Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
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How is it known that proteins are polymers of amino acids?
I read the following here.
In 1902, Emil Fischer and Frank Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one ...
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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 ...
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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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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 ...
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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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Testing whether an unknown powder is wheat gluten (at home)?
Last week, I ordered wheat gluten to make seitan. I received some powder and attempted a recipe, which mixes 100g of water with 100g of gluten to form a sticky dough. However in my case, I only got a ...
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Calculate IC50 from fluorescence kinetic
I have an assay in which a fluorescence signal is generated when the enzyme reaction progresses. The fluorescence signal increases until a maximum is reached. Than it keeps constant. The first 1 h ...
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What can I do if a peptide won't go in solution in a biological assay?
I have working on the realisation of on assay, that is intended to examine the activity of a protein. The assay works in a way, in which the product of the target enzyme is transfered by a support ...
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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
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Non-toxic alternative to borax for use in slime chemistry?
I understand that sodium tetraborate decahydrate ($\ce{Na2B4O7•10H2O}$) and water is the primary binder for PVA glue based slimes.
We have learned borax is not good for the ground water, or marine ...
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Effect of presence of competitive inhibitor on observed reaction constant
Suppose there is a solution of enzyme, its substrate, a competitive inhibitor, and a suicide inhibitor. The reaction rate constant for the reaction of the suicide inhibitor with the enzyme is known. ...
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Effect of competitive inhibitor on substrate inhibition
In an enzyme that undergoes substrate inhibition, how would the presence of a competitive inhibitor affect said substrate inhibition? Would the substrate concentration at which substrate inhibition ...
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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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Why Does Milk Seal Sidewalk Chalk?
I work at a public library and we recently had a sidewalk chalk hour for families. Someone gave us a tip that if we brush milk with a paintbrush over the finished chalk drawings, it helps seal them ...
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Why does this lysozyme powder not look crystalline?
I am very new to protein crystallography and visualization. I have been asked to take photos through an optical microscope of the lysozyme powder directly as-is from the supplier. I suspended some of ...
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By what mechanism does amylase catalyze hydrolysis?
I've recently been learning bits and pieces of starch metabolism, and am wondering if anyone could explain exactly what is going on when alpha or beta amylase "cleaves" the 1-4 glycosidic ...
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Does the word "restraint" have any special meaning in the case of protein or biochemistry?
The following screenshot is taken from the book The Encyclopedia of Physical Science & Technology, volume: Biochemistry, Edition: 3rd, Page-197.
The text says:
FIGURE 3 Schematic representation ...
user124269
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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?
user124269
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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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Is it possible to replace 3-mercaptopropionic acid with 2-mercaptoethanol to solubilize avian eggshell membrane to soluble eggshell membrane protein?
Is it possible to replace 3-mercaptopropionic acid with 2-mercaptoethanol to solubilize avian eggshell membrane (ESM) to soluble eggshell membrane protein (SEP)?
Most literature suggested the use of ...
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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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Do whey proteins precipitate with heat?
I am currently studying about the biochemistry of yoghurt and when reading about the effect of heat in milk proteins specifically whey, my book says that heat can denature whey proteins.
So after the ...
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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 ...
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Why is collagen fibre autofluorescent?
Why is collagen fibre autofluorescent? Proteins with increased amount of trp, tyr, phe tend to fluoresce but I don't think collagen fibre has increased percentage of any of them. Some say collagen ...
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Why do hydrogen bonds between atoms of the polypeptide backbone, form both helix and pleated structures, instead of only one structural type?
Proteins have segments of their polypeptide chain/chains that can be repeatedly coiled or folded into helix and pleated structures, respectively. This is due to hydrogen bonds between partially ...
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Why are proteins made up of alpha amino acids and not beta amino acids?
Why are proteins made up of alpha amino acids and not beta amino acids? Or gamma amino acids? My idea on this would be that a world with beta or gamma amino acids would be too complicated? Is that ...
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what is the meaning by 'species' of glycine? [closed]
The question ask for the species of the (i) glycine hydrochloride (ii) glycine titrated with NaOH. When they mentioned 'species', what did they mean by it?
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How to calculate absolute charge of a protein [closed]
My understanding is that hydrogen bonds formed by proteins require the NH2 / COOH to be neutral. Hence to find out when the hydrogen bonds are the strongest will depend on the absolute charge of the ...
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How is geometry optimization of small molecules different from the protein folding problem?
My layman's understanding is that finding the ground state geometry of small molecules is "hard". I don't have a good sense of how hard though. I suppose there are applications where methods ...
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Contaminants in Ion Exchange Chromatography significance?
I am a high school senior and decided to do a project on the essential amino acid composition of varying vegan protein mixtures. I have run into a problem concerning protein purification. One of the ...
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Any cheap way to test whether a given powder has high protein content?
Protein powders are used as dietary supplements. The photo below is for whey protein powder, which usually has about 24 grams of protein per scoop:
Image: © jirkaejc/Getty Images
Unfortunately, many ...
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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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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?
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How does one derive a KD from an equilibrium titration experiment? I am definitely making a mistake somewhere
Any help would be greatly appreciated. Thank you in advance.
If I have an antibody A and a target B, and experimentally titrate the antibody against a single concentration of B, and then measure the % ...
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What does the word "dynamics" mean in the context of proteins or biomolecules in general?
What does it mean by “dynamics” when we say “dynamics of protein” or “dynamics of biomolecules”? For instance, McCammon's paper has the title "Protein Dynamics" [1]. What does the word “...
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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 ...
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Can we compare absorbance of two peptides when the read concentration from Qubit Protein Assay are different?
I have two peptide A and B. And I would like to know the solubility level of these peptide in certain solute. For that purpose I use Qubit Protein Assay.
The Qubit readout I get is this:
Note that ...
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How to calculate concentration of a protein based on known concentration and mw of other protein
I have a Peptide A (mw = 5074Da), the table below showed
measured concentration by Qubit from 5uM up to 80uM solution.
All under 20uL solution.
Below is the standard plot for Peptide A (not sure if ...
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Why does a big protein move during gel electrophoresis but to a lesses extent through a size exclusion column?
A big protein going through gel electrophoresis will be forced through the gel, it will drift a small way and will show on the top of the gel, while in size exclusion, the big protein is not forced to ...
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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 ...
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How does protein denaturation speed change with temperature? [closed]
So this is something that I had been wondering since middle school. We "roughly" know that protein denaturation occurs above a temperature of 72 degrees Celsius, and is the reason why it is ...
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Is the 3D spacing arrangement of atoms in chemical bond always unique?
I would like to ask if the 3D spacing arrangement of atoms in chemical bond configurations are always unique, please?
For example, glycine consists of the set of atoms HHNCHHCOOH. Does there exist a ...
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Best description of forces/ mechanisms that stabilize the interaction between a hydrophobic protein binding pocket and a hydrophobic ligand
This is a more theoretical or definition question that is related to the terms "hydrophobic effect", "hydrophilic interaction", and "van der Waals' forces" (and others I ...
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How does ethanol separates salts from proteins [closed]
Grad student here messing around with famed TRIzol isolation protocol and looking to optimize the protein yield at the end. There are more direct ways to get protein from a sample but I like getting ...
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Troubleshooting an AutoDock Vina error on Chimera: “Could not find an atomic number for Hn Hn”
After minimizing a ligand (prepared with MarvinSketch) and preparing a target enzyme to dock said ligand onto (collected from RCSP PDB — 5DGN (Crystal structure of human FPPS in complex with compound ...
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Q-TOF vs Q-orbitrap MS data
I recently had the opportunity to analyze the same (intact protein) sample on an Agilent QTOF and a Thermo Q-Exactive, and noticed that in addition to having a moderately higher resolution the ...
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Loss of entropy and solvation energy in proteins
I am reading a chapter on protein stability. One section outlines the role of salt bridges or ion pairs in the stability of a protein. The excerpt goes as follows (italization added for emphasis):
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What do sequence numbers in PDB files actually mean and why don't they match the sequence?
I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry ...
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Hypothetical Alternative for Nitrogen [closed]
Recently I was surfing the internet and I found thisWikipedia article.
It states that
The element silicon has been much discussed as a hypothetical alternative to carbon. Silicon is in the same group ...
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What is "tail" in case of secondary structure of protein? [closed]
What is a "tail" in the case of the secondary structure of a protein?
How does it influence the "protein assignment" task?
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