Questions tagged [proteins]

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

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14 views

What is the chemical composition of the liquor from egg-white?

I am following traditional techniques using egg white to make a glaise for gold leaf embossing on to leather. The glaise dries on to the leather, gold leaf is laid on it, a heated diestamp is applied ...
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Protein-Protein binding affinity

I am a complete novice at Protein-Protein interactions but needed a bit of clarity. I have a model that produces binding affinity between a drug and a viral target in terms of Kd values. I want to ...
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Why are isomers of parathion less active acetylcholinesterase inhibitors than paraoxon?

Parathion itself has been found to be a very weak inhibitor of acetylcholinesterase. It normally requires metabolic activation and the conversion into paraoxon in the body to actually start exhibiting ...
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What is the chemical reaction behind ginger milk curd?

Pouring hot milk into ginger juice solidifies the milk. All I know is that ginger juice contains Zingibain that could break down milk proteins into smaller polypeptides. I'm confused as though why is ...
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Why are S-thiocarbamates less toxic than carbamates?

According to Haley and Rhodes, neostigmine bromide (alternatively known as Prostigmine) has an LD50 in mice of around 0.165 mg/kg by IV injection. Pubchem claims that this is also the LD50 for ...
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Molecular dynamics simulation of a protein in acidic medium

I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
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21 views

Reaction rate constants for the inhibition of cholinesterases by various carbamates

Darvesh et al. [1] have conducted a study on the anticholinesterase activity of various carbamates derived from phenothiazine. The authors measured the inhibition rate constants of rivastigmine for ...
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2answers
94 views

How would I make a basic protein folding algorithm? [closed]

On the face of it it doesn't seem especially difficult. Model the amino acids as solid objects linked together. Approximate the 3D force fields around them using a coarse approximation, then set the ...
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1answer
63 views

How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?

Thanks for some online resources (i.e. here) I have an understanding of what X-Ray Crystallography does. By blasting X-Rays at a crystal and recording the scattering patterns on a plate behind the ...
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80 views

Why are hydrogen bonds in an antiparallel beta sheet stronger than those in parallel beta sheets?

Beta sheets are illustrated as such in most diagrams, where: In an antiparallel B sheet, the polypeptide strands are arranged such that a C=O and an NH from adjacent strands face each other, and the ...
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2answers
102 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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20 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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92 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
64 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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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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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
69 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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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 ...
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1answer
82 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 ...
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1answer
64 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
61 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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31 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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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 ...
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1answer
61 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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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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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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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
75 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 ...
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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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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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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
57 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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162 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 ...
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1answer
161 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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How to use Google’s Alpha-fold to predict 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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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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261 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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61 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
76 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
108 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
41 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
83 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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258 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 ...
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194 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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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
62 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 ...
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1answer
212 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
67 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
562 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