Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
177
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How can all amino acids point outwards from an alpha helix, if peptides are mostly trans?
My textbook in biochemistry ("Biochemistry" - Berg,Tymoczom Gatto, Stryer) tells me that:
"Almost all peptide bonds in proteins are trans" (p. 40)
At the same time, it states the ...
2
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2answers
203 views
Lysozyme crystals versus NaCl
If someone has some experience with lysozyme crystals I would be interested in knowing whether any of the images below seem likely to be lysozyme. Solutions were made with powdered lysozyme ($\pu{50 ...
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28 views
What do natural hybrids of peptides and nucleic acids look like?
Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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19 views
Mechanism of Action of Carbachol
Carbachol (carbamylcholine chloride) is known to be a cholinergic agent. Does it work as an indirect agonist by inhibiting acetylcholinesterase, as a direct agonist of acetylcholine receptors, or is ...
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1answer
36 views
What does it mean by spatial neighbor?
What does it mean by a spatial neighbor (SN) in the case of a protein residue or protein chain?
Why is it different or special as opposed to other neighbors?
2
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1answer
52 views
What is the maximum length of peptide which considered to be hard for synthesis by the current technology?
I am a molecular biologist and work with recombinant proteins. I am wondering what the cut point, in terms of length, is at which I should produce the peptide using heterologous expression rather than ...
2
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1answer
43 views
How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?
When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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1answer
26 views
How can I calculate the distances between residues of a protein? [closed]
Suppose, we have a protein (16PK).
We are considering a 5-residue segment/window.
If we assume ASN10 to be the ...
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1answer
68 views
What does the following diagram represent?
Suppose, the following is a diagram of a protein's polypeptide chain:
What does this diagram represent?
What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid ...
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26 views
Can Amphotericin B cross a lipid bilayer membrane in its zwitterionic form when it is loaded in the aqueous core of a liposome?
Can Amphotericin B cross a lipid bilayer membrane in its zwitterionic form when it is loaded in the aqueous core of a liposome? Or must it be uncharged in order to cross the lipid bilyer membrane of ...
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1answer
32 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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106 views
What is the meaning of this data from a protein data bank (PDB) file? [closed]
The following rows are part of a large dataset:
...
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3answers
274 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.
...
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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),...
7
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1answer
45 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 ...
5
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1answer
594 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, ...
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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 $\ce{COOH},$ ...
6
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4answers
759 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 ...
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1answer
77 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 ...
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1answer
30 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, ...
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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 ...
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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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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
406 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. ...
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
34 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 ...
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1answer
34 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 ...
7
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1answer
154 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 ...
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0answers
32 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 &...
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21 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 ...
4
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1answer
121 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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56 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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47 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 ...
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0answers
42 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 (...
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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 ...
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2answers
126 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 ...
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1answer
145 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 ...
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1answer
624 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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2answers
231 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 ...
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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 ...
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4answers
98 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 ...
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1answer
70 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?...
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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?
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0answers
277 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 ...
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1answer
301 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 ...
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37 views
Does HI-6 form a covalent adduct with acetylcholinesterase?
According to sources provided below, the oxime HI-6, or Asoxime Dichloride, as it is also called, besides being a reactivator of acetylcholinesterase that has been inhibited by organophosphorus ...
2
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1answer
156 views
Is a beta pleated parallel sheet always formed from more than one peptide?
I can conceptually grasp the beta pleated anti-parallel sheet by imagining a curved length of string i.e. one polypeptide, starting with the N- terminus on the left and ending with the C-terminus at ...
