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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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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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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Spectroscopic methods for quantifying peptides/proteins with or without Tryptophan or Tyrosine content

I have several peptides (20-50 amino acids long) which I want to quantify the solubility/concentration in a solvent at certain temperature and pH. These peptides may or may not contain Tryptophan or ...
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How to look for different transcripts for a protein?

I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein. However, when I look it up online, there is no clear organized data on different ...
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What's the best way to purify my His tagged protein? Supernatant super viscous after first sonication?

I am trying to purify my his-tagged protein of interest, disulfide isomerase. It is about 40kDa and is cloned in pET28a vector, at XholI and NdelI, and expressed in BL21. I'm having issues with my ...
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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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What are protein iBAQ abundance values in SWATH mass spectrometry?

I am reading a journal paper where they used SWATH mass spectrometry to quantify the abundance of proteins in synaptosomes isolated from different species. I am trying to determine whether some ...
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What is meant by ‘local structure’ of proteins?

The EBI/EMBL training course includes the following definition of Secondary structure of proteins: Secondary structure refers to the regular, local structure of the protein backbone, stabilized by ...
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Does alternative splicing contribute to the diversity of enzymes?

I understand the role of alternative splicing in generating protein diversity, but for enzymes specifically, is alternative splicing responsible for the diversity of it? My professor told me something ...
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Why do some amino acids have more synonymous codons than others?

In the standard genetic code (above), tryptophan and methionine are coded for by a single codon, other amino acids such as phenylalanine by two codons, isoleucine by three codons, and some by four or ...
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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 enhanced chemiluminescence in western blots, will the horseradish peroxidase eventually get used up?

I am learning about enhanced chemiluminescence in Western blots. I have read online that in enhanced chemiluminescence that horseradish peroxidase (HRP) catalyses the oxidation of luminol to 3-...
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is pepsin able to break down proteins into amino acids in human stomach? [closed]

I'm trying to find out if pepsin can break down proteins into amino acids after they are converted to peptides. Is pepsin able to separate amino acid monomers from the peptides? can you please show me ...
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1 answer
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Does mass spectrometry data have units?

I am reading some journal papers about the proteome of certain brain structures. In these papers, they used mass spectrometry to identify the proteins that were present in the brain structure as well ...
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Can cell adhesion molecules have intrinsic enzymatic activity?

I am learning about cell adhesion molecules (CAMs), and I know that they mediate cell-cell and cell-extracellular matrix adhesion via homophilic and heterophilic interactions. I have read that CAMs ...
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Western blot trouble shooting - low voltage and yellow sponges during/after transfer

I have a western blot troubleshooting question that I haven't been able to find the answer to in manufacturer troubleshooting guides. As a bit of background, I was transferring 2 western blots ...
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1 answer
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What do the colors mean in representations of amino acids?

I've seen sequences of amino acids depicted using colors, which I imagine correspond to whether the side chain is charged, etc. I can't figure this out, though, and I'm not a biologist or biochemist. ...
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mRNA vaccines: Can a spike protein by itself have different side-effects than the virus itself? [duplicate]

I was wondering, is it possible for the isolated spike protein, as resulting from an mRNA vaccine, to cause harmful side effects in an individual, that would not have developed in that individual if ...
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Should Secondary Antibody Bind better through adsorption than using an EDC Linker?

Recently, I conducted an experiment to compare the use of EDC versus passive adsorption. I attempted to immobilize goat anti-rabbit HRP secondary antibody to Carboxylated polystyrene beads via EDC ...
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Do the cadherins involved in adherens junctions and the cadherins in desmosomes "communicate" at all?

I think I have a basic understanding about the function of these cytoskeleton-linked junctions, and they can link one cell to another and the interaction of cadherins of adjacent cells give the ...
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Slightly different sequences returned by BLASTP

Probably this is very trivial but I am self-learning bioinformatics and I don't know who to ask for this kind of stuff. Also, apparently it is really hard to find information on general topics like ...
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Where can I get info about A. thaliana proteins' locations?

I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's ...
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Arrangement of Amino Acids in the Protein alphabet

I am a software engineer with little knowledge of molecular biology. However I am trying to understand some bioinformatics computer code where the protein alphabet appears to be represented as the ...
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What protein(s) bind together the calcium carbonate tiles in abalone shell to give it strength?

The articles that I've been able to find on the structure of abalone shells mention that they consist of calcium carbonate plates connected by proteins, but don't name the proteins. These proteins are ...
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What other sites do non-competitive inhibitors bind to apart from allosteric sites?

I learned competitive inhibition and non-competitive inhibition. My teacher told me that we should say that non-competitive inhibitors bind to somewhere on the enzyme apart from active sites. I ...
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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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How are some exotoxins heat-stable, despite being proteins?

While studying microbiology, I came across bacterial exotoxins and endotoxins. It's understandable that endotoxins are lipopolysaccharides and hence heat stable. Exotoxins are proteins and hence heat ...
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How many different proteins are able to form prions?

The Wikipedia article on prions and other sources seem to only talk about variants of PrP protein. I think I remember a previous version of Wikipedia saying something about another protein able to ...
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What does 'disordered' mean in the 'Family & Domains' section of UniProt?

I am looking at information about a protein called CD83 antigen on UniProt. On the page for the protein, in the 'Family & Domains' section, it says that between amino acids 60-81, the region is '...
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Number of membrane proteins of a particular type per cell

Is it possible (or meaningful) to count how many proteins (protein copy number?) of a certain type a given cell has on its surface? For instance, say there is some membrane integral protein ...
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1 answer
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Why are IMAC and gel filtration combined?

In a practical course I used an Biorad Profina system to purify a protein with a histidine tag. The device uses a column for IMAC and one for gel filtration. Why are these two devices combined in one? ...
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8 votes
1 answer
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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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2 votes
2 answers
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Does baking soda interfere with digestion when cooked into food?

Baking soda is useful for tenderizing meats and leavening baked goods. In the case of meats, it allegedly breaks down proteins/amino acids. However, does this usage pose a risk to digestion? Could the ...
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Do transcription factors need to undergo extensive post-translational modification?

Some proteins need additional processing to become fully functional, for example NiFe-hydrogenases need to be cleaved by endopeptidases for some of their subunits to be active. Is it known whether ...
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Determine directionality of backbone from electron density map

I am given a polypeptide with three electron density maps at different resolutions; 1.85, 2.5 and 3.5Å. And from this I am to determine at which resolution you could be certain about the ...
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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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Intelligence of nervous system vs other human intelligence? [closed]

Viral proteins are shown to be used in intelligence such as for memory: https://www.sciencedaily.com/releases/2018/01/180111141450.htm I wondered since proteins able to form prions are the most ...
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4 votes
1 answer
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Why would this viral strain-specific antiserum fail to immunoprecipitate the same (98% identical protein) from another strain?

I'm reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC392475/ and I can't work out why a certain immune serum didn't work on the same viral protein but from different strains. The serum ...
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Predicting protein folding with Alphafold

I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ ...
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Ways to predict the preservation of functional domains in fusion proteins

My lab is synthetically creating fusion proteins consisting of an enzyme attached to a zinc finger through a linker. We can attach the zinc finger to the enzyme at either its N-terminus or its C-...
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5 votes
2 answers
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Meaning of ‘motif’ in molecular biology

I would like to understand the meaning of the term motif as used in molecular biology. In an article in Nature Biotechnology, Patrik D’haeseleer states: Sequence motifs are short, recurring patterns ...
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How does the shape of a protein determine its function?

There is currently much interest in protein folding and the problems in predicting how the sequence of amino acids determines how proteins fold into specific shapes. Accounts of this generally mention ...
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4 answers
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What is 'protein' in food?

I know that proteins perform a lot of functions and as a result there are a lot of different types of proteins in our bodies. When I eat food that has x grams of 'protein', what is this? A homogenous ...
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Which genes/proteins constitute the core components of the circadian clock?

What the title says. For instance in Drosophila melanogaster and Mus musculus (see Patke et al. 2020) the CLOCK, CYCLE/BMAL, CRYPTOCHROME, PERIOD setup seems to be conserved. But other components also ...
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Has life on Earth explored the entire space of genomes?

Recently I came across a 2008 article, the authors of which argue that in fact the space of protein sequences is not as large as it might seem, and that life on Earth has most likely already explored ...
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2 votes
1 answer
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What is the point of calculating extinction coefficients of a protein without Cys residues?

ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value ...
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9 votes
1 answer
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Why can't H3O+ ions pass through aquaporins?

Aquaporins are proteins that facilitate the movement of water (and related molecules) through cell membranes. (Also, these transport proteins are very specific about what they transport.) ...
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2 answers
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Is alternative splicing possible in the same cell?

I know alternative splicing is possible in different cell types of an organism, or within the same cell at different developmental stages. There are several examples like this. But are there any ...
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When subtracting background from a Western blot image, does the method of subtracting background signal have to be the same for all blots analysed?

I am analysing some Western blot images and I want to subtract the background signal for my protein bands of interest. Previously, the way that I subtracted background was to draw a rectangle (that ...
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2 votes
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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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