Questions tagged [proteins]
Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.
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What are the secondary structure requirements for cell-penetrating peptides AKA protein transduction domains
Cell penetrating peptides.
Cell penetrating peptides (CPPs) are a class of short amino acid sequences which are sufficient for crossing cell membranes and delivering themselves along with any attached ...
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What is the fastest way to crystallise lysozyme (for student course)?
High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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How do non-ionic polymers help precipitate proteins?
Some non-ionic polymers (e.g. chitosan and polyethylene glycol) are also commonly used as protein precipitating agents. What is the principle of protein precipitation resulting from the addition of ...
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What are the most common proteins inside cells, by mass?
I'm interested in the most abundant proteins inside cells by total mass of the protein (for example average for a whole human or for specific organs/tissues/cell lines).
It is quite easy to find that ...
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Can any molecule become a hapten?
Hapten are small-molecules, that can only become immunogenic when conjugated with a carrier protein. I was wondering if all small-molecules can become haptens (eg. by synthetic conjugation).
Given ...
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What is the median concentration of spike antigen in COVID positive patients?
I am searching for the plasma spike concentration in COVID patients. The closest possible reference I found claims that spike was only detectable in 5 of 64 COVID-19 positive patients.
However, their ...
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How do scientists determine the nature of ions passing through a channel/carrier/pump?
The NCE (Sodium Calcium Exchanger) transports 3 Na+ inside the cell for 1 Ca2+ outside.
How did we figure this out, and other mechanisms of this sort?
If it were a protein, we could tag it with GFP. ...
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Why does heating kidney beans at a low temperature potentiate the toxicity of phytohaemagglutinin?
I recently found out that red kidney beans contain a relatively high amount of the toxic lectin, phytohaemagglutinin.
An article on phytohaemagglutinin on the FDA website states:
Several outbreaks ...
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Relative densitometry from SDS PAGE
I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software.
My questions are ...
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Is it possible to crystallize proteins so that the crystal has a normal concentration of potassium chloride?
I've been learning about protein crystallography, and how crystals are made. A lot of the crystallization processes involve gradually changing variables (protein concentration, pH, salt concentration,...
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Does the SARS-CoV2 spike protein passively diffuse through the nuclear pore complex?
I found this thread which is worth reviewing as context to my question(s) since there is some overlap in potential discussion, although it's concern is with mRNA ingress rather than spike protein.
...
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Is CRISPR mediated RNA editing less specific and less efficient than DNA editing?
According to this diagram, the high efficiency and the high specificity of CRISPR lies in its reversible binding with the target DNA. The Cas protein unzips the target DNA and have the gRNA to base ...
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Mass spectrometry: What is meant by the 'most intense peptide ions' in data dependent acquisition (DDA) mode?
I am learning about data dependent acquisition (DDA) mode in mass spectrometry from this online resource. I have come across the following statement:
In DDA mode, the mass spectrometer selects the ...
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How many of each structural component of SARS-CoV-2 are there?
I'm interested in the composition of SARS-CoV-2, including how many copies of each protein are present in an assembled virus, as well as the overall mass and density. There are a few recent papers ...
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Do egg-whites dry as right-handed helices?
Do egg-whites dried at cool temperatures form mostly right-handed helices, and if so is there an explanation for this? Because there is so much (mostly crystal-related) research a quick search did not ...
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Estimating diffusion constant of a protein based on number of amino acids
Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, ...
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Are there any enzymes without aromatic amino acids?
I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just ...
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How are animal patterns encoded in the dna?
After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this ...
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Proteins folds: relation to splicing and post-translational modification?
Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?
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Do non-pathogenic organism not have PAMPs? Are there any research paper which proves that a certain microbe is non-pathogenic?
According to this
PAMPs are delivered along with additional information that can be
used by the host to distinguish pathogenic from nonpathogenic
microbes and thereby guide the ensuing innate ...
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Plant vs animal protein digestibility?
The protein scoring methodologies ( https://en.wikipedia.org/wiki/Protein_Digestibility_Corrected_Amino_Acid_Score) rate plant proteins of a lower quality than animal proteins. Now I can understand ...
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How do spiders get silk from their spinnerettes?
I'm 13 and writing a report on spiders. How do they use the silk protein gel from the spinnerets? How does it get from the spinnerets to the web? P.S. I know how silk is created, all the way up until ...
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Would this be called a complex?
When an intermediate is formed between a substrate and an enzyme, this is called an enzyme-substrate complex.
When a molecule is bound to its respective transfer protein, (the molecule being ...
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Determine secondary structure (per residue pair) from a protein contact map
Given a protein map contact map (which for this particular case is a matrix of all Ca-Ca atoms in protein 1a3a that are less than 8 Angstroms):
Question: For each ...
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Is there a cellular mechanism that detects Ribosomal damage?
What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to
what happens when a cell sustains damage of some ...
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Can't resolve protein with native PAGE
This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After ...
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Removal of the Initial Methionine in Venus for FRET
I'm working on building some FRET reporters. In addition to a cleavage site (of varying composition from 15-18AA), a 1 AA linker, I'm using Venus and Cerulean.
Initially I was worried that 18AA ...
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Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?
I'm talking about this type of post-translational modifications. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature ...
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Immunoaffinity chromatography: avoiding damage to the antibodies from proteases
What are the possible methods to prevent the digestion of antibodies (mainly Polyclonal) by proteases during affinity chromatography?
I read some papers about doing modifications to the anitbodies:
...
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Can the protein extinction coefficient be calculated on a 3D structure pdb file?
I have so far only seen programs that work on monomeric amino acidic (1D) sequences, like ProtParam, but now that more 3D protein structure predictions can be trusted, I wonder if there is an ...
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Comparison of different glassy matrices for protein immobilization at room temperature
I am completely new to protein biology experiments. I care about experiments where proteins are immobilized near a surface with the help of a glassy matrix or similar materials.
I am looking for a ...
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Do some plant proteins have no domains?
I've always been under the impression that all proteins consist of at least one domain (with the exception of intrinsically disordered proteins). However, I've come across some things which challenge ...
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In phospho/pan analysis in Western blots, what is best way to normalise to an internal loading control?
I am analysing the expression of a protein kinase X that is a phosphoprotein through Western blots. I have labelled the membrane for both the phosphorylated form of the protein and also for the total ...
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Would the amino acid profile of lab-grown human meat perfectly match the dietary nutritional amino acid requirements for humans?
Whey protein is the food which has the most ideal (yet not perfect) amino acid profile for humans, whereas gelatin for example has a very poor and incomplete amino acid profile for humans. Would human ...
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How to find a model organism's standard data about proteome size and genome size?
I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc.
I found www.uiprot.org
and I made ...
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Does glycerol in E.coli culture media somehow inhibit the lac-operon?
I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
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Why do nattokinase and serratiopeptidase remain effective when given orally, but not insulin?
Why do nattokinase and serratiopeptidase not break down in the stomach and intestines?
Article says that serratiopeptidase is absorbed in rats intestines after oral intake - https://iubmb....
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Appropriate regeneration of StrepTrap HP columns for FPLC
My question is related to protein purification using a ÄKTA FPLC.
We used StrepTrap HP Columns (1 ml column Volume (CV)) from GE Healthcare Life Sciences to purify a strep-tagged protein. In the first ...
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Do carrier proteins constantly open and close or do they only work when a substance binds to them?
What causes carrier proteins to change shape ?
Do they need energy to change shape? If that is true, how are they involved in Facilitated diffusion ?
By changing shape, do we always mean opens from ...
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Fluorescence assays to identify protein concentration without adding a large peptide sequence?
I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. ...
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Why do BRAF mutations appear more in skin cutaneous melanoma?
When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
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Net electrical load of a peptide
I have to determine the electrical charge of the next peptide chain:
C - E - H - P
I know that this page is not there to raise doubts about this style, but I have looked for resources on the ...
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What attaches plant cells to the cell wall?
In animal cells integrins span the plasma membrane and attach the cell membrane to the extracellular matrix. I was wondering how are plant cells attached to the cell wall? Is it just the middle ...
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Do GPCRs have 7TMHs?
I've screened a non-redundant set of GPCRs acquired from UniProt. I found a handful of examples of record IDs that contain more than the 7 TMHs. For example Q89609 and P20905, both of which have been ...
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To which SCOP Class corresponds the following secondary structure?
I need to classify this protein into one of the SCOP class (all $\alpha$, all $\beta$, $\alpha +\beta$, $\alpha/\beta$, or small protein).
I'm having difficulties understanding the difference ...
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Protein/ligand affinity databases?
Is there any database that contain binding affinities reported in litterature for different proteins and ligands?
I have checked uniprot already and it does not seem to included any binding affinity ...
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String-db locally downloaded
I need a ppi network of cancer and it should have 200k to 300k proteins (nodes)
As the web inteface don't allow more than 2000 ...
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Why do my peptide samples turn yellow and red?
The protocols for (brain) tissue digestion I am trying out are: lysis (buffer containing 0.1% SDC or SDS in 100mM TEAB + phosphatase inhibitor which is sort of yellow), reduction with TCEP, alkylation ...
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Degradation of PMSF in protein extract while dialysing - safe for feeding to animals?
I would like to use the protease inhibitor PMSF in enzyme isolation. The obtained enzyme diamine oxidase (or better the protein extract) is tested oral on dogs.
According to Wikipedia, PMSF has a ...
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When can helices form coiled-coils?
The other day, my teacher suggested we find out whether a chain of the following amino acid sequence would be able to form a coiled-coil:
N-KIAEVRAQYEDVANKVRLIVE-C
...
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