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 $\mathrm{d^6}$...
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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:
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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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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
user28429
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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 ...
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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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user93950
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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 ...
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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 ...
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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 ...
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