Questions tagged [proteins]

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

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2
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1answer
73 views

How to predict amine donor in biochemical reactions (whether glutamine or aspartate)?

In biochemical reactions amine $(\ce{-NH2})$ transfer is done in multiple pathways (e.g. urea cycle, purine biosynthesis etc.). In many of the situations glutamine donates amine group (e.g. xanthosine ...
3
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2answers
99 views

What is the mechanism of AChE inhibition by Onchidal?

A naturally-occuring neurotoxin, called Onchidal, produced by a species of sea slug acts as an irreversible inhibitor of acetylcholinesterase. The structure of Onchidal is presented below: How and ...
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0answers
33 views

What is "protein redox conformation"?

From an article by Frye et al. [1]: Reduced glutathione (GSH) is the major intracellular redox buffer and is essential in free radical scavenging, redox homeostasis, maintenance of protein redox ...
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0answers
37 views

Hydrolysis of phosphoryl-oximes

When acetylcholinesterase that has been inhibited by an organophosphorus compound is reactivated by an oxime, a phosphoryl-oxime is formed, which is then somehow hydrolyzed in the blood. One study ...
3
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1answer
67 views

Can aged acetylcholinesterase be reactivated?

it is a well-known fact that certain phosphorus compounds can inhibit the enzyme acetylcholinesterase, and that the treatment of poisoning with such compounds is administration of atropine and some ...
5
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0answers
122 views

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-...
2
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0answers
36 views

Why are carbamates capable of inhibiting acetylcholinesterase?

Certain carbamate compounds, such as the insecticide carbaryl or the Edgewood carbamates such as EA-3990, can inhibit the enzyme acetylcholinesterase. Unlike organophosphorus compounds, however, they ...
2
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2answers
181 views

What exactly makes a carbon atom "α" in a protein residue?

I'm a computer scientist and have no biochemical background, but was working on a project recently that had me going through a lot of protein residues for one reason or other. Feel free to correct me ...
3
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0answers
32 views

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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0answers
13 views

Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
5
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1answer
114 views

What is a secondary shell in an enzyme?

I've searched the internet for a definition of what the different shells in enzymes/proteins are and haven't found a good answer. This Nature article, which is about an enzyme that catalyzes Kemp ...
3
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2answers
219 views

Generating electron density from protein coordinate (PDB)

Normally protein coordinates are generated from electron density, such as that from X-ray scattering experiment. In my case, I want the reverse - PDB to electron density mesh. I thought it was more ...
2
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1answer
236 views

Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]

I am completely new to using OpenBabel software. I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
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2answers
2k views

How to use Google’s Alpha-fold to predict the structure of a two-protein complex?

Alpha-fold won the CASP13 and CASP14 competitions last year and this year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence. Google has ...
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0answers
79 views

Differences in efficacy of oxime reactivators in organophosphate poisoning

Compounds containing an oxime functional group, such as 2-PAM and obidoxime, are used in the treatment of poisoning with organophosphorus compounds. These oximes reactivate the enzyme ...
1
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1answer
59 views

Can someone explain the article below? [closed]

This is the article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611670/ I'm not a Chemist, so I can't understand the article very well. The conclusion states that the molecules tested should not ...
9
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2answers
338 views

AChE Aging time of organophosphorus compounds containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the OPC phosphorylates the serine-203 residue of the enzyme. If the enzyme is not reactivated ...
4
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0answers
72 views

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 ...
1
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1answer
134 views

What is the correct term of a chemical formula for very large molecules if not just "chemical formula"? [closed]

I know that many molecules, wihch I as a non chemist, might define as "small" if their two dimensional diagram can be sketched on an A4 page, are often formulated; ...
1
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1answer
189 views

Acid-Temperature coagulation of milk

I was making coffee with a cup of boiling milk which was 2 days old. I used instant coffee powder and some sugar for the making of it. Tried to make a very hot coffee but usually prefer medium hotness....
1
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1answer
44 views

Estimating protein binding and disassociation

I don't have a background in the area of drugs or pharmacokinetics/Pharmacodynamics but I am trying to understand about protein binding. I was going through this paper. If $C_b$ is the ...
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2answers
85 views

Does water in big cities get heated (boiled) for treatment?

I live in Bangkok and read how water comes to customers here: I understand from the chart that water go through Thon Buri treatment plant (west Bangkok) and Mahasawat treatment plant (east Bangkok) ...
5
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2answers
606 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 ...
4
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3answers
263 views

Fitting multiple pKa's

I have three histidine residues that are next to each other in a protein. When I compute the fraction of unprotonated states for each individual histidine as a function of $\mathrm{pH}$ my titration ...
4
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0answers
148 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 ...
0
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1answer
69 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 ...
4
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1answer
236 views

What does "parallel in-register" mean for a protein structure in a fibril?

I read a paper by Ross and Poirier [1, p. S12] which has the following lines (see section Commonalities of amyloid structure) that describe the structure of protein in a fibril: The most ...
2
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1answer
84 views

Why can DAP be used to elute a protein in affinity chromatography?

A little background: as part of my bioinformatics degree I have to take Protein Chemistry course, but I miss chemistry basics (have CS background), so that's why I'm asking the following question. We ...
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2answers
629 views

What dictates cathode vs anode nomenclature use?

what was the justification for the use the cathode and anode terminology in IEF? There is no redox taking place in IEF, just proteins interacting with an electric field
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2answers
77 views

Can I normalize my data in order to compare it?

I have three chromatograms of the same eluted protein but at different concentrations, since it got diluted during purification process) and hence peak maximums at very different absorbances. The ...
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1answer
41 views

How should I interpret and present my total protein amount? [closed]

I have a problem. I have purified a protein with method A and then B. After method A I have a protein concentration of 20 mg/ml and after method B a concentration of 18 mg/ml. Method B is dialysis and ...
2
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1answer
743 views

How to pool fractions after chromatography?

I used chromatography to purify my protein and now I have fractions with different concentrations ranging from 1-16 mg/ml. Should I pool all these fractions or just the ones with high concentration (...
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0answers
21 views

Choice of buffer pH to avoid aggregation

I want to purify IgG which has a theoretical pI of 6.4-9.0 with an anion exchange column. I also want to keep the pH of my buffers as low as possible and "outside" the range of the pI to prevent ...
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1answer
449 views

How do I calculate the correct sample concentration for my measurements?

I will measure absorbance for measurement of protein concentration. The sample solutions are prepare in serial dilutions to the volume of 100 uL to obtain a certain concentration of the protein in ...
4
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1answer
81 views

Can a protein complex be a machine? [closed]

Discussing an article with friends we began discussing whether a protein complex that punches holes in cells (membrane attack complex) would be considered a machine. Now, my friends are biochemistry ...
2
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2answers
97 views

Purifying cysteine containing peptides

I would like to purify my peptide having cysteine residue by using HPLC. It is known that thiol containing peptides undergo oxidation and form disulfide linkages. In order to prevent it I used proper ...
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0answers
74 views

Correct Generalization for Adair Equation?

I know how to derive the Adair Equation for n binding sites the long way, writing n+1 mini equations and linking them to relate all sub $K_b$ values to $K_{b-intrinsic}$. Tried to find a general ...
6
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3answers
388 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 ...
1
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1answer
47 views

Chemical Equilibria - Fraction Bound equation based on Kd, [R], [L], [RL], is actually an average?

Let's say 150 stem cells express exactly 150 copies of the same mebrane antigen X. While all differentiated cells express exactly 15 copies of X. To the cell mixture you add a large amount of 0.2 μM ...
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0answers
39 views

Which Flocculant/Coagulant is ideal for harvesting Algae?

While dealing with Algae fit for human consumption (as protein supplements), which is the most suitable coagulant/Flocculant available? Factors to consider: 1) Cost Effectiveness (for instance poly ...
3
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1answer
249 views

Why is casein hydrophobic?

According to this source hydrophobic behaviour occurs when a molecule does not have a charge or is neutral and therefore cannot be attracted to the negative nor positive parts of water. Casein has an ...
3
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1answer
95 views

Can glucose and insulin exist in the same container without reacting?

Someone asked if glucose and insulin could be mixed in the same container and used as an injection to provide a quick energy boost. I'm not interested about the medical part of this question, but just ...
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0answers
64 views

Developing a lab to identify the concentration of casein in organic milk

I am currently attempting to create a feasible lab design that will enable me to identify the concentration of casein protein in organic milk without having to use spectroscopy. Thus far I have ...
4
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1answer
3k views

Why is copper(II) sulfate added drop by drop during the Biuret test?

The Biuret test is a test for proteins. The procedure is to add a strong base, such as NaOH, to dissolve the protein. After that, copper(II) sulfate is added drop by drop into this until a (violet) ...
5
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1answer
1k views

Can =NH2+ in Arginine's side chain form hydrogen bonding at physiological pH?

I know that at physiological pH, Arginine will have its $\ce{=NH}$ protonated to $\ce{=NH2+}$. I was wondering if this $\ce{=NH2+}$ can still form a hydrogen bond by being a donor? And does the ...
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1answer
45 views

Molecular dynamics after modeling a protein loop. Necessary?

Firstly, I am postign this question to both chemistry and physics stacks exchange as I am not sure to which it belongs and to use the benefits from both sites. I have modeled missing loops in a PDB ...
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0answers
36 views

cluster of milk [closed]

I have a problem with milk when we are making yogurt in factory. When the milk pass through the machine it clogs the filter of the machine because the cluster that formed on the filter. My question is ...
4
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1answer
1k views

Is chitin actually protein?

Recently insects are featured as a protein rich source for human nutrition. That humans can really digest chitin through chitinase enzym has been only recently confirmed. But, does the chitin shell ...
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1answer
64 views

Why Greek yogurt has higher protein concentration?

During fermentation, no nitrogen is added and the number of amino acid molecules cannot increase. Why does it have a higher protein concentration than milk?
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1answer
759 views

Formating chemical equations for proteins binding in hugely complex configurations

In a previous question I asked about a simple case, I'm now trying to write equations for proteins that bind multivalently. In the simplest case proteins $A_1$ and $A_2$ can bind to up to two $L$ ...