Questions tagged [proteins]

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

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1
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2answers
69 views

To which extent is protein folding conserving subprotein structures?

I am actually a pure mathematician, who stumbled over this paper «Protein-Folding Analysis Using Features Obtained by Persistent Homology» by Ichinomiya et al. (Biophys. J. 118, 2020, 2926-2937; link),...
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1answer
36 views

In solid-phase peptide synthesis, why are the formation of aspartimides a problem but not “glutamides”?

I'm studying solid-phase peptide synthesis (SPPS) at the moment, and a common problem is the formation of aspartimides, which disrupt the synthetic process. I understand how they form and why are they ...
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1answer
547 views

SARS-CoV - relative size of the spike protein

I am taking an online course in image analysis and have been asked to use the attached image to determine the size of the SARS-S protein of the SARS-CoV relative to the total of its proteins. However, ...
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0answers
36 views

Is there a computer program capable of showing protein conformational changes based on pH?

As it is known, changes in pH change the attractions between the groups in the side chains of the protein. Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ ...
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4answers
638 views

Ramachandran plot Phi(ϕ) Psi(ψ) dihedral angle Convention for Zero, Positive and Negative value- old and new

Update: possible duplicate: What is the precise definition of Ramachandran angles?. Question modified. G.N. Ramachandran et al, in their own work (PMC) (DOI), did not used phi(ϕ) and psi(ψ) as we use ...
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1answer
72 views

Carbon atoms types in amino-acids [closed]

I'm looking for a table or another kind of schema where I can find which type of carbon atoms (sp3, sp2 etc.) are present in each amino-acid. In my biochemistry books these informations are not ...
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1answer
27 views

Do phosphoryl thiocholines, their uncharged analogs, and other organophosphates, interact differently with Acetylcholinesterase?

As asked in the title, would the various salts -such as hydrochloride or methyl iodide- of V-Agents interact any differently with acetylcholinesterase compared to the neutral compound? For instance, ...
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0answers
17 views

How carbon nanotube sensors works?

How carbon nanotube sensors works? Is the protein (or chemical compound used as part of the sensor) placed inside the tube or where is it placed? and how is the technology used to place the protein ...
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12 views

Improving protein solubility in Water solvent (food science)?

I am trying to form a solution involving mixing my protein shakes. I am using a vegetable protein and it has poor solubility. Is their another protein I could use to entrap it to improve solubility? ...
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32 views

Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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23 views

Differences in AChE inhibition kinetics between VX and VR

According to the referenced paper, VR has an AChE inhibition reaction rate constant almost 4 times that of VX. Interestingly, its reaction rate constant for aging of the enzyme is less than that of VX,...
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382 views

Why does denaturation of albumen protein cause pH of solution to increase?

I'm interested in the denaturation of proteins by alcohols, specifically by ethanol. I have devised a simple experiment in which I inject solutions of ethanol (of variable concentrations) into ...
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0answers
14 views

Structure-Activity Relationship of Chlormephos and Parathion

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/k. ...
2
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0answers
30 views

How can DI water inhibit peroxidase activity?

I'm troubleshooting an IHC staining issue, and according to Thermo-Fischer's website, "Deionized water can sometimes contain peroxidase inhibitors that can significantly impair enzyme activity.&...
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1answer
33 views

Determination of metal state from protein X-ray structure

Many proteins or enzymes contain metal ions within their active sites. These metals are often directly involved in the reaction catalysed bu the enzyme. In certain cases the function is well known and ...
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1answer
32 views

Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group

I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation ...
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30 views

Why is Chlormephos highly toxic despite requiring metabolic activation?

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/kg. For ...
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1answer
123 views
+50

Are all protein tetramers considered to be “dimers of dimers”?

Is every tetramer thought to be a dimer of dimers? Because even if every subunit is unique in structure, it could be a heterodimer of heterodimers? Or is the term "dimer of dimers" reserved ...
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22 views

Right conductivity of protein sample for Protein A purification of human IgG?

A sample from a cell culture has some IgG and this is to be purified using protein A chromatography. Based on the chromatography handbook from GE-Healthcare/Cytiva, the protein sample should have &...
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19 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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1answer
117 views

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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49 views

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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41 views

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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39 views

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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0answers
24 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
115 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
120 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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1answer
373 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 β-sheet, the polypeptide strands are arranged such that a $\ce{C=O}$ and an $\ce{NH}$ from adjacent strands face each ...
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2answers
188 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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22 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
97 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
68 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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77 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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211 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
224 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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37 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
119 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
70 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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2answers
99 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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0answers
33 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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0answers
34 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
67 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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0answers
120 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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0answers
36 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 ...
2
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2answers
140 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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0answers
31 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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0answers
13 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 ...
5
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1answer
98 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
203 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
194 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....