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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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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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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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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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 ...
Damocle Damoclev's user avatar
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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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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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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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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 ...
weddegege's user avatar
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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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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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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 ...
Son of Sevenless's user avatar
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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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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?
WaterMolecule's user avatar
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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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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,...
Damocle Damoclev's user avatar
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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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cancer cell - antigen presenting cell

We all know that if normal cell contains virus inside it, normal cell has mechanism inside it that can detect that it has abnormality inside(virus) and what it will do is present the virus's protein(...
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immune system - how does adaptive work without innate?

The way I understood immune system is that: phagocytes detect viruses and present it on their surface and become antigen presenting cells. Then, T-helper cells try to bind to these phagocytes that ...
Giorgi Lagidze's user avatar
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What is the oligomeric state of Leptospira LipL32 protein?

Does anyone know the oligomeric state of the mature and functional lipoprotein lipL32 in Leptospira? It's an outer membrane-bound protein. In its mature state, the signal peptide (residues 1-20) is ...
Anthony Nash's user avatar
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Is it possible to crystallize proteins so that the crystal has a normal concentration of potassium chloride?

I've been learning about protein crystallography, and how crystals are made. A lot of the crystallization processes involve gradually changing variables (protein concentration, pH, salt concentration,...
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Is there any reagent that can help me obtain the protein in a 14 μm tissue without damaging the morphology of the tissue

I need to extract proteins, but I want to protect the morphology of the tissue. Can I use lysis buffer directly?
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How many proteoforms are theoretically possible?

Initially, I was going to ask how many proteins were possible. But, while researching the question, I learned the word proteoform and have been reading a lot of stuff I don't really understand, but ...
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Molecular Signaling: Why is it more difficult to study membrane-bound signaling molecules compared to soluble ones?

I am reading the textbook Neuroscience (6th ed.) by Dale Purves and colleagues. In one of the chapters (Chapter 7, Molecular Signaling within Neurons), I am reading about the different types of ...
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Why can't protein pumps reuse phosphate groups?

I am currently in AP Bio, and our textbook has a diagram of a sodium-potassium pump: If I am understanding correctly, every time this cycle occurs, an ATP is hydrolyzed in step 2 to produce a new ...
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Why are there so many carbonic anhydrase structures in the Protein Data Bank?

I've been looking through PDB — the Protein Data Bank — and I noticed that the protein with the most structures is human carbonic anhydrase II (UniProt: P00918), with over a thousand X-ray structures. ...
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Is retinoblastoma truly an autosomal dominant condition?

I am getting, in my opinion, very conflicting information from sources about the inheritance of retinoblastoma, a type of cancer. Hereditary retinoblastoma is associated with defects in the gene ...
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Comparison of different glassy matrices for protein immobilization at room temperature

I am completely new to protein biology experiments. I care about experiments where proteins are immobilized near a surface with the help of a glassy matrix or similar materials. I am looking for a ...
Ben's user avatar
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Examples of passive membrane transport proteins that only transport in one direction and their mechanism

I would like to know about those transporters with alternating-access-type mechanism, that can only efficiently shuttle molecules in one direction but the other direction is severely kinetically ...
symmetrickittens's user avatar
2 votes
1 answer
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Is there are theoretical limit to the number of proteins possible and their respective structure?

I saw an article saying that DeepMinds AI has catatogued every protein known to science. I guess "known to science" and what is the theoretical limit is not exactly the same thing but the ...
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Does the recent concern over several papers about Aβ*56 call into question the association of Alzheimers Disease with any amyloyd beta oligomer forms?

The news item by Charles Piller just published in Science BLOTS ON A FIELD? A neuroscience image sleuth finds signs of fabrication in scores of Alzheimer’s articles, threatening a reigning theory of ...
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What is the relationship between stress granules and circular RNAs?

I have read that circRNAs act as sponges for miRNAs and that stress granules help reduce chronic cellular stress and they are composed of proteins and RNAs. I'm interested in the relationship between ...
Shadan Alrawi's user avatar
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What came first: the ribosome in which RNA is read, or the RNA to encode for the ribosome proteins? [duplicate]

It's a bit like the chicken-and-egg problem. Ribosomes need proteins because they are partially made of them. Where can they get their proteins? They read the base sequence in mRNA entering them, ...
Felicia's user avatar
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Does the SARS-CoV2 spike protein passively diffuse through the nuclear pore complex?

I found this thread which is worth reviewing as context to my question(s) since there is some overlap in potential discussion, although it's concern is with mRNA ingress rather than spike protein. ...
Ben Shaman's user avatar
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1 answer
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How does tetracycline transactivator localize to the nucleus? Where is the nuclear localization signal?

Proteins typically use a nuclear localization signal (NLS) to localize to the nucleus. Tetracycline transactivator (TTA) needs to work in the nucleus, but I did not find an NLS in the structure. ...
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Why is protein turnover necessary or important for cells to function?

Cells constantly create new proteins in order to maintain their normal function, this is called protein turnover. Why is that? Do the old molecules wear out as time passes, so that they need a ...
Georgi Popov's user avatar
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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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