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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24 views

Protein structure prediction from amino acids sequence

Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict ...
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A balanced diet with the minimum carbon footprint

Many studies shows that 1 kg of non-vegetarian food as 3-4 times more carbon footprint than 1 kg of vegetarian food. I think that does not represent the complete picture food from animal sources are ...
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Why can't we use biological process to manufacture items to save energy?

I see many variety of things made by nature around me - I am talking about things made as a result of biological processes. For example: Trees make wood Plants make variety of fruits (some are soft, ...
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How many proteins could participate in a complex

Disclaimer: I’m a computer science student with minimum knowledge of biology. I’m working on an algorithm to cluster proteins in Protein-Protein-Interaction Networks to find protein-complexes. While ...
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Available Protein sequence alignment dataset and HMM model

I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to generate noisy copies of the consensus sequence ...
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Are there any proteins assembled from non-adjacent parts of the genome?

Many proteins are assembled from multiple exons with the introns between adjacent exons being spliced out. But are there any proteins that have unrelated to them exons in the middle of their sequence? ...
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How does protein protect itself from the protease of the same organism?

In a German podcast about the coronavirus, the professor is saying that a piece of meat has protease on its surface, i.e. protein destroying enzymes (which would destroy most virus materials on its ...
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Meaning of “Domain with function to find” (FIIND)

From NALPs: a novel protein family involved in inflammation. FIIND - Domain with Function to Find. What is the meaning of this name? Does it mean "Domain with an unknown function"? I'm ...
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Can DNA be used directly to determine the age of a mutation?

I've studied that proteins found in a sample as biochemical evidences for evolution. Its variation in structure and configuration can be used to date the age when that mutation occured, effectively ...
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single nucleotide polymorphism and protein domain

I have a list of nsSNPs (e.g. rs121918549) and I want to know what are the protein domains that contain those nsSNPs. Can someone suggest a way to do so (some online database/tool)? Thanks in advance
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What's the role of bromelain in pineapple?

Bromelain refers to one of two proteases found in pineapple and its relatives. Like other proteases, many believe it has therapeutic uses and it's the subject of a lot of research. But what role does ...
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network with all the interactions of the alpha-synuclein protein

I would like to make a network with all the interactions of the alpha-synuclein protein (in homo sapiens), that is, I would like to visualize the pathways where this protein participates, I would also ...
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Glycocylation or glycosylation?

I came across a few sources that refer to glycocylation. Is this the same as glycosylation? See for instance page 237, or the abstract in this paper. ...
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Type VII collagen binds type IV collagen?

What are the functions of type VII collagen ? My book says it 'binds type IV collagen', does that just mean it binds type IV collagens together to form a sheet or a network of type IV collagen for ...
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Why don't carrier proteins require energy to change shape?

I know that carrier proteins can be used for both passive and active transport, but I am referring to the facilitated diffusion aspect. Even though facilitated diffusion via carrier protein goes along ...
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How to filter the PBD databank for “single-domain proteins with full length 3D-structures solved”

I am trying to reproduce a machine learning model that has been developed here. As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a ...
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Need either a [similar] ribosome to the following few | a heuristic for finding [similar] macromolecule given 20 others

Background : Hi! I am running a small experiment dealing with structural heterogeneity of the ribosome, actually of ribosomes across all domains of life. It's entirely computational: I get cryoEM ...
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How much of the genotype-phenotype map do we understand in HIV?

From what I understand, viruses have very small genomes relative to those of standard model organisms used in biological research. For example, according to Wikipedia, "the HIV genome contains nine ...
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Does destroying a virus envelope make the virus inactive?

Some viruses have a lipid envelope around their protein capsid. The envelope can be dissolved with soap, but does that still leave the capsid and interior genetic material intact? If so, is the virus ...
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Protein content in chemical composition of different phyla?

The protein content in the human body is roughly 15%, what are the percentages for other organisms? Bacteria, plants, fungi, protozoa, etc.
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How does a protein molecule enter a cell through the cell membrane? [closed]

I can't find a good explanation as to how a whole protein molecule enters a cell membrane. Is it through endocytotic vesicles, with the help of ATP? How does this occur? Thanks for the help!
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Which proteins are part of the most different protein complexes?

Let n be the number of different protein complexes (as defined here) that a protein may be a stable part of for a considerable amount of time (and not only transiently). Which proteins have the ...
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Genes and proteins with a significantly inbalanced composition

According to Wikipedia, the median size of a protein-coding gene is 26,288 bp which makes it possible (from statistical considerations) that the nucleotides C, G, A, T appear in roughly equal amounts ...
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Cell type = gene expression spectrum?

I wonder if it is correct to say that the type of a cell is essentially its spectrum of expressed genes, i.e. the rates at which it produces specific proteins. As these rates may change (e.g. during ...
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Are the 70s ribosomes in archaea similar to the 80s ribosomes in eukarya

I understand that archaea are closer to eukarya than they are to bacteria (especially in the proteins of their RNA polymerase) but are they also similar in their ribosomes? (despite having different s ...
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In the notch signaling pathway, what is Fringe activating?

Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330 I want to know what is Fringe activating. It is not pointing to another gene or ...
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Can the human body store protein?

I am interested to know if a human body can store protein. Absolutely for the bodybuilders, does it really matter if they divide their protein consumption during the day or eat all of it in one meal ...
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Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

I read in Wikipedia: While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as ...
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AChE aging time of organophosphates containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the organophosphate phosphorylates the serine-203 residue of the enzyme. If the enzyme is not ...
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How to analyze phosphorylation shift by western blot?

I want to see the phosphorylation shift in my protein of interest. I have created a point mutation in my protein. so that it will not able to go for the phosphorylation compare to my control. i want ...
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If a gene is missing from an operon that structures a protein, then would that protein not be made properly?

From my understanding, operon is a series of genes that are regulated by a single promotor. In many cases genes in an operon form subunits of a protein. I obtained a genome in my study and looked for ...
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Statistics: How are protein species distributed over cell types?

There are roughly 10,000 to 20,000 protein species in the human proteome (while I've seen also numbers of 500,000 to 1,000,000). Furthermore, there are roughly 200 different cell types in the human ...
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Bimodal frequency distribution of size of protein loops

The graph of number of amino acid (AA) residues in a loop Vs the frequency of their occurrence in proteins largely follows a tending-to-zero pattern. However, there appear to be some specific number ...
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How are proteins reused in the body? [duplicate]

Part of what we eat are proteins, and our body is in part build of proteins. Are the proteins of the body build based on proteins in food at all? Are proteins in food directly reused in the body, or ...
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What difference in proteins radius of gyration can be considered significant?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein. When comparing two protein radius of gyration, what difference can be ...
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Why is dimethylmercury so poisonous? [closed]

According to the Wikipedia article Karen Wetterhahn, Karen Wetterhahn died after only a very small amount of dimethylmercury got absorbed through the gloves. What is it about the way the body works ...
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Is brewer's yeast a good source of protein for humans?

I read that brewer's yeast protein is not a "real protein" and is not usable by non-ruminants. Is that true? If yes, how can I know what kind of protein is good for humans (especially athletes)
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KRAS gene and K-Ras Mutations

This question pertains to the KRAS wikipedia page, and I just want to double check and clarify my own understanding of how this mutation works in cancer. It states: K-Ras protein acts like a ...
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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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What happens to embedded membrane proteins after a vesicle is formed?

When an animal cell is going through endocytosis it cell surrounds a food particle, and the membrane swallows it, creating a vesicle within the cell. However, what happens to the embedded ...
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Are Hsp70 proteins only activated in response to heat shock?

Hsp70 proteins are chaperones that assist in protein folding in my plant physiology textbook it says the Hsp70 proteins were discovered by inducing heat shock. But do they only work in response to ...
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How to get a list of kinases that phosphorylated a particular protein?

I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue. I want to know which proteins could have ...
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Is mucus significantly affected by the presence of ions?

In mucus, there is besides water and the mucins (Proteins for mucus), there are Ions like $Ca^{2+},Na^{+}$, etc. I have read that These Ions can Control the mucus swelling, i.e. the volume that the ...
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Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a ...
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Protein folding

I've two questions 1. Is free ATP available in the cytoplasm of the cell? 2. In the protein folding funnel, prions and other misfolded proteins are located at the local minima of the graph. If ATP ...
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Do carrier proteins constantly open and close or do they only work when a substance binds to them?

What causes carrier proteins to change shape ? Do they need energy to change shape? If that is true, how are they involved in Facilitated diffusion ? By changing shape, do we always mean opens from ...
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is consuming collagen actually good for skin/joint health? [duplicate]

A coworker of mine insists on drinking a very expensive collagen supplement for their skin health. It seems like a gimmick- Doesn't the digestive process breakdown proteins to their constituent amino ...
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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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Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
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Is it scientifically feasible to compare two samples of different sizes, while values in each sample are average numbers?

I want to compare result from my protein docking experiments to various protein structures of the same protein. I have two samples and in Sample 1, I have ...

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