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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Does pdb file contain one single protein

A pdb file defines a protein data bank. Does it contain only one protein? https://raw.githubusercontent.com/geohot/corona/master/proteins/1ubq.pdb example this file is a protein data bank. I am not ...
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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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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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Presence of S-P or T-P residues in pin1 proteins [closed]

I was under the impression that pin1 proteins contain at least one of these residues, yet when I accessed the three different protein sequences available on Wiki, none of them reflected this. ...
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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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In a Western blot, when analysing phosphoprotein bands can you normalise against total protein or do you need to use a loading control?

I am doing Western blot data analysis and I have probed my membrane with phospho-specific antibodies against a phosphoprotein (it is a protein kinase) of interest. I have also probed my membrane with ...
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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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Recommendations on books about statistical analysis for Western blot data?

I have run a couple of Western blots and I am planning on doing more in the future. My goal is to combine the results from the different Western blots and perform a statistical analysis in order to ...
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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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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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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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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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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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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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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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Compatibility between spytag/spycatcher versions

Background SpyTag and SpyCatcher are peptides which can associate via a spontaneous amide bond. Because of this, they can be fused to proteins of interest as tags to cause the proteins to bind. There ...
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What's superposition and thread in RosettaCM?

I'm a beginner in structural biology. I had a question while reading a paper on RosettaCM. What does RosettaCM's superposition and thread mean? I googled it. As a result, the following results were ...
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In western blots, do loading controls have to be proteins that are in equal amounts in each lane?

I have recently done a Western Blot and I am doing data analysis on my blots. I am studying the protein GSK3, which is a phosphoprotein. I have labelled my membrane against active GSK3 and inactive ...
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What are the units of the band intensities in a western blot image?

I have done a Western blot and I am measuring the band intensities in Image J. Using the rectangle tool, I have outlined the band and then calculated the area and the mean intensity of the band. I ...
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What is meant by “opposing plasma membrane” with respect to cell adhesion molecules?

I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about cell adhesion molecules (CAMs) and I have come across the following: CAMs are involved in homo‐ or ...
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Is the phrase “transmembrane segment” equivalent to the transmembrane domain of a protein?

I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about the cell adhesion molecule NCAM2 and I have come across the following: The overall structure of NCAM2 ...
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How are integral monotopic proteins synthesized? Is it the same process as a transmembrane integral protein or are they different?

In a book I was reading, they state that secretory proteins and integral transmembrane proteins are synthesized in the same manner. But, they don't mention how integral monotopic proteins are ...
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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 Invertase catalyse the hydrolysis of other sugars other than sucrose?

I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a ...
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What does q stands for in Gq/11 alpha subunit?

Sorry for asking, I am not capable to find what does the q stands for in Gq/11 alpha subunits.
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Confusion regarding the Kir2.1 inward-rectifying potassium channel

I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being ...
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What is the thickness of the membrane if only alpha helixes are embedded of a transmembrane protien?

Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å Please read: The reason I didn't submit my ...
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Calculating sequence divergence score for a protein from identity or similarity score?

I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue ...
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Which enzymes use ATP?

It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well ...
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Western blotting: what common tweaks do you make to the protocol and why would you make membrane cuts?

I'm building an app which helps researchers plan out Western blots, record protocol tweaks and receive warnings in the app if: you're trying to multiplex antibodies of similar molecular weight on the ...
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What are the effect of radioactivity on grey wolves in Chernobyl?

I am doing some research about the effects that radioactivity has and is having on grey wolves in Chernobyl and more particularly on their genetics, but maybe also looking at the populations in the ...
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Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles

First Question : RNA interference - small-interference RNA in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin this Figure is Shown my question is : if the foreign RNA ...
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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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How can carnitine enter the mitochondrial matrix without OCTN2?

Some people have defects on the gene SLC22A5, giving them problems with their OCTN2 transport protein (Organic cation transport). OCTN2 transports carnitine into the mitochondial matrix where it can ...
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Does hydrolysis of carbohydrates, proteins, and fats occur in the small intestine?

Does the hydrolysis of carbohydrates, proteins, and fats occur in the small intestine? I have researched this and just cannot seem to get a clear-cut answer. Perhaps I am misunderstanding something? ...
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What happens when you mix catalase found in yeast with a small, medium, and large amount of isopropyl alcohol and hydrogen peroxide?

I conducted an experiment trying to see what isopropyl alcohol does to the catalase found in yeast's catalytic activity. I can not make sense of the results which showed that a 1:10 ratio and 1:1 ...
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What does the acronym ‘PIN’ stand for referring to PIN proteins in plants?

There are so called PIN proteins, or PIN-formed proteins, in plants. What does this acronym mean? Wikipedia briefly explains the function of the protein but not the origin of the name. It's not ...
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Will dissolved proteins pass through a 0.2 micron filter?

Given that there may be exceptions, can you usually expect protein to pass through?
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Why can't plain water be used in dialysis? Why is buffer used?

I read that buffer is used in dialysis because usage of water could cause precipitation of proteins but I don't really understand why and how water can cause precipitation of proteins and buffer ...
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Are there any online resources for finding the signaling pathways that two proteins both belong to?

I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these ...
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What does ΔC and ΔN mean with regards to a protein sequence?

I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement: Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the amino-...
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Did Mendel believe that proteins are hereditary substances?

Scientists first thought that proteins, which are found in chromosomes along with DNA, would turn out to be the sought-after genetic material. Proteins were known to have diverse amino acid sequences, ...
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Do we find protein not of cellular origin in nature?

I read once that we have two sources for proteins: Protein that is made in cells Protein that is made in labs However, based on Miller–Urey experiment, it's argued that amino acids can be made from ...
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How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
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What are the different types of helices in protein secondary structures and how do they differ?

What are the different types of helices in protein secondary structures and how are they differentiated? In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5. In the ...

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