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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Why doesn't treating neurons with a high sodium solution depolarize their membranes?
I am reading a journal paper, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:
We found that ...
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What are possible tweaks when a protein expression from a plasmid shipped on paper fails?
In my group we recently tried to express a protein necessary to perform an analytical method in BL21(DE3). The first two attempts did fail and no colonies did grow on the agarose. I hear, that the ...
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How do I assess the conservation of a protein function across different homologs, isoforms, biosimilars?
I am studying toxicology where the presence of a "toxic" function is more important (in context) than a protein's ancestry. After scanning the lit, homology modelling seems to be the best ...
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How does comparing shuffled proteomes to the unshuffled ones help us understand independent protein adaptation?
From 'Protein and DNA Sequence Determinants of Thermophilic Adaptation', by Konstantin B Zeldovich, Igor N Berezovsky and Eugene I Shakhnovich (Published: January 12, 2007 | https://doi.org/10.1371/...
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What protein or other process does the peptide BPC-157 come from?
BPC-157 is a peptide for which there were some studies that suggest that it can help with wound healing and gastrointestinal problems in some animal models. In 2022 the World Anti-Doping Agency added ...
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How to choose a method for upregulating an endogenous protein?
What factors affect the method that should be chosen to engineer a cell line that upregulates an endogenous protein? I am mostly asking permanent or long-term expression of nuclear proteins in ...
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Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?
An acquaintance provided me with this article1. I can't understand for sure what it is about.
My acquaintance said that it proves that time for generation of even the simplest proteins is on a ...
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MSA cluster and MSA depth
I was reading the AlphaFold paper and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate.
I had a hard ...
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What is the purpose of using two layers of gel in SDS- PAGE?
I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about ...
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Sequence identity and coverage in multiple sequence alignment of proteins
This might be naive since I am very new to the field, but I wonder about the difference between sequence identity and coverage in multiple sequence alignment of proteins. I imagine the calculation ...
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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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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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If Viruses use Host Proteins, why don't Immune Cells attack Host Cells?
The Wikipedia article for Viral Proteins contains the following line:
Thus, viruses do not code for many of their own viral proteins, and instead use the host cell's machinery to produce the viral ...
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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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How do i find and download targets of drugs which are in DrugBank?
Recently, I am focused on drugs and their interactions. But since I am new in this field, using experts experience would help me a lot. I have downloaded DrugBank xml file from DrugBank website and ...
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How to convert Kilo Units (KU) to mg? [duplicate]
Im searching for AChE (Acetylcholinesterase) and on sigma-aldrich it is showing 2 KU or 2000U/mg of protein and on MedChemExpress it is showing 50mg then how can we calcute how much will be the drug ...
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Does poop have protein?
Popular health advice suggests that one shouldn't consume >30g of protein at a time (without a gap of ~3 hours, or otherwise depending on the type of protein), because only so much can be digested ...
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What is the best way/kit to extract total proteins from biopsy tissue?
I need to extract total protein from 2mm skin biopsies for western blots.
I was thinking about miRNeasy Micro Kit (50) Cat. #217084 while it's ok for total RNA ...
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Question on protonation/deprotonation of amino acid side chains
I understand that actual pKa of amino acid side chains is greatly influenced by the surrounding environment. I am trying to deeply understand the equilibrium between protonated and deprotonated form ...
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Are all proteins translated by the RER ribosomes destined for the Golgi apparatus?
The proteins translated by the free ribosomes can fold in the cytoplasm and never go through the endomembrane system. But when the endomembrane system is described, it is always stated that the ...
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Efficiency of molecular motors vs. human-made motors
On the wikipedia page for "Molecular motor", it says "In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors." without any ...
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What is the precise definition of "cytokine"?
For example, both bone morphogenetic protein 4 and nerve growth factor are paracrine signaling proteins which promote growth of their respective tissues, and both are known to have some effect on the ...
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What is the danger of biasing the sampling when using Monte carlo in protein/peptide structure prediction
I am reading this paper in the link.
In introduction, paragraph 3, the last few lines are as follows
In theory, MC methods can be as ac-
curate as MD methods, but MC may suffer from lower efficiency ...
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Relationship between an Integrin-binding peptide and the Collagen type that it models
Recently, I have been investigating whether collagen can interact with integrin α2 (the product of human gene ITGA2). There is a structure in the protein data bank (...
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Confused about the transport of materials across cell membranes
I am very confused about how exactly substances are transported across cells. For example, if a cell is placed in a hypertonic solution, the cell loses water. If the cell is placed in a hypotonic ...
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Sequence homology of cytokeratins
I am reading https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962860/ and do not understand what it means by high sequence homology of cytokeratins in the following text:
"Sequence homology of ...
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How do proteins 'know' where to go?
I've just found once again this famous animation I've been curious about for many years:
https://youtu.be/WFCvkkDSfIU?t=213
Here's a screenshot from the animation:
The green blobs (proteins, I ...
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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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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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Protein in fruits
Why do fruits have such a low protein content (with a few exceptions) ? Don't seeds need protein while growing up? In comparison, the egg of a hen contains lots of protein, used to make a chick.
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What are the benefits of elucidating the three-dimensional structure of a protein?
I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we ...
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Essential amino acids
Humans and the majority of animal species cannot synthesize essential amino acids (Info: Campbell biology 9th edition). However, meat, eggs, et cetera provide all required essential amino acids. And ...
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Are channel proteins considered a type of integral protein or peripheral protein?
I have conducted research, and unfortunately, I am unable to conclude whether channel proteins are considered a type of integral or peripheral protein. Based on my understanding, channel proteins are ...
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Do we need to underline the name of a gene while handwriting?
While teaching about the cry genes and the Cry proteins in Biology class, my teacher told us that the names of genes are always written in lowercase and should be italicized, and the name of protein ...
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Do GPCRs such as this chemokine receptor legitimately have these extended coils?
I've been using alphafold to generate some GPCRs from uniprot protein sequences (in the image is CCR2) but have noticed that there are these really long coils coming out of both the extra and ...
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How to prepare the standard curve solution for Proline estimation
My aim is to estimate proline content from plant tissues using Ninhydrin method with a spectrophotometer(colorimetric method). Briefly, Proline when in contact with Ninhydrin yield a colured solution ...
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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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The springlike behavior of titin problem
I am currently reading a textbook (Molecular Biology of the Cell, 6th ed), and this problem on p. 170 is driving me crazy. I read through the solution given in this book but I couldn’t understand it ...
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Do voltage-gated channels in a neuron use ATP
I have a question about action potentials in a neuron.
Do voltage-gated sodium and potassium channels use ATP? I mean when they are closed or when they want to open the gate, do they use ATP?
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Endospores contact with surfaces
I am currently studying endospores-forming bacteria. To be specific B.subtilis. I noticed that the formed spores have strong contact "grip" with the surface it is forming on. For example, ...
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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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Meaning of “cognate genes encode the basic biological functions of proteins”
In the introduction to a review article entitled “Interpreting the protein language using proteomics” the author uses the term ‘cognate genes’ in a manner which I do not understand:
Whereas cognate ...
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What enzyme could you use to delipidate lipidated serine?
I have a protein with a serine modified with an O-octanoyl group (ester linkage). What enzyme could I use to remove this group? Could I use a lipase, such as pancreatic lipase?
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Why is random protein selection not used more often in biotech to create proteins with desired enzymatic activity?
mRNA/cDNA display allows random libraries of up to ~ 10^13 proteins to be subject to selection for binding to arbitrary binders. In the listed studies, proteins selected for ATP binding also had ATP ...
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What is the difference between a protein and a factor?
In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors?
I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly ...
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Boundary of a cell and its membrane - position definition and jargon problem
Can extracellular be extramembrane/intramembrane?
Definition of Extracellular here:
Extracellular matrix: The extracellular matrix is a complex network of material such as proteins and ...
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Are "antibodies" and "immunoglobulins" really the same things?
Wikipedia says that NCAM (CD56) glycoprotein belongs to Immunoglobulin (Ig) superfamily.
A the same time, its article on antibodies equates them with immunoglobulins. NCAM is obviously not an antibody,...
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Is there a way to refine a low resolution Cryo-EM structure using high resolution partial crystal structures?
I'm working on running simulations of human topoisomerase IIa. These are best done by starting with high resolution structures to ensure the system is as accurate as possible. However, no crystals ...
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How does the energy we get from food transform into mechanical motion at the cellular level?
I am curious how, food broken down into glucose powers the movement of proteins in our cells (e.g., in muscle fibers for example).
Is the thermal energy converted to kinetic energy somehow?
As a ...
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What has caused life to choose this unfathomably tiny subset of all possible proteins?
I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ...
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