Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
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Fe(II) NMR of deoxy-hemoglobin
As the article mentions, Fe-NMR is generally never carried out because of its low sensitivity. However, the article also says Fe(II)-NMR is possible because Fe(II) is sufficiently diamagnetic. Are ...
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2answers
48 views
Why don't proteins form branched polymers?
My reference book (Princeton Review for SAT Chemistry Subject Test) mentions that:
Proteins and carbohydrates are both polymers; however, only
carbohydrates commonly form branched polymers. Glycogen ...
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19 views
Calculating stock solutions
In the question it mentions that the protein forms dimers. Does that affect the RFM of the protein when I use it in my calculations (10kDa). For example for part a, would it just be. 0.01/10, 000 = 1 ...
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4answers
89 views
If I hard boil eggs in a pressure cooker, will I get the same results regardless of altitude?
This seems like it should be obvious but for some reason (my chemistry is very rusty) I'm having a hard time articulating why the hardboiled egg recipe in an instant pot should yield the same results ...
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1answer
60 views
Turn Alpha Helix into Beta Pleat
Beta sheets have the peptide backbone parallel whilst the alpha helix has a curled backbone.
But the thing I can't get around my head is why would the same protein always fold into one of these shapes?...
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72 views
Which amino acids can be totally synthesized? [closed]
I can't find information regarding which amino acids (say the proteinogenic ones or in general) can be totally synthesized. Is there a reference?
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36 views
Why is it rational that salt-bridges (in proteins) are described as a combination of H-bond and ionic bond?
This is a fundamental question that came to me as I was trying to draw the electrostatic attraction between Aspartate (D) and lysine (K). I have always considered the charge on nitrogen, in the lysine ...
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1answer
26 views
How to tell the difference between lysine and the N-terminal amino acid in DNP labeling?
The N-terminal amino acid of a protein can be identified by reacting the N-terminal amine with FDNB (1-fluoro-2,4-dinitrobenzene), or Dansyl chloride, or Dabsyl chloride, then digesting the protein ...
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29 views
Does HI-6 form a covalent adduct with acetylcholinesterase?
According to sources provided below, the oxime HI-6, or Asoxime Dichloride, as it is also called, besides being a reactivator of acetylcholinesterase that has been inhibited by organophosphorus ...
2
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1answer
72 views
Is a beta pleated parallel sheet always formed from more than one peptide?
I can conceptually grasp the beta pleated anti-parallel sheet by imagining a curved length of string i.e. one polypeptide, starting with the N- terminus on the left and ending with the C-terminus at ...
2
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1answer
62 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 ...
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1answer
60 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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29 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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25 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
52 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 ...
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99 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-...
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68 views
Peak broadness and artifact peaks in intact antibody MS?
I am having an issue where the MS for my antibody (intact/nonreduced, deglycosylated by PNGase) shows multiple clusters of what appear to be ghost peaks after deconvolution, and the main peak is ...
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31 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 ...
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2answers
61 views
What exactly makes a carbon atom “Ī±” 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 ...
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24 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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18 views
Short description for destriptors output by PaDEL-Descriptor
I am trying to implement this paper & it uses PaDEL-Descriptor to get additional features. To be specific they extracted:
Bond count: number of single, double, triple bond including and excluding ...
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0answers
12 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 ...
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1answer
44 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 ...
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2answers
155 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
146 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
290 views
How to use Googleās 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 ...
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74 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 ...
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2answers
239 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 ...
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0answers
58 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 ...
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1answer
70 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
76 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
40 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) ...
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2answers
220 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
173 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 ...
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83 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
53 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
206 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 ...
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1answer
51 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
528 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
61 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
30 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
312 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
19 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
113 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
79 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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2answers
63 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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49 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 ...
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3answers
243 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 ...
