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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1answer
60 views

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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Do Prawns (Prawn, banana, wild, flesh, raw) have all essential amino acids or just Tryptopham?

Looking at the amino acid composition of banana Prawns (wild, flesh, raw) on the Australian food composition database at https://www.foodstandards.gov.au/science/monitoringnutrients/afcd/Pages/...
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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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44 views

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 ...
4
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1answer
116 views

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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1answer
63 views

How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

I have two datasets, from different sources, that I need to compare. The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
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Do phagocytes need antibodies to be able to engulf pathogens (to function)?

I recently saw a question about monoclonal antibodies, that are specific to a certain virus, being split (into their constant and variable regions via an enzyme), and the question asked whether some ...
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1answer
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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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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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154 views

Which lipoprotein has the highest protein content?

I know that HDLs have the highest protein/lipid ratio but know that the HDLs are very small molecules too and I couldn’t find the exact answer for this question. I mean, by amounts which of these ...
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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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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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2answers
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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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2answers
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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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3answers
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Protein structure prediction from amino acids sequence

Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict ...
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1answer
56 views

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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4answers
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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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What happens when you tag a protease with its own degradation tag?

I've been learning about the ClipXP, ClipAP, and Lon proteases. They are proteases from the AAA+ family, which seek out proteins tagged with certain peptide sequences, unfold them, and chop them up. ...
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2answers
270 views

Can DNA sequencing of food provide quantitatively the fraction of protein from chicken vs soy?

update: New York Times X, 2021: The Big Tuna Sandwich Mystery: For about $500, his lab could conduct a PCR test — which rapidly makes millions or billions of copies of a specific DNA sample — and ...
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445 views

Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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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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Which proteins are part of the most different protein complexes?

Let n be the number of different protein complexes (as defined here) that a protein may be a stable part of for a considerable amount of time (and not only transiently). Which proteins have the ...
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1answer
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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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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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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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1answer
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Can you use images taken at different exposure times in western blot image analysis?

I am doing Western blot data analysis where I have images from a number of experiments (where the samples in the experiments are biological/technical replicates). For each experiment, I labelled the ...
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1answer
31 views

When analysing phosphoproteins via Western blot, why is total protein level of the target protein recommended as an internal loading control?

I am analysing the expression of a protein kinase via Western blots, and it is a phosphoprotein. I have labelled my membrane with antibodies against the phosphorylated form of the protein (using ...
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Why do you need to calculate the lane normalisation factor when doing western blot data analysis?

I am learning about western blot data quantification from some online resources. I have read about methods to normalise the data. I have seen in a number of resources, such as this handbook and this ...
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1answer
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Meaning of "Domain with function to find" (FIIND)

From NALPs: a novel protein family involved in inflammation. FIIND - Domain with Function to Find. What is the meaning of this name? Does it mean "Domain with an unknown function"? I'm ...
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How many times is a single strand of mRNA translated into a protein?

In other words, is the mRNA damaged or somehow "marked completed" in the translation process? Or does it pop out the other side of a ribosome ready to be translated again? If the latter, how ...
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Is the kinase domain of a protein kinase the same as the catalytic domain?

I am learning about protein kinases and I have read that the protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. I am wondering ...
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1answer
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Is sonic hedgehog a gene or a protein or both?

Is sonic hedgehog a gene or a protein or both? I think sonic hedgehog is okay as a name for a chemical. Having said that, I am a little bit concerned about the way sonic hedgehog seems to mean the ...
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1answer
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SARS-CoV - relative size of the spike protein

I was given the task of determining the percentage of the S-protein of the SARS-CoV relative to the total of its proteins from the attached image. However, I have been given no explanation of the ...
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1answer
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Can a constitutively active kinase be highly regulated?

I am studying the protein kinase GSK3 and I am learning about the regulation of its activity. Many journal papers that I have read have stated that GSK3 is unique because it is a constitutively active ...
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1answer
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Does the mRNA of the covid19 spike protein contain any nuclear localization signals

Does the covid19 spike protein amino acid sequence, as used in the covid19 vaccines, contain a nuclear localization signal. Because if they do, isn't there a chance that the RNA can find its way to ...
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1answer
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Are there any online resources that have a list of post-translational modifications and their molecular weight?

I am studying a protein and I am interested in learning about all the post-translational modifications that it has (as I am analysing it via Western blot). I have found a list of the post-...
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1answer
55 views

Can Western Blots be used to quantify the activity of a protein?

I am new to Western Blot analysis and I have recently done my first two. I am studying a phosphoprotein (a protein kinase) that can be both activated and inactivated via phosphorylation at a specific ...
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How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?

I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19....
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389 views

Does the term 'protein expression' refer to the production of proteins only or also their regulation?

I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific ...
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1answer
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How do G proteins move?

G proteins consist of an alpha subunit and a beta/gamma subunit. These proteins are involved in various cellular signalling process. From what I have understood, the alpha and gamma subunits have ...
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How to combine data points from different western blots into one graph?

I am doing Western blot data analysis and I have data from two different western blots. In my two Western blots, I have labelled for the same proteins. I am comparing knockout (KO) samples against ...
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Question about total protein normalisation in western blot image analysis

I am analysing western blot data and I am using total protein normalisation using Ponceau S. My supervisor and I have agreed to use total protein normalisation for my western blots instead of using ...
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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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1answer
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What is the best way from remove background signal from a band when doing Western blot image analysis?

I am doing image analysis of a Western Blot in Image J. I have calculated the total intensity of my protein bands of interest through outlining each band using the rectangle tool in ImageJ, and ...
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1answer
39 views

What is background signal in a Western blot?

I have done a western blot and I want to remove the background signal when doing densitometry analysis of my protein bands of interest. I have read some articles online such as this one regarding high ...
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In Western blot, is Ponceau S a valid loading control if band intensities vary between lanes?

I have done a Western blot and I am using Ponceau as a loading control to normalise my measurements against a protein of interest. For my Western blot I have a number of wild-type and knockout samples ...

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