Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
221
questions
4
votes
3
answers
415
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.
...
user93950
1
vote
2
answers
105
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),...
- 21
7
votes
1
answer
159
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 ...
- 71
5
votes
1
answer
658
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, ...
- 181
1
vote
0
answers
46
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 $\ce{COOH},$ ...
- 111
7
votes
4
answers
4k
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 ...
user36001
0
votes
1
answer
298
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 ...
- 293
1
vote
1
answer
52
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, ...
- 1,264
2
votes
0
answers
31
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 ...
3
votes
1
answer
66
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 ...
- 1,264
3
votes
0
answers
34
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,...
- 1,264
4
votes
2
answers
828
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 ...
- 151
2
votes
0
answers
132
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
votes
1
answer
96
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 ...
1
vote
1
answer
250
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 ...
- 39