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Questions tagged [proteins]

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

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How can I determine if there are π-π interactions between an amide and an aromatic ring in a protein?

In a crystal structure I've determined, a triazole ring on my ligand appears to be stacking with a tyrosine (top in picture): However, there is also an amide, courtesy a glutamine, near it (bottom). ...
Nick T's user avatar
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23 votes
2 answers
4k views

Why is the cyanide ion toxic?

As the title implies, what is the molecular basis of cyanide toxicity? I did some searching around at the CDC and it only states that it prevents cells from using oxygen. I also read how it could take ...
Aubrey Champagne's user avatar
17 votes
2 answers
4k views

What makes heat resistant proteins heat resistant?

We were doing the chapter Biomolecules in class the other day, and a doubt popped up once we reached the section on proteins. We were taught that the stuff that keeps proteins together are: Ionic ...
paracetamol's user avatar
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15 votes
1 answer
5k views

What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?

Deoxymyoglobin ($\ce{Mb}$) is known to have iron in the +2 oxidation state; I believe this was deduced from its magnetic moment, which corresponds to four unpaired electrons in high-spin $\mathrm{d^6}$...
orthocresol's user avatar
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14 votes
2 answers
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Why do unboiled eggs last longer than boiled eggs?

Just like the title says, I watched this video https://youtu.be/CHMY4G9gTPA and then became intrigued.
Nick Lim's user avatar
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10 votes
2 answers
1k views

Why do the physical properties of an egg shell change when the egg shell is exposed to vinegar for a week?

When an egg is kept in vinegar for one week, its hard calcium carbonate shell changes into a soft rubbery membrane. As vinegar is weak acetic acid, how does vinegar change calcium carbonate into a ...
DARYL JOSEPH.G's user avatar
10 votes
1 answer
726 views

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
  • 111
10 votes
2 answers
846 views

AChE Aging time of organophosphorus compounds containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the OPC phosphorylates the serine-203 residue of the enzyme. If the enzyme is not reactivated ...
user73910's user avatar
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9 votes
4 answers
3k views

Does quantum mechanics play a role in protein folding?

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. However, for the initial micro-steps of folding, when an atom, or a configuration of atoms, can ...
yariv's user avatar
  • 101
8 votes
1 answer
298 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
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8 votes
2 answers
834 views

Why aren't chaperones considered catalysts?

I'm reading about protein folding on Wikipedia and I stumbled on a bit about a class of proteins called chaperones that aid in the folding of proteins by: ...reducing possible unwanted aggregations ...
Melanie Shebel's user avatar
8 votes
1 answer
4k 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 ...
Heat's user avatar
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8 votes
1 answer
304 views

How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?

There are proteins with intrinsic symmetries. For example: I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
0x90's user avatar
  • 924
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
8 votes
3 answers
3k views

Is it known for sure that bases feel slippery because of the production of soap/surfactant?

Discussion around the question Why does bleach feel slippery? has started me thinking about the saponification explanation for the slippery feeling of basic solutions. According to Wikipedia: ...
uhoh's user avatar
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7 votes
2 answers
1k views

What is the difference between crystal structures of proteins, organic and inorganic materials?

From the definition of crystal and the main differences between crystalline and amorphous material, it is known that crystal formation requires ordered bonding between atoms or molecules. How can ...
M.ghorab's user avatar
  • 497
7 votes
4 answers
3k 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 ...
user avatar
7 votes
2 answers
3k views

How to use Google’s Alpha-fold to predict the structure of a two-protein complex?

Alpha-fold won the CASP13 and CASP14 competitions last year and this year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence. Google has ...
0x90's user avatar
  • 924
7 votes
2 answers
2k views

Peptide bond formation involving side chains of charged amino acids

Peptide bonds are formed as such: Aspartic acid, glutamic acid and lysine all contain either one extra $\ce{-COOH}$ or $\ce{-NH2}$ group in them. Why does that extra group not participate in peptide ...
Aniruddha Deb's user avatar
7 votes
1 answer
809 views

Protein Data Bank: Asymmetric Unit/Biological Assembly

For a schoolproject I have to interpret the 3D structure of an imatinib-BCR ABLC kinase complex. When I visited the PDB website I downloaded the PDB file corresponding to this complex. Once I opened ...
user21398's user avatar
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7 votes
1 answer
236 views

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 ...
Nicholas's user avatar
7 votes
1 answer
152 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 ...
Rob C's user avatar
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6 votes
1 answer
3k views

Can =NH2+ in Arginine's side chain form hydrogen bonding at physiological pH?

I know that at physiological pH, Arginine will have its $\ce{=NH}$ protonated to $\ce{=NH2+}$. I was wondering if this $\ce{=NH2+}$ can still form a hydrogen bond by being a donor? And does the ...
EllBe '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
  • 61
6 votes
1 answer
3k views

Mechanism of protein precipitation with TCA

In practice, TCA (trichloroacetic acid) is widely used for quantitative protein precipitation, but so far I have failed to discover the exact mechanism of TCA action. I highly doubt it's just the ...
Đorđe Timotijević'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
  • 169
6 votes
1 answer
1k views

How to write an entire trajectory into a single PDB file?

I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library. With VMD if I do ...
0x90's user avatar
  • 924
6 votes
1 answer
970 views

Is there a chemical test for gluten?

I am looking for a chemical test for the presence of gluten: however, having looked online for such a thing, all the results seem to be about 'home testing kits' (presumably for people with a gluten ...
user5374's user avatar
6 votes
1 answer
203 views

Biomolecular energy functions and entropy

From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
Opt's user avatar
  • 163
6 votes
1 answer
221 views

Protein purification with Cobalt

Cobalt exhibits a more specific interaction with histidine tags, resulting in less nonspecific interaction than nickel. For this reason, cobalt is the preferred divalent cation for purifying His-...
Plutonium94's user avatar
6 votes
3 answers
1k views

What is the precise definition of Ramachandran angles?

The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
Jennifer M.'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
5 votes
3 answers
190 views

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
5 votes
2 answers
857 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 ...
Simon's user avatar
  • 161
5 votes
3 answers
2k views

Why are protein hydrophobic cores denatured by heat when entropic forces should be favoured at high temperature

The hydrophobic interaction is thought to be driven by an entropic force. If it is, shouldn't hydrophobic interactions be stronger at higher temperatures, where states of higher entropy are favoured? ...
Jory's user avatar
  • 235
5 votes
1 answer
657 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, ...
Logi's user avatar
  • 181
5 votes
1 answer
1k views

Is chitin actually protein?

Recently insects are featured as a protein rich source for human nutrition. That humans can really digest chitin through chitinase enzym has been only recently confirmed. But, does the chitin shell ...
J. Doe's user avatar
  • 189
5 votes
1 answer
411 views

Is the structure of a crystalized protein the native one?

When one finds the 3D structure of a protein by crystalizing it and then making a X-ray experiment, how does one know that the geometrical configuration of the crystal is the same (or even close) to ...
user avatar
5 votes
1 answer
211 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
5 votes
1 answer
7k views

Why is copper(II) sulfate added drop by drop during the Biuret test?

The Biuret test is a test for proteins. The procedure is to add a strong base, such as NaOH, to dissolve the protein. After that, copper(II) sulfate is added drop by drop into this until a (violet) ...
QuIcKmAtHs's user avatar
5 votes
1 answer
4k views

Why does capping after each coupling in Solid phase peptide synthesis improve the results?

Why does capping after coupling improve results during solid phase peptide synthesis (SPPS)? The Case: I have conducted a lab experiment where we coupled three Fmoc-protected amino acids, and did a ...
CuriousTree's user avatar
5 votes
1 answer
441 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 ...
nsg's user avatar
  • 153
5 votes
2 answers
14k views

What happens to the t-butyl cation in the TFA deprotection of a t-butyl ester?

I am a first-year chemistry graduate student and I am currently learning how to synthesize proteins. I have reached a stage in the process where I need to deprotect a carboxylic acid moiety protected ...
Don_S's user avatar
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5 votes
1 answer
370 views

Alternative to Hanging Drop Crystallization

Forgive my ignorance if I am way off, but I was having a look at the crystallization of a number of different substances (e.g. proteins) through the hanging drop vapour diffusion method. The examples ...
user1829564's user avatar
5 votes
1 answer
229 views

Thermal stability of charged and uncharged alpha helices (the concept of alpha-helix capping)

I just learned that charged alpha helices are less thermally stable than uncharged ones. The only difference I see between them would be a larger dipole moment in the charged helix, but how would this ...
ste's user avatar
  • 662
5 votes
1 answer
1k views

How to make a sephadex slurry

I want to purify crude alpha-amylase with column chromatography. I am using a spehadex 75, but for some reason I can't find any information on how to make the slurry. I can quickly find a lot of ...
Peter's user avatar
  • 51
5 votes
1 answer
2k views

Using electronegativity and atomic size to compare acidity of cysteine with serine

In proteins, the alcohol group of serine is generally more difficult to deprotonate than the thiol group of cysteine. Serine and cysteine respectively: In the literature, the explanation given is ...
Nobody's user avatar
  • 320
5 votes
1 answer
580 views

Tandem mass spectrometry: a1 and immonium ions

In tandem mass spectrometry of proteins one will usually end up with a mix of $b$ and $y$ fragments but also $a$ fragments and immonium fragments. My problem is that wouldn't an $a_1$ ion be the exact ...
Matthieu Kratz's user avatar
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
5 votes
0 answers
68 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 ...
user73910's user avatar
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