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 α-keratin a fully functional protein?

Is α-keratin before it coils with another polypeptide, makes chains, and build intermediate filaments a fully functional protein? I mean, is the single monomer of α-keratin a protein or does it have ...
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Which is actually better for you - lyophilized vs hydrolyzed collagen peptides?

From my research and the common selling feature of hydrolyzed proteins and collagen peptides that they offer the highest absorption rate. This however does not relate to amino acid synthesis, as ...
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Can genetic circuit alone alter protein structure?

I would like to know if there are examples of genetic circuits, that usually appear in synthetic biology, can modify aspects of protein structure (allosteric sites, regiospecificity, and so on) i.e. ...
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Why is the amount of protein variants in a human genome higher than gene variants?

Why does the human genome have more protein variants than gene variants? Is this because of PTMs?
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Iterative macrocyclic design in drug design [on hold]

Suppose that I have some proteins (for example, kinase) that their structures are completely determined (cryo-EM, crystal structure from X-ray crystallography). Given that I have raw peptides, I want ...
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What inactivates pepsin in infants?

In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach. Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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What's a good reference for learning about recombinant proteins?

I'm looking for books and articles that can bring me up to speed on the design, expression, and purification of mammalian proteins in recombinant systems, both in E. coli and in more complex systems ...
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Can protein/codon chirality be described in tRNA molecules? [on hold]

Is left-handed chiral protein and right-handed chiral RMS factored in to the tRNA molecuar structure? If so, how.
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What aggregates can be seen in reduced SDS-PAGE? [on hold]

Can dimers and trimers of a Ig's heavy chain and light chain be seen in SDS-PAGE reduced with heat and 2-ME? Or will they be reduced to monomers? Thanks in advice!
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Dipeptide approximations for making Ramachandran plot [on hold]

How did Ramachandran arrived at his plot? Did he consider only the nearest neighbor amino acids and their steric clashes? In general all those interactions in protein are electrostatic in nature which ...
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Lysozyme amino acid sequence: N-terminal extension

I looked up the amino acid sequence of lysozyme here: http://www.biology-pages.info/L/Lysozyme.html Then I crossed referenced that with the lysozyme sequence on UniProt: https://www.uniprot.org/...
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What is the function of spongin in sea sponges?

Sea sponges (Porifera) use different types of skeletons to support their structures. Some skeletons are built from minerals, some are built from proteins like spongin, and some use both. My question ...
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Can denatured GFP show fluorescence?

GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we ...
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Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
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Do residue sequence numbers in PDB files correspond to the positions in the backbone?

In other words if two residues have sequence numbers, say, 20 and 21 then are they next to each other in the backbone? If no (or not necessarily) then is there any way to find consecutive residues ...
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Relationship between Communication Proteins and Gap Junctions

What is the relation between communication proteins and gap junctions? Do the communication proteins make up gap junctions or something?
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How exactly is casein digested?

I mean it seems first step is rennin or pepsin digestion in stomach - then what happens with remaining peptides? I am interested in the whole process from casein to amino acids. Is there brush border ...
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Preserved alpha complementation over evolutionary time?

Has the result of alpha-complementation ever happened via mutation through evolutionary time, and been preserved in modern day organisms? In other words, has a functional gene product ever been split ...
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How do organophosphates actually work?

The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine ...
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Can protein structure be determined by X-Ray Diffraction in a single image?

I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration ...
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What is the subcellular location of synthesis of non-essential amino-acids?

What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this? I thought the whole point of DNA is coding for how to ...
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How can I get the yield of my purified immunoglobulins?

In order to get the yield of IgY through a set of purification steps, what method can I use? Thanks in advice!
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How can I change my buffer system for protein purification?

I have a protein that I purified in PBS buffer, pH 7. I will do dialysis to remove salt and will then further purify the protein with ion exchange chromatography. I will need to use another buffer (...
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What buffer should I choose for IEX chromatography for purifying IgY

I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
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conversion of distance matrices to pdb/coordinates

I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...
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What does “count in gene set” mean?

I am trying to understand the analysis generated by STRING. In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498". What ...
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What does “PDPN+ cells” means?

Are they podoplanin positive cells (cells that tested positive for podoplanin)? "...though it has been shown that podoplanin (PDPN+) cells analogous to mouse FRCs are found in human secondary ...
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What is the relationship between Ca- and Na-ions and mucins and why?

According to Wikipedia https://en.wikipedia.org/wiki/Mucin#Secretion mucins (Proteins that form mucus) obtain viscoelastic properties by the Exchange of sodium and Calcium Ions. What is Happening ...
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Why does the ratio type III collagen:type I collagen increase after a tendon injury?

I read on {1}: Type III collagen has accumulated at the rupture site [of human Achilles tendon] probably due to microtraumas and the subsequent healing process. […] The increased content of type ...
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Why are dietary recommendations for methionine consumption combined with cysteine?

I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids (source: wikipedia). I don’t understand why they pair Methionine + Cysteine: ...
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Why is glycine considered a nonpolar amino acid but a polar molecule?

Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins? Also, is the backbone of a protein nonpolar?
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How are multiples transmembrane proteins translocated or embedded in the membrane?

This image is in the textbook, Molecular Biology of the Cell. I understand why the start and stop transfer sequences must alternate, but why is there 2 consecutive start transfer sequences at the N ...
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How much nucleoside triphosphate is required to form one peptide bond during protein synthesis?

I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, ...
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Genes of the electron transport chain

Where are the genes of proteins that make the electron transport chain of mitochondria?(are they in in the nucleus or they are in the dna of the mitochondria itself?) Thanks for this answering system ...
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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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Why do protein solutions have to be alkalised in biuret test?

I’ve read that CuSO4 solution reacts with peptide bonds that connect amino acids to create a violet colour, but the instructions always tell me to add NaOH solution to the protein solution before I ...
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Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
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Preparing sample for SDS PAGE

I have more than 10 cell lysate samples (70 µL each) whose concentration varies from 1.9 mg/mL to 4.8 mg/mL. I have 5X and 2X SDS sample buffers. I would like to prepare SDS PAGE samples in such a way ...
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Why are prions in animal diets not destroyed by the digestive system?

According to CBC: Mad cow disease is the common name for a condition known technically as bovine spongiform encephalopathy, or BSE. [...] The only known source of mad cow disease is from animal-...
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Where can I find and download HMMTOP training set?

I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the ...
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Are SLC52A2 and GPR172A really the same?

The official HUGO gene nomenclature page says that GPR172A (Gamma-hydroxybutyrate receptor) and SLC52A2 (riboflavin transporter, member 2) are the same. The sequence reported by Andriamampandry seems ...
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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 ...
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Backbone hydrogen bonds between adjacent amino acids in a protein?

Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO? Are there any examples of such situations in proteins and how common are they? If ...
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Intein Splicing

Currently I am trying to read and understand this paper on intein splicing. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/22001202 However, I'm a little confused with Figure 4. Why do the ...
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Does digestion require hydrochloric acid?

Would our digestion function any differently if we secreted something else, like sulfuric or nitric acid, instead? I'd assume an acidic environment may be required, but not sure if chloride is also ...
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If overcooked hard boiled eggs show these green sulfide rings, why do scrambled/fried eggs not show this?

In the image above, the dark green rings are ferrous sulfide rings, caused when the sulfur from the egg white reacts with the iron in the egg yolk when the egg is overcooked. I was wondering, given ...
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How do you interpret the resulting bands of gel zymography?

I would like to clear up some things for gel zymography. I understand that bright bands show proteolytic activity. But which molecular weight do these bands correspond to? Is it the weight of the ...
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How does the immune system recognize harmful proteins?

How does the human immune system detect whether a protein happens to be a protein found in the body that is supposed to be there, a bacterial toxin that should be inactivated, an already inactivated ...
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What is a secretion target family protein?

I came across this link: https://www.genome.jp/dbget-bin/www_bget?btw:BF38_3398 What is this protein, is it a secreted effector protein or is it something else? What is the difference between type ...