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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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1answer
295 views

What characteristics of the protein folding process ensure that the energy landscape is a funnel?

The folding funnel hypothesis states that the energy landscape that proteins observe when they fold is funnel shaped with a single global optima. This ensures that no matter what sequence of folds the ...
2
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1answer
268 views

What's the difference between prions and prion-like proteins?

If I added a prion domain to a protein, does that make the protein a prion-like protein or would it be considered a prion at that point? I'm trying to understand what prions are, how they aggregate ...
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0answers
109 views

Protein/ligand affinity databases?

Is there any database that contain binding affinities reported in litterature for different proteins and ligands? I have checked uniprot already and it does not seem to included any binding affinity ...
3
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1answer
202 views

If bortezomib, a cancer drug, inhibits cell proteasomes, wouldn't resulting protein aggregate in normal cells further increase the risk of cancer?

Bortezomib is an anti-cancer drug that inhibits the proteasomes of cancer cells, allowing proteins that stop cell growth to fold and perform their function. However, wouldn't bortezomib also affect ...
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0answers
49 views

String-db locally downloaded

I need a ppi network of cancer and it should have 200k to 300k proteins (nodes) As the web inteface don't allow more than 2000 ...
16
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3answers
1k views

Is prion a term used to describe the normal form of the protein as well as the disease causing form?

I've been reading my textbook and it refers to prions as a normal protein with a helpful function but it can turn into a disease causing form. However, I look in my other textbook and it refers to the ...
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0answers
47 views

Biogrid interaction protein network

I need a ppi network for cancer or Alzheimer . I'm using BioGrid , In the search field I can specify the gene id only , I want to know how can I make an interaction network for one of the disease ? ...
3
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1answer
206 views

R Stringdb bioconductor

I 'm using STRINGdb package from biconductor to manipulate String database of ppi I'm newbie and I don't find the documentation of the package useful for me . I wanna extract the associated network ...
0
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1answer
35 views

Retrieve the associated annotation from Uniprot

I have a dataset that I extracted using Cytoscape and STRINGAPI Hoz can I retreive the annotation of that network from uniprot as it has more than 1k proteins . and doing it manually is not possible
2
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2answers
73 views

Predicting DNA nucleotide bases sequence from fully formed protein

I know there are many algorithms (and a lot of different implementations) that allow predicting the outcome of protein synthesis given a set of nucleotide bases present in the DNA. In other words, ...
1
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0answers
41 views

Cytoscape export network

I'm using Cytoscape to visualise a ppi network having 2000 proteins ... I m trying to export it but the supported format are only cytoscype formats not a usable ones and for the table format the ...
3
votes
1answer
46 views

Are bacterial RNA polymerases distributed evenly throughout the cell or localized?

Bacterial cells aren't internally compartmentalized with membranes (like eukaryotes). This naturally leads to an image of a homogeneous interior, but bacterial cytoplasm isn't homogeneous. Case in ...
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0answers
41 views

Human Papillomavirus E7 (HR HPV16)

So there's a protein that binds to E7 viral protein, I want to remove a sub domain of the protein to see which exact domain the E7 binds to. What is the procedure for this? Edit: I believe the virus ...
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0answers
106 views

Pelleting bacterial cells using centrifugation and getting proteins in the supernatant

Do significant amount of proteins from cells find their way in supernatant during pelleting? If the answer is yes then I see two ways in which protein can be in the supernatant . 1) Through lysis ...
0
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0answers
83 views

STRING DATABASE export graph

I'm using STRING database to export a network that I'm going to integrate in Neo4j . I cant find the format to export data as a network I have tried all of the ones in the export tab but none seem to ...
3
votes
1answer
170 views

How are collagen fibers in skin aligned with respect to skin surface?

I read in one paper that collagen fibers in dermis are randomly oriented in direction with respect to the skin surface. I can't locate that paper now. However, I came across this paper that indicates ...
4
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2answers
480 views

Should there be separate Ramachandran plots for an amino acid in different contexts?

I understand the nomenclature of the phi and the psi angles of the alpha-Carbon atoms in protein stucture, but I am confused by the Ramachandran plot. Each alpha-Carbon atom (magenta) makes two ...
0
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1answer
46 views

Do mutations in one bacterial strain have the same effect in other strains within the same species?

I would assume so, since they are the same species after all. I am asking this because I am doing a bioinformatics project for school and I cannot find any protein mutations for the specific bacterial ...
5
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1answer
77 views

Generate mesh surface from protein structure

What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated. I'd prefer the output to be a ...
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0answers
29 views

Predict if a given protein can pass through the intestine

Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein can pass through the intestine or not?
2
votes
2answers
6k views

Why does Edema occur in Kwashiorkor?

Edema in lower leg and face is a symptom of Kwashiorkor. It is the most distinguishing feature of it which distinguishes it from Marasmus. Why would decrease in amount of proteins cause Edema? Why ...
19
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1answer
2k views

Why are sushi proteins called “sushi”? What are the origins of this name?

Does anybody know why complement control proteins (also short consensus repeats) are called "sushi" proteins? Is there any special reason for their name?
6
votes
1answer
511 views

How many proteins are in the Earth's proteome? [closed]

Humans alone have thousands of proteins. With that in mind, it seems like the total number of proteins among all species would be very large. Are there any available estimates for how many proteins ...
3
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2answers
179 views

How were the first genes isolated from genomic or cDNA libraries without already knowing a hybridization probe?

Let us go back in time to around 1975. It is my understanding that at that point (or at least by the end of the decade), both genomic and cDNA libraries had been created for a few organisms, e.g. ...
3
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1answer
99 views

Sephadex column for alpha-amylase

I want to purify crude alpha-amylase with column chromatography. I am using a spehadex 75, But for some reason I can't find any information on how to make the slurry. I can quickly find tons of ...
6
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3answers
98 views

Protein in fruits

Why do fruits have such a low protein content (with a few exceptions) ? Don't seeds need protein while growing up? In comparison, the egg of a hen contains lots of protein, used to make a chick.
3
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1answer
68 views

Is Sda a protein, or is it a protein domain of DnaA?

I initially thought that a domain was a specific part of a protein, with it given tertiary structure, to which a given molecule is able to bind. (I think I recall phrases such as "the haem binding ...
2
votes
1answer
399 views

Protein content in sprouted beans

I have checked on Wikipedia which says that sprouted mung beans has way less protein than normal one, while on web you will find articles saying sprouted beans are best, which is true, how do I eat ...
2
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0answers
407 views

Why do my peptide samples turn yellow and red?

The protocols for (brain) tissue digestion I am trying out are: lysis (buffer containing 0.1% SDC or SDS in 100mM TEAB + phosphatase inhibitor which is sort of yellow), reduction with TCEP, alkylation ...
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2answers
76 views

Database of known human proteins

Is there an up-to-date database of known human proteins that is easily accessible using Python libraries?
0
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1answer
92 views

What is GST RhoA fusion protein?

Would you please explain to me what GST RhoA fusion protein means and how it differs from RhoA protein? I am a kind of doing an experiment using this protein.
4
votes
2answers
73 views

Etymology of PAX proteins

What is the reasoning behind naming proteins first found in Drosophila as paired box? All I could find on internet is that it was first found in Drosophila as a protein with paired domain, but I ...
3
votes
1answer
86 views

Translation of RNA into proteins

What's the least number of tRNA molecules needed to form a polypeptide chain that contain 50 amino acids of 15 types? I know that each type of amino acid has at least one unique type of tRNA that ...
1
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1answer
88 views

Protein diet composition

I have read that non veg food are better for proteins while veg food is deficient in either one or other protein. If it is so are herbivores protein deficient always in case of animals as well as ...
3
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1answer
73 views

How can antibodies in rapid antibody tests be kept at room temperature without denaturing?

The normal temperature for long term antibody storage is around -20 degrees Celsius. However, when developed into rapid antibody tests, they can be kept at room temperature for prolonged periods. How ...
4
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2answers
286 views

Betaine HCl stomach pH

It seems betaine HCL is often recommended for those suffering from "low stomach acid" -- which, as I understand, is having too high stomach pH for proper digestion (especially for proteolysis via ...
3
votes
1answer
159 views

Can I dry digested protein sample over weekend in a vacuum concentrator?

I have digested with trypsin the tissue protein extract for mass spectrometry, and forgot to transfer the sample from the SpeedVac to the -80C freezer. As I did this on Friday, I can transfer the ...
5
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1answer
173 views

Excess protein consumption effect on kidney

How does excess protein consumption through food as well as through supplements affect body especially kidneys? Why it is advice to consume low protein diet during summer ?
2
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1answer
498 views

Purpose of intensive protein synthesis in G1 phase of mitosis

What is the purpose of intensive protein synthesis in G1 phase of mitosis, and what purposes do these synthesized proteins serve? Why are lipids and carbohydrates not synthesized intensively as well?
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2answers
1k views

When does histone synthesis occur in relation to DNA replication?

Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?
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1answer
1k views

What inactivates pepsin in infants?

In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach. Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
4
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1answer
71 views

What is the secondary structure distribution per AA in the Human proteome?

If one would classify each amino acid to either be in a Coil, Beta strand or Alpha helix what would be the distribution of these classes in the human proteome? Is it 33%-33%-33% or is it biased? If ...
1
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1answer
171 views

What difference do trans and cis configurations of amide groups bring to the polypeptide chain?

Hi I was just wondering whether there would be any difference to the structure of the polypeptide chain, or any changes to a proteins characteristics, if it has more amide groups with a cis or trans ...
6
votes
1answer
436 views

What happens to the enzymes produced by the digestive system?

Our digestive system produces a lot of enzymes and they help to catabolize the food, and after completing their work are they excreted out or as they are also made up of proteins are they catabolized ...
4
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1answer
283 views

About the formation of protein [closed]

There is a question in my textbook which asks: "What does the glucose produced from photosynthesis form?" However one of the answers said that glucose forms protein. But I'm quite sure that amino ...
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0answers
29 views

Cows milk protein transferability through breast milk

I understand that cow's milk protein(casein) transfers through breast milk via the mother's diet. I'm looking for the process as in what hormone does it bind to to allow this process in some women ...
3
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0answers
85 views

Degradation of PMSF in protein extract while dialysing - safe for feeding to animals?

I would like to use the protease inhibitor PMSF in enzyme isolation. The obtained enzyme diamine oxidase (or better the protein extract) is tested oral on dogs. According to Wikipedia, PMSF has a ...
6
votes
1answer
58 views

For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?

I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics. PBPs cross-link adjacent pentapeptides to form ...
4
votes
1answer
69 views

Subset of Protein Crystal Structures (from PDB)

Is there a well-accepted subset of the Protein Data Bank set of protein structures that: Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural ...
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2answers
8k views

Do all proteins start with methionine?

Start codon AUG also codes for methionine and without start codon translation does not happen. And even the ambiguous codon GUG codes for methionine when it is first. So does this mean that all ...