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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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How to prevent small-protein smearing in SDS-PAGE?

I am doing SDS-PAGE for ubiquitin-6xhis (9.6kDa), and all my hand-cast gels produce a smeared band (see image). I typically use 5% acrylamide for stacking, 15% for resolving gel layers. I don't ...
Tom Murphy's user avatar
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How do you determine the structure of a molecular recognition feature (MoRF) after it binds to itself?

I have a protein that has a roughly 10 residue chain that registers at a MoRF in MoRFPred and MoRFchibi. I have the PDB files to correlate the known structure of the protein with the site of the MoRF; ...
vdg's user avatar
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Knock-Out (KO) Mice

We have generated an induced KO mice line for a specific gene. However when i perform IF staining I can still see substantial levels of the protein for this specific gene produced, even though the ...
shaii's user avatar
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Binding modes of a protein on a planar surface graphene

Can a protein have different binding modes on a flat even surface like graphene? For a surface like Graphene oxide I can understand, since it has several oxygenated groups on its surface that makes it ...
Roshan Shrestha's user avatar
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What is the difference between "microproteome" and "peptidome"?

I know that "peptide" is sometimes used to refer to both microproteins and short peptides derived from longer proteins (post-translational), but I do not know whether this extends to "...
kate allerton's user avatar
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Best way to predict the effects of deletion mutations on protein function?

I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of ...
aquaporin's user avatar
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If protein is mostly used by the body for purposes other than extraction of energy, why are calories from protein relevant?

Non-biologist speaking here. As you can probably see from the title, I'm having trouble wrapping my head around concepts related to the body's energy balance amd the role of macronutrients. Let me ...
ilovemaths's user avatar
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Does it make sense to calculate the phospho protein (serine) : phospho protein (threonine) of the same protein in western blot?

I want to indirectly measure the nuclear accumulation of DARPP protein through phosphorylation. Their nuclear transport is controlled by phosphorylation of Threonine 34 and Serine 97 residues. S97 is ...
oklu's user avatar
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How is opsin of rhodopsin is different from that of iodopsin? [closed]

Rhodopsin contain retinal, an aldehyde of vitamin A and opsin protein and iodopsin also contains retinal along three different types of opsins namely erythropsin, chloropsin and cyanopsin. But kind of ...
Venkatesh Choudhary's user avatar
3 votes
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Why UniRef representative sequences in UniProt are so long?

I found that some sequences in UniRef90 database are tens of thousands amino acids long. I read UniProt official documentation and figured out that these sequences are the representative sequences of ...
dearname's user avatar
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What is the optimal pO2 concentration for automated reactor batch mode EColi expression?

I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? ...
raptorlane's user avatar
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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 ...
raptorlane's user avatar
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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 ...
MHamel's user avatar
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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/...
Growing6884's user avatar
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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 ...
Christian's user avatar
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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 ...
Gumpf's user avatar
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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 ...
Jack's user avatar
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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 ...
Jack's user avatar
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6 votes
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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 ...
Gumpf's user avatar
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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 ...
Orca's user avatar
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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 ...
Shreyash Yadav's user avatar
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750 views

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 ...
Abhimanyu Pallavi Sudhir's user avatar
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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 ...
Lara's user avatar
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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 ...
Science123's user avatar
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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
2 votes
2 answers
143 views

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 ...
nullspace's user avatar
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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 ...
Candlebeam's user avatar
3 votes
2 answers
121 views

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 (...
Wan NIE's user avatar
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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 ...
Patrick Chan's user avatar
24 votes
3 answers
6k views

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 ...
Vladislav's user avatar
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3 answers
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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 ...
Nawaz_04's user avatar
1 vote
1 answer
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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 ...
qwerty's user avatar
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1 answer
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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 ...
Juhi Kumari's user avatar
2 votes
0 answers
124 views

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: ...
Alpha's user avatar
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4 votes
1 answer
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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
1 vote
0 answers
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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, ...
Anwar Elhadad's user avatar
2 votes
0 answers
43 views

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 ...
719016's user avatar
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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
1 vote
1 answer
55 views

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 ...
symmetrickittens's user avatar
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35 views

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 ...
bonCodigo's user avatar
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4 votes
1 answer
735 views

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
8 votes
1 answer
103 views

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 ...
Paul's user avatar
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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(...
Giorgi Lagidze's user avatar
1 vote
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37 views

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
1 vote
0 answers
21 views

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
3 votes
0 answers
55 views

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,...
Alex I's user avatar
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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?
Ming's user avatar
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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 ...
Curious Layman's user avatar

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