniruddha Deb's user avatar
6 votes
3 answers
1k views

What is the precise definition of Ramachandran angles?

The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
Jennifer M.'s user avatar
5 votes
1 answer
411 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 ...
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4 votes
0 answers
341 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 ...
Geek's user avatar
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4 votes
3 answers
407 views

What is the difference between structure assignment and structure prediction?

I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning. ...
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4 votes
1 answer
164 views

Why are isomers of parathion less active acetylcholinesterase inhibitors than paraoxon?

Parathion itself has been found to be a very weak inhibitor of acetylcholinesterase. It normally requires metabolic activation and the conversion into paraoxon in the body to actually start exhibiting ...
user73910's user avatar
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3 votes
0 answers
88 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 ...
Abijah's user avatar
  • 197
3 votes
1 answer
286 views

What is the molecular mechanism behind oncotic pressure?

I can't wrap my head around the idea of oncotic pressure and osmolarity, logically. I imagine a blood vessel. It is filled with proteins, like a ton of proteins and solutes. So this means, according ...
Paze's user avatar
  • 703
2 votes
1 answer
110 views

Calculate IC50 from fluorescence kinetic

I have an assay in which a fluorescence signal is generated when the enzyme reaction progresses. The fluorescence signal increases until a maximum is reached. Than it keeps constant. The first 1 h ...
raptorlane's user avatar
1 vote
1 answer
196 views

How to calculate concentration of a protein based on known concentration and mw of other protein

I have a Peptide A (mw = 5074Da), the table below showed measured concentration by Qubit from 5uM up to 80uM solution. All under 20uL solution. Below is the standard plot for Peptide A (not sure if ...
littleworth's user avatar
1 vote
1 answer
158 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 ...
0x90's user avatar
  • 924
0 votes
1 answer
118 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 ...
Aditya Shrivastava's user avatar