Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
57
questions with no upvoted or accepted answers
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Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?
I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
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Why are S-thiocarbamates less toxic than carbamates?
According to Haley and Rhodes, neostigmine bromide (alternatively known as Prostigmine) has an LD50 in mice of around 0.165 mg/kg by IV injection. Pubchem claims that this is also the LD50 for ...
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Interaction of trifluoroacetates with acetylcholinesterase
There exists a substance called TMTFA, or 3-(N,N,N-Trimethylammonio)-2,2,2-trifluoroacetophenone. It is known for being able to inhibit acetylcholinesterase at femtomolar concentrations. The TMTFA-...
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Calculating the energy of a molecule using probability distributions
I wish to calculate the energy for a protein where the position of all the C-alpha atoms is known.
One way is to calculate the pairwise distances between the atoms and then look up a probability ...
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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 ...
- 89
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Is there a model for (quality of) two-component-polymerization (dependent on e.g. concentration)?
Sadly my chemistry background is only from high school (I'm a roboticist), but I try my best to explain the problem:
Situation: Lets say I have two water based solutions/suspensions. One contains ...
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Assessing stability of protein used for interaction experiments after changing buffer from tris to HEPES
I have a protein with a theoretical $\mathrm{pI}~9.0$ currently stored in $\pu{25 mM}$ tris and $\pu{250 mM}$ $\ce{NaCl}$ $(\mathrm{pH}~8)$ at $\pu{−80 °C}.$ I need to do experiments in HEPES at $\...
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Histidine-Boc deprotectection
A question on Fmoc-solid phase peptide synthesis (SPPS). Is Boc-protected Histidine too labile? Merck's website shows Boc is labile to treatment with Piperidine. Anyone with such experience?
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Differences in AChE inhibition kinetics between VX and VR
According to the referenced paper, VR has an AChE inhibition reaction rate constant almost 4 times that of VX. Interestingly, its reaction rate constant for aging of the enzyme is less than that of VX,...
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Normal Mode Analysis of proteins
I'm trying to do Normal Mode Analysis for my MD trajectory. I'm following Amber tutorial (http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm) which uses an example of estrogen ...
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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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Are there super(calorie-)dense foods?
It’s commonly reported that there are 9 kilocalories per gram of fat, 7 per gram of alcohol, and 4 per gram of carbohydrates or protein. But these figures (with the exception of that for alcohol, ...
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Positive charge on a zwitter ion at pH=7?
I faced this question. But I am having some problems understanding the solution to this:
How can the negative charge on the peptide vanish on $\pu{pH = 7}$? Suppose, we have some $\ce{H+}$ donor on ...
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Reason for differences in AChE aging/reactivation kinetics between neutral and charged organophosphorus inhibitors
According to the referenced papers, acetylcholinesterase that has been inhibited by an organophosphate possessing thiocholine as its leaving group is more susceptible to reactivation by oxime ...
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How are enzyme inhibition constants assayed for "multi-inhibitors"?
Suppose there is a suicide inhibitor of an enzyme that reacts with the enzyme to form an inactive enzyme and another product. This "Another product", however, is capable of acting as a ...
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