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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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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What is the best way to find which domains in a list of InterPro IDs are catalytic?

What is the best way to find which domains in a list of InterPro IDs are catalytic? (In this case, we are looking at human enzymes and their domains' InterPro IDs.) Thanks in advance! Setz
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Where did the first proteins, without the aid of ribosomes, came from?

In order to make proteins, a cell uses ribosomes, which itself is a structure made out of proteins. The first ribosome couldn't have been created with the help of ribosomes though, as the ribosomes ...
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Why are some protein sequences known but their 3D structure isn't?

Why are there some proteins that have a known amino acid sequence, but their 3D structure is not known? Wouldn't finding the former in a lab lead to the discovery of the latter? Please correct me if I ...
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What is a Protein contact map, and how do I read one?

Protein contact maps are symmetrical and look great, but how does one read one? 'Understanding contact patterns of protein structures from protein contact map and investigation of unique patterns in ...
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Do proteins generally contain phosphorus and sulfur?

I've heard that proteins generally contain six main elements - carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. I know that proteins are made from amino acids. Amino acids are composed of ...
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Are there any proteins not found in the brain that are affected by prions?

A prion is an abnormally folded protein that is capable of causing otherwise normal proteins to also misfold and become prions. They are responsible for causing diseases such as Kuru and Creutzfeldt–...
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How can protein allergens be passed from mother to baby via breastmilk is proteins are broken down after ingestion?

All over the Internet new mothers are urged to avoid dairy products, a slew of vegetables and even beef if their child displays symptoms of reflux. In the case of dairy, for instance, it is said that ...
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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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How do anticholinesterase pesticides kill nematodes?

Compounds that inhibit the enzyme acetylcholinesterase are commonly used as pesticides. In animals with centralized respiratory systems controlled by the nervous system, poisoning with an ...
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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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What is “irrational” drug/molecule design?

Both the papers "Directed evolution: the 'rational' basis for 'irrational' design" by Tobin et al. and "Rational and 'Irrational' Design of Proteins and Their Use in Biotechnology" ...
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How are proteins containing other elements encoded?

If I understand correctly, proteins are formed by associating each three-letter DNA sequence to a certain amino acid. Yet there seem to be proteins which contain elements such as copper, which isn't ...
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Is this basic gene diagram correctly labeled?

I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what ...
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Why do nattokinase and serratiopeptidase remain effective when given orally, but not insulin?

Why do nattokinase and serratiopeptidase not break down in the stomach and intestines? Article says that serratiopeptidase is absorbed in rats intestines after oral intake - https://iubmb....
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Do people with higher body hair growth (eg. Women with hirutism) need more protein? [closed]

Hair is protein. Does that mean that the body of a woman with hirutism is using more than usual protein to make hair and thus she needs more for building and repairing muscles?
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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 [closed]

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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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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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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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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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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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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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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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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Why is sickle cell trait expressed in half of all cells rather than all cells containing half-sickled haemoglobin

If sickle cell trait is due to be heterozygous with respect to a single gene mutation on the haemoglobin β-globin chain, why is it the case that ~50% of RBCs are sickled rather than half of the ...
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Why are prions in animal diets not destroyed by the digestive system?

According to CBC: Mad cow disease is the common name for a condition known technically as bovine spongiform encephalopathy, or BSE. [...] The only known source of mad cow disease is from animal-...
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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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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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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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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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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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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 peanut proteins similar to chicken meat proteins?

I'm studying amino acids content in vegetable food. I was looking at peanut protein and noticed its similarity with chicken meat, as you can see in the table below (quantities are measured in grams). ...
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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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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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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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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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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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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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