Questions tagged [proteins]

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

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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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34 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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107 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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65 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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102 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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54 views

Is there a model for (quality of) two-component-polymerization (dependent on e.g. concentration)?

Sadly my chemistry background is only from high school (I'm a roboticist), but I try my best to explain the problem: Situation: Lets say I have two water based solutions/suspensions. One contains ...
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1answer
315 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 ...
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69 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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28 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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67 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 ...
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123 views

Are there super(calorie-)dense foods?

It’s commonly reported that there are 9 kilocalories per gram of fat, 7 per gram of alcohol, and 4 per gram of carbohydrates or protein. But these figures (with the exception of that for alcohol, ...
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1answer
212 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 ...
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23 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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25 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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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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33 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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22 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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124 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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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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34 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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76 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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78 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 ...
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458 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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38 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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376 views

NAMD free energy calculations (FEP, Alchemical)

I am trying to calculate the absolute free energy of a protein-ligand-complex using the free energy perturbation theory. Following the alchemical route in this tutorial, I have calculated eight MD-...
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38 views

Effect of protein hydrophobicity on metal interaction

I'm studying how metals and proteins interact (metal-protein complexes). I've found that almost all proteins could bind with metal at higher $\mathrm{pH}$ values, but also found some proteins showed ...
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112 views

RCSB PDB - how to choose between multiple copies of the same protein?

I want to map the location of missense mutations on a protein, SERPINB3. I intend to do this using PyMol and download the protein structure from RCSB PDB. However, ...
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34 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 ...
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31 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 ...
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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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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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58 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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37 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 ...
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84 views

Do proteins have a smell?

Proteins are heavy and not so volatile. Does it mean that pure proteins do not have a smell?
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772 views

Why do Bence-Jones proteins behave differently in urine heat test?

The preliminary test for proteinuria (proteins in urine) is precipitation/turbidity on heat due to denaturation. This turbidity should not disappear when 10% acetic acid is added - to differentiate ...
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157 views

Energy required to break salt bridges in peptides and proteins

Is there a way to calculate the energy required to break a salt bridge in a peptide or on the exposed surface of a protein in aqueous solution? Is there any useful literature on this topic? I'm ...
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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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27 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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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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21 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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54 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
65 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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What exactly is meant by the structures 2-alpha beta and alpha 2-beta 2?

In the context of protein quaternary structure. What exactly is indicated by 2αβ and α2β2 structures? What distinguishes the two forms and is this nomenclature only used for a dimer of dimers?