Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
96
questions
0
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0answers
15 views
Shear simulations of protein in water with Gromacs [on hold]
Hi I am doing protein with water simulations. I am trying to shear the box using deform mdp option. It works for 0.001nm/ps but if deform the box at higher rate for example 0.1 nm/ps or 1nm/ps this is ...
3
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2answers
367 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
1
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2answers
56 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 ...
-1
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1answer
26 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 ...
0
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1answer
67 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 (...
1
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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 ...
-1
votes
1answer
15 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 ...
0
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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
76 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 ...
1
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0answers
17 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
120 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
vote
1answer
30 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
28 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
78 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
74 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
40 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
233 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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vote
0answers
26 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 ...
1
vote
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
votes
1answer
662 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 ...
-2
votes
1answer
55 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?
1
vote
1answer
356 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
votes
2answers
48 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
283 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 ...
1
vote
1answer
75 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
230 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 ...
-1
votes
1answer
199 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
105 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
votes
1answer
3k 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
votes
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
482 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 ...
0
votes
1answer
75 views
How to read these graphs and what are they called?
How does one interpret/read the following graph (found here) as well as on wikipedia or
What are these called?
3
votes
0answers
57 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 ...
4
votes
1answer
340 views
Mono-oxidized and dioxidized tryptophan
I'm translating a Russian text in which there is the following diagram of tryptophan degradation:
Further on in the text, hydroxytryptophan is called "the mono-oxidized form" (моноокисленная ...
8
votes
2answers
545 views
Why aren't chaperones considered catalysts?
I'm reading about protein folding on Wikipedia and I stumbled on a bit about a class of proteins called chaperones that aid in the folding of proteins by:
...reducing possible unwanted aggregations ...
15
votes
1answer
2k views
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 $\mathrm{d^6}$...
0
votes
1answer
792 views
Is protein folding thermodynamically favourable? If yes.. why? [duplicate]
The second law of thermodynamics dictates that the sum of entropy of the universe is always increasing. Is the process of protein folding a spontaneous process which is increasing the entropy? Is this ...
4
votes
1answer
213 views
How to measure a distance along the surface of a protein in a PDB
I would like to measure the distance between two active sites in a protein complex (pdb), but I do not find a straightforward way to do it.
To be more precise I need the distance along the surface ...
4
votes
1answer
704 views
Using baking soda paste (alkaline) to “neutralize” honeybee venom (acidic). Is this scientifically sound?
I recall reading (courtesy: my 9th grade Chemistry text-book, chapter Acids, Bases and Salts), something along the lines of:
Bee venom is acidic. This is why the area of skin (stung by a bee) is ...
2
votes
2answers
159 views
Why is the E2 protein important for protein degradation?
In the ubiquitination process, the E2 protein transfers ubiquitin from E1 to E3. Why can't E1 work with E3 directly to tag some protein with ubiquitin? Going further, why can't one of the E(1-3) ...
3
votes
1answer
147 views
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 ...
4
votes
0answers
102 views
How to make a sephadex slurry
I want to purify crude alpha-amylase with column chromatography. I am using a spehadex 75, But for some reason I can't find any information on how to make the slurry.
I can quickly find tons of ...
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votes
1answer
83 views
Collagen: similarity of human to fish and meat amino acids [closed]
I am looking for a collagen supplement for my partner who has joint pain, bone pain, fatigue associated with ligaments, flaccid skin problems, and is just over 40. As she does not eat fish or meat, ...
2
votes
0answers
384 views
proteolysis - how to determine the partial or completeness of the cleavage reaction?
Though the question is about biomolecules, we agree the underlying functions, formation, degradation etc come down to chemistry, (then physics and maths). I am posting it here to receive an ...
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0answers
79 views
Do proteins have a smell?
Proteins are heavy and not so volatile. Does it mean that pure proteins do not have a smell?
6
votes
3answers
956 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:
...
2
votes
0answers
35 views
Antiprion effectiveness of phenol
I am investigating ways to reliably decontaminate instrumentation that has come into contact with mammalian prions. Chaotropic salts and extreme pH are good at inactivating prions by disaggregating ...
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0answers
2k views
Terminology: what's the difference between “monomer” and “protomer”?
Using definitions from Wikipedia, a protomer is defined as "the structural unit of an oligomeric protein. It is the smallest unit composed of at least two different protein chains that form a larger ...
5
votes
1answer
702 views
Using electronegativity and atomic size to compare acidity of cysteine with serine
In proteins, the alcohol group of serine is generally more difficult to deprotonate than the thiol group of cysteine.
Serine and cysteine respectively:
In the literature, the explanation given is ...
