Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
115
questions
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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 ...
4
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1answer
27 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
135 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
114 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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1answer
194 views
How to use Google’s Alpha-fold to predict a two-protein complex?
Alpha-fold won the CASP competition last year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence.
Google has released its code a few weeks ...
2
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0answers
64 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 ...
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1answer
57 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 ...
6
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1answer
128 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 ...
3
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0answers
50 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
56 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;
...
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1answer
23 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....
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1answer
37 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
82 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
199 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
144 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
43 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
52 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
votes
1answer
193 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
49 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 ...
3
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2answers
462 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
58 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
27 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
136 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
16 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
33 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 ...
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0answers
13 views
Do I have to take the sample buffer into account when determining the protein concentration?
I am measuring the absorbance of a protein that is dissolved in a certain buffer. I know the extinction coefficient for this protein in this buffer.
In order to be in the good absorbance range I have ...
4
votes
1answer
78 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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0answers
21 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
41 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 ...
4
votes
3answers
200 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 ...
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1answer
33 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
34 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
votes
1answer
120 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
votes
1answer
81 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
45 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 ...
5
votes
1answer
412 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
41 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
33 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
891 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
58 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
521 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 $L$ ...
3
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2answers
72 views
Why does the isoelectric range decrease as an Alanine chain grows longer?
The pK1 and 2 values for alanine are 2.3 and 9.7. In the dipeptide Ala-Ala, they are 3.1 and 8.3 and in tri-peptide Ala-Ala-Ala, they are 3.3 and 8.0. Why does this trend in pKa values exist? Why does ...
8
votes
1answer
287 views
How to dock aggregated structures comprised of “elementary” protein units like LEGO pieces?
There are proteins with intrinsic symmetries. For example:
I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
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1answer
86 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 ...
6
votes
1answer
262 views
How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
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votes
1answer
234 views
How to visualize a crystal from a unit cell PDB and how to draw the unit cell's axes? [closed]
I am looking at the following PDB experimental data:
Length (Å) Angle (°)
a = 155.72 α = 90.00
b = 155.72 β = 90.00
c = 106.16 γ = 120.00
I find it hard to ...
6
votes
1answer
107 views
Biomolecular energy functions and entropy
From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
3
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1answer
5k views
What happens to the t-butyl cation in the TFA deprotection of a t-butyl ester?
I am a first-year chemistry graduate student and I am currently learning how to synthesize proteins. I have reached a stage in the process where I need to deprotect a carboxylic acid moiety protected ...
2
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0answers
76 views
Calcium concentration in NMDARs e Nitric Oxide Synthase
My question is related to calcium $\ce{Ca^{2+}}$ concentration in NMDA receptors and nitric oxide synthase. I've found a very simple model that describes how the time change of calcium can be related ...
2
votes
1answer
668 views
What is the difference in the effect of DTT (Dithiotreitol) and SDS (sodium dodecyl sulfate) for PAGE?
In class, we have studied that when running a polyacrylamide gel with our protein sample to separate the proteins by molecular size, we can use several techniques, among which we have denaturing PAGE ...
