Questions tagged [proteins]

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

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31 views

Troubleshooting an Autodock Vina Error on Chimera: "Could not find an atomic number for Hn Hn"

After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply ...
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111 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 ...
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2answers
54 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): ...
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16 views

What are the initial experiments to hypothesize or decide the method of protein degradation?

For a protein of interest, How to determine it’s degrading method— protease or proteasome? Is it possible through bioinformatics? What are the initial experiments to hypothesize or decide the method ...
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1answer
69 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 ...
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1answer
74 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 ...
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1answer
34 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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2answers
115 views

How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
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1answer
46 views

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 ...
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2answers
227 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
39 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?
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1answer
63 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 ...
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1answer
58 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
30 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
76 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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27 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
34 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
119 views
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3answers
294 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
76 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),...
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1answer
57 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 ...
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1answer
613 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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37 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 $\ce{COOH},$ ...
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4answers
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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
88 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
34 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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24 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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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? ...
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35 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 ...
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24 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,...
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2answers
434 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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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. ...
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36 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.&...
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1answer
37 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
38 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 ...
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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
160 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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42 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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25 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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1answer
130 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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73 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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52 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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53 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
138 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
194 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
944 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 ...
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2answers
296 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 ...