Questions tagged [proteins]

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

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5
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2answers
8k 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 ...
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1answer
28 views

Protein drug conjugate exercise

I am supposed to draw the structure of a derivative of the following structure which could be used to make a protein drug conjugate. And then I should draw the reaction for the protein modification. ...
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1answer
63 views
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2answers
187 views

What is the difference between structure assignment and structure prediction?

I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning. ...
7
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1answer
151 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 ...
4
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1answer
3k 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) ...
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2answers
73 views

To which extent is protein folding conserving subprotein structures?

I am actually a pure mathematician, who stumbled over this paper «Protein-Folding Analysis Using Features Obtained by Persistent Homology» by Ichinomiya et al. (Biophys. J. 118, 2020, 2926-2937; link),...
6
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4answers
675 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 ...
7
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1answer
40 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 ...
3
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2answers
94 views

Explaining a biochemical reaction (protein labelling, e.g. with fluorescent probes)

I am an immunology master student without prior knowledge of biochemistry. Could someone explain to me the following 6 reactions? What I want to understand is why exactly the reactions happen at this ...
1
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1answer
27 views

Do phosphoryl thiocholines, their uncharged analogs, and other organophosphates, interact differently with Acetylcholinesterase?

As asked in the title, would the various salts -such as hydrochloride or methyl iodide- of V-Agents interact any differently with acetylcholinesterase compared to the neutral compound? For instance, ...
3
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1answer
833 views

Denaturing of Proteins and Nucleic Acids - Effect of Temperature (Heating vs Cooling)

Heating a protein/nucleic acid will disrupt inter-molecular and intra-molecular forces in the tertiary structure. It will also interfere with the shape of the active site if the protein. Does this ...
5
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1answer
568 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, ...
1
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0answers
36 views

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 $\ce{COOH},$ ...
7
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2answers
2k 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 ...
0
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1answer
76 views

Carbon atoms types in amino-acids [closed]

I'm looking for a table or another kind of schema where I can find which type of carbon atoms (sp3, sp2 etc.) are present in each amino-acid. In my biochemistry books these informations are not ...
1
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0answers
17 views

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 ...
0
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0answers
12 views

Improving protein solubility in Water solvent (food science)?

I am trying to form a solution involving mixing my protein shakes. I am using a vegetable protein and it has poor solubility. Is their another protein I could use to entrap it to improve solubility? ...
2
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0answers
34 views

Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
3
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2answers
99 views

What is the mechanism of AChE inhibition by Onchidal?

A naturally-occuring neurotoxin, called Onchidal, produced by a species of sea slug acts as an irreversible inhibitor of acetylcholinesterase. The structure of Onchidal is presented below: How and ...
3
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0answers
23 views

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,...
4
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2answers
389 views

Why does denaturation of albumen protein cause pH of solution to increase?

I'm interested in the denaturation of proteins by alcohols, specifically by ethanol. I have devised a simple experiment in which I inject solutions of ethanol (of variable concentrations) into ...
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0answers
28 views

Structure-Activity Relationship of Chlormephos and Parathion

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/k. ...
6
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1answer
418 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 ...
2
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0answers
32 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.&...
2
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1answer
33 views

Determination of metal state from protein X-ray structure

Many proteins or enzymes contain metal ions within their active sites. These metals are often directly involved in the reaction catalysed bu the enzyme. In certain cases the function is well known and ...
6
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1answer
647 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 ...
1
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1answer
32 views

Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group

I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation ...
2
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0answers
30 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 ...
2
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0answers
26 views

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 &...
4
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1answer
119 views

Why are isomers of parathion less active acetylcholinesterase inhibitors than paraoxon?

Parathion itself has been found to be a very weak inhibitor of acetylcholinesterase. It normally requires metabolic activation and the conversion into paraoxon in the body to actually start exhibiting ...
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0answers
20 views

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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0answers
51 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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0answers
42 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 ...
3
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1answer
127 views

Effect of His-tag on enzyme activity

In my biochemistry laboratory class, I designed an experiment to study the effect of a His-tag on enzyme activity. First, I measured the activity of the His-tagged enzyme. Then, I cut off the His-tag (...
2
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0answers
41 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 (...
2
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0answers
24 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 ...
2
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2answers
121 views

How would I make a basic protein folding algorithm? [closed]

On the face of it it doesn't seem especially difficult. Model the amino acids as solid objects linked together. Approximate the 3D force fields around them using a coarse approximation, then set the ...
0
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1answer
130 views

How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?

Thanks for some online resources (i.e. here) I have an understanding of what X-Ray Crystallography does. By blasting X-Rays at a crystal and recording the scattering patterns on a plate behind the ...
2
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2answers
195 views

Why don't proteins form branched polymers?

My reference book (Princeton Review for SAT Chemistry Subject Test) mentions that: Proteins and carbohydrates are both polymers; however, only carbohydrates commonly form branched polymers. Glycogen ...
0
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1answer
68 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?...
0
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0answers
22 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 ...
1
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1answer
182 views

Acid-Temperature coagulation of milk

I was making coffee with a cup of boiling milk which was 2 days old. I used instant coffee powder and some sugar for the making of it. Tried to make a very hot coffee but usually prefer medium hotness....
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4answers
97 views

If I hard boil eggs in a pressure cooker, will I get the same results regardless of altitude?

This seems like it should be obvious but for some reason (my chemistry is very rusty) I'm having a hard time articulating why the hardboiled egg recipe in an instant pot should yield the same results ...
3
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0answers
77 views

Which amino acids can be totally synthesized? [closed]

I can't find information regarding which amino acids (say the proteinogenic ones or in general) can be totally synthesized. Is there a reference?
2
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1answer
70 views

How to predict amine donor in biochemical reactions (whether glutamine or aspartate)?

In biochemical reactions amine $(\ce{-NH2})$ transfer is done in multiple pathways (e.g. urea cycle, purine biosynthesis etc.). In many of the situations glutamine donates amine group (e.g. xanthosine ...
2
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2answers
91 views

Purifying cysteine containing peptides

I would like to purify my peptide having cysteine residue by using HPLC. It is known that thiol containing peptides undergo oxidation and form disulfide linkages. In order to prevent it I used proper ...
5
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1answer
99 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 ...
2
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0answers
232 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 ...
0
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1answer
241 views

How to tell the difference between lysine and the N-terminal amino acid in DNP labeling?

The N-terminal amino acid of a protein can be identified by reacting the N-terminal amine with FDNB (1-fluoro-2,4-dinitrobenzene), or Dansyl chloride, or Dabsyl chloride, then digesting the protein ...