Questions tagged [proteins]

Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

Filter by
Sorted by
Tagged with
5
votes
2answers
84 views

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 ...
1
vote
1answer
92 views

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 ...
3
votes
1answer
79 views

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 ...
2
votes
0answers
36 views

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....
-2
votes
1answer
41 views

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?
8
votes
3answers
326 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 ...
1
vote
0answers
35 views

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 ...
3
votes
1answer
85 views

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 ...
-1
votes
1answer
50 views

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 ...
2
votes
1answer
65 views

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? ...
1
vote
1answer
42 views

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 ...
2
votes
1answer
59 views

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 ...
3
votes
1answer
51 views

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 ...
0
votes
0answers
15 views

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 ...
1
vote
1answer
29 views

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. ...
0
votes
1answer
646 views

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 ...
0
votes
0answers
28 views

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 ...
0
votes
0answers
39 views

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 ...
0
votes
1answer
37 views

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 ...
2
votes
1answer
86 views

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 ...
0
votes
0answers
11 views

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.
1
vote
0answers
28 views

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!
1
vote
1answer
106 views

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 ...
2
votes
0answers
30 views

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 ...
1
vote
1answer
29 views

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 ...
11
votes
2answers
2k views

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" ...
2
votes
2answers
520 views

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 ...
9
votes
1answer
162 views

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 ...
-1
votes
1answer
118 views

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 ...
0
votes
1answer
48 views

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 ...
6
votes
1answer
305 views

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 ...
3
votes
1answer
52 views

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 ...
1
vote
1answer
112 views

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 ...
1
vote
0answers
31 views

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 ...
-1
votes
1answer
81 views

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 ...
0
votes
0answers
39 views

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)
1
vote
1answer
57 views

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 switch ...
2
votes
0answers
107 views

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 ...
1
vote
1answer
43 views

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 ...
1
vote
0answers
21 views

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 ...
3
votes
1answer
25 views

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 ...
1
vote
1answer
24 views

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 ...
1
vote
1answer
55 views

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 ...
0
votes
1answer
139 views

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 ...
2
votes
0answers
40 views

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 ...
0
votes
1answer
157 views

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 ...
1
vote
0answers
55 views

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 ...
1
vote
0answers
93 views

Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
-1
votes
1answer
66 views

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 ...
2
votes
0answers
59 views

Fluorescence assays to identify protein concentration without adding a large peptide sequence?

I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. ...

1 2
3
4 5
18