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Questions tagged [proteins]

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

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Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?

I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
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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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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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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 ...
Chris's user avatar
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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 ...
Geek's user avatar
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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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Assessing stability of protein used for interaction experiments after changing buffer from tris to HEPES

I have a protein with a theoretical $\mathrm{pI}~9.0$ currently stored in $\pu{25 mM}$ tris and $\pu{250 mM}$ $\ce{NaCl}$ $(\mathrm{pH}~8)$ at $\pu{−80 °C}.$ I need to do experiments in HEPES at $\...
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Histidine-Boc deprotectection

A question on Fmoc-solid phase peptide synthesis (SPPS). Is Boc-protected Histidine too labile? Merck's website shows Boc is labile to treatment with Piperidine. Anyone with such experience?
Science123's user avatar
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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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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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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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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, ...
SudoSedWinifred's user avatar
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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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Reason for differences in AChE aging/reactivation kinetics between neutral and charged organophosphorus inhibitors

According to the referenced papers, acetylcholinesterase that has been inhibited by an organophosphate possessing thiocholine as its leaving group is more susceptible to reactivation by oxime ...
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How are enzyme inhibition constants assayed for "multi-inhibitors"?

Suppose there is a suicide inhibitor of an enzyme that reacts with the enzyme to form an inactive enzyme and another product. This "Another product", however, is capable of acting as a ...
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Is there any special meaning to the angle between two peptide planes?

Take a look at the following image: Is there any special meaning to the angle between two peptide planes (marked with red arrow heads)? If so, why isn't a specific name (like phi, psi, etc.) given?
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Protein/polypeptide nomenclature, residue number superscripted or not?

When referring to a specific residue number of a given amino acid, should the residue number be superscripted or simply affixed? For example, When referring to a Tryptophan residue at the 147th ...
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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 ...
Dare to ask-I dnt mind punishm's user avatar
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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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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 &...
Keine's user avatar
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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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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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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 ...
CuriousTree's user avatar
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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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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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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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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 ...
Angelo Giuseppe Spinosa's user avatar
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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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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 ...
aag's user avatar
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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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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 ...
user36264's user avatar
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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, ...
Slavatron's user avatar
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Why is AChE inhibited by triflates not susceptible to reactivation?

According to a report, certain esters of trifluoromethanesulfonic acid are capable of acting as irreversible inhibitors of acetylcholinesterase. Also, 3-PAM, while capable of reactivating AChE ...
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How come in biuret test the copper sulfate doesn't react with the sodium hydroxide?

As I understand the color change in the biuret test is due to the formation of a complex between the peptide (with more than 2 peptide bonds) and the $\ce{Cu^2+}$ ion, from $\ce{CuSO4}$. But before ...
CaptainAmerica Whyso's user avatar
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What are the available cheap proteins that are much less soluble than BSA

Currently, as a beginner, I'm performing solubility analysis (with UV based spectrometry) for practices. The protein I'm using now is BSA. This is widely used and cheap option. I'm now looking for a ...
littleworth's user avatar
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Spectroscopic methods for quantifying peptides/proteins with or without Tryptophan or Tyrosine content

I have several peptides (20-50 amino acids long) which I want to quantify the solubility/concentration in a solvent at certain temperature and pH. These peptides may or may not contain Tryptophan or ...
littleworth's user avatar
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What do natural hybrids of peptides and nucleic acids look like?

Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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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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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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1 vote
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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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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 ...
Ahmed Rast's user avatar
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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 ...
Michelangelo's user avatar
1 vote
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202 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 ...
ThermoRestart's user avatar
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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 ...
prashanth manohar's user avatar
1 vote
0 answers
113 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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1 vote
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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 ...
Polisetty's user avatar
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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 ...
JustSomeBoy's user avatar
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Strange Binding Curve DNA:Protein Interaction

So I did some DNA:Protein Interaction studies using Fluorescence Polarisation Assays. I have fluorescently labelled DNA and add my Protein of interest. Down below you see an exemplary plot of the ...
TheChemist's user avatar
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What is the industrial alternative to dialysis?

I want to separate a recombinant protein from imidazole. Both of them are in a solution of pH 8. I was thinking of using ion exchange chromatography with cationite: the imidazole being positively ...
MathEnthusiast's user avatar