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Questions tagged [proteins]

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

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3 answers
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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 ...
powerful_bob'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
3 votes
0 answers
28 views

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 $\...
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
2 votes
0 answers
22 views

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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1 answer
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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 ...
Alduno's user avatar
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2 votes
1 answer
110 views

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 ...
raptorlane's user avatar
2 votes
1 answer
71 views

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 ...
raptorlane's user avatar
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0 answers
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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 ...
Don Aborah's user avatar
-2 votes
1 answer
123 views

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 ...
Shannon Strong's user avatar
3 votes
1 answer
101 views

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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2 votes
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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 ...
user73910's user avatar
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6 votes
1 answer
143 views

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 ...
Rachel's user avatar
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10 votes
1 answer
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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 ...
Mack's user avatar
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2 votes
1 answer
87 views

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 ...
Matthew Finger's user avatar
2 votes
2 answers
141 views

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 ...
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2 votes
0 answers
68 views

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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1 vote
0 answers
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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 ...
user73910's user avatar
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0 votes
1 answer
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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 ...
Aina Razali's user avatar
2 votes
0 answers
93 views

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 ...
sat0ri's user avatar
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0 answers
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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 ...
CaptainAmerica Whyso's user avatar
1 vote
0 answers
87 views

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
8 votes
1 answer
297 views

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 ...
Yushi Li's user avatar
  • 197
1 vote
3 answers
402 views

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 ...
Growing6884's user avatar
0 votes
2 answers
534 views

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 ...
saturn20005252's user avatar
-3 votes
1 answer
46 views

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?
Nku's user avatar
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1 vote
0 answers
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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 ...
TheRavenSpectre's user avatar
6 votes
2 answers
238 views

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 ...
theQman's user avatar
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3 votes
1 answer
101 views

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 ...
I do not want to put my name's user avatar
0 votes
1 answer
264 views

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 ...
caveman's user avatar
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5 votes
0 answers
68 views

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 ...
Doe Pual's user avatar
  • 107
3 votes
0 answers
31 views

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
1 vote
1 answer
770 views

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 % ...
Justin's user avatar
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0 votes
1 answer
132 views

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 “...
user avatar
1 vote
0 answers
106 views

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
3 votes
1 answer
174 views

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 ...
littleworth's user avatar
1 vote
1 answer
196 views

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 ...
littleworth's user avatar
0 votes
1 answer
69 views

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 ...
yahel abraham's user avatar
1 vote
0 answers
77 views

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
-4 votes
1 answer
420 views

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 ...
Shikhar Jaiswal's user avatar
5 votes
2 answers
512 views

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 ...
user avatar
2 votes
1 answer
137 views

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 ...
William Wong's user avatar
1 vote
0 answers
51 views

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 ...
TheCodeNovice's user avatar
1 vote
1 answer
632 views

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 ...
Mas's user avatar
  • 447
8 votes
1 answer
2k views

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 ...
oryza's user avatar
  • 133
2 votes
2 answers
233 views

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): ...
Brian Blumberg's user avatar
5 votes
1 answer
209 views

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 ...
Gunther Schadow's user avatar
-3 votes
1 answer
130 views

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 ...
classy_BLINK's user avatar
0 votes
1 answer
77 views

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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