Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
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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
17 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
33 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
78 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
191 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
122 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
38 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 ...
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1answer
50 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
189 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
42 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
431 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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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
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 ...
2
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1answer
110 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
20 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
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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 ...
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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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30 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
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3answers
181 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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33 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
107 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
80 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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43 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 ...
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1answer
347 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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27 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 ...
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1answer
829 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
471 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 $L$ ...
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2answers
52 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 ...
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1answer
286 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
84 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
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1answer
255 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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1answer
223 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 ...
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1answer
106 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
4k 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 ...
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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
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1answer
626 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 ...
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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
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0answers
58 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
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1answer
369 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
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2answers
569 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 ...
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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
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1answer
859 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
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1answer
226 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
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1answer
781 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 ...
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2answers
167 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) ...
