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
113 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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854 views

What are the characteristics of a promising drug?

The drug development industry is a multi-billion dollar economy powered by a multitude of research bodies from industry and academia. A big risk is that drug development costs are in the tens of ...
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Why do food items expire?

Why do food items and medicines expire after sometime?
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516 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
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Effect of 2,3-bisphophoglycerate (2,3-BPG) on haemoglobin

When 2,3-bisphophoglycerate (2,3-BPG) binds to haemoglobin, a higher partial pressure of oxygen is needed to bring about 50% saturation of with oxygen. What is the physiological significance of this ...
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What is the “mucin net”?

From Giulia Enders, Gut: The Inside Story of Our Body’s Most Underrated Organ Mucins are proteins that form the main constituent of mucus. They help provide hours of fascination and fun for young ...
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Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
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484 views

Why do raw prawns turn red after sitting in vinegar?

Yesterday morning I put some raw prawns (shell removed) into vinegar (more specific this one), and put them in fridge. When I came back at night all of them turned red, which looks cooked, except ...
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Assays for detecting RNA binding with protein

In a project I'm working on, we are designing a system where specific RNAs bind to proteins - an important part of this is to test whether the RNA binds when we modify the proteins in some way. What ...
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2answers
977 views

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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1answer
2k views

What is the difference between gene expression and protein synthesis? [closed]

I have no idea what I'm supposed to do. Can someone please help me? What is the difference between gene expression and protein synthesis?
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Do non-pathogenic organism not have PAMPs? Are there any research paper which proves that a certain microbe is non-pathogenic?

According to this PAMPs are delivered along with additional information that can be used by the host to distinguish pathogenic from nonpathogenic microbes and thereby guide the ensuing innate ...
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338 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 ...
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Will a sandwich assay work with a GST 26 antibody/protein?

I have a GST 26 kda antibody, and want to use it in a sandwich lateral flow assay. Are there enough epitope regions for both antibodies to bind to the protein?
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1answer
54 views

Is Ellman's reagent specific for low molecular weight proteins and thiols?

Is it still possible to quantify cystein rich low molecular weight proteins such as Metallothionein in a given sample using Ellman's reagent if the sample is contaminated with some high molecular ...
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1answer
113 views

Do non-functional (‘junk’) protein sequences exist?

For DNA one can distinguish between protein-coding DNA sequences, i.e. nucleic acid sequences inside DNA (vs. non-coding sequences) DNA sequences that do not code for proteins but are transcribed ...
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Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in ...
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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 ...
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How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
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Is it possible to isolate and analyse intermediates of protein folding?

I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form. While studying structural biology, I only came to know the forces that ...
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1answer
82 views

How does radiolabeling work?

Protein turnover can be measured by calculating the "decay" or loss of radio-labeled proteins in the blood, for example, but I am confused at how this calculation works. Wouldn't the radioactive ...
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1answer
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Protein molar mass from Uniprot ID?

I have a long list of uniprot IDs. How can I get the mass of the "canonical" isoform for each? Ideally from some Python library.
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Is osteoid an uncalcified substance?

I recently learned about Osteoid (the substance secreted by osteoblasts during intramembranous ossification), and I read that it was an "unmineralized organic component of bone." Now, does this mean ...
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202 views

How do membrane proteins find their target locations?

The question might be asked for any kind of "bound" proteins, but I'd like to restrict it to membrane proteins. Assuming membrane proteins (or their main parts) don't (or aren't) build in situ but at ...
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1answer
152 views

Is there any way to make protein pass through cell membrane?

Protein cannot pass cell membrane because it's a large molecule. Until now, is there any technique that can make protein pass through the cell membrane in vivo? I want to create a protein-drug that ...
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What is the shortest mRNA the ribosome can read to produce a peptide?

This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome. In general, Glutathione has a "gamma" ...
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Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
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1answer
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How would one go about identifying unknown cell cycle checkpoint proteins (i.e., cyclins)?

No this is not 'homework'. I'm a PhD student, and this was something brought up at the end of a journal club recently, and one of the PIs posed this question and told us to think about it. It sounds ...
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818 views

Does pepsin digest plant protein?

This may sound trivial, but... Protein is sourced from plants and animals. Pepsin and HCl digest meat (animal protein). Does pepsin also digest plant-based proteins? I took a look at few articles ...
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1answer
2k views

What is a complex? [closed]

In my text book it says that "Troponin" is a complex of Troponin C, I and T. In this sense, what is the relation between Troponin complex and C, I, T?
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Since the matter in the brain is recycled every few days how does consciousnesses work?

Since parts of the brain are recycled every few days does that mean that materialistic theories of consciousness don't work?
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966 views

Life cycle of proteins

I try to get a picture of the life cycle of a protein (considered as a specific molecule). This is how I can imagine it: After the cell is born a protein molecule is synthesized by gene expression ...
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Etymology of vimentin [closed]

What is the etymology of the intermediate filament , Vimentin?
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The difference between the beta-sheets and the quaternary structure of proteins

My biochemistry book says that beta-pleated sheets is a form of secondary structure of proteins, and it is formed between two or more polypeptide chains. I wonder why the sentence in bold doesn't ...
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248 views

Which of the three is true for insulin receptors?

I have seen the following question in a Cell Biology exam: Which of the following is true" Insulin has an hydrophobic Signal Peptide and the insulin receptor does not have an hydrophobic Signal ...
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What do you call mRNAs that translate to the same protein?

For example AUAACC and AUCACG in distinct mRNAs may both be translated to the same dipeptide Ile-Thr.
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What are some examples of non-homologous sequences having similar functions?

I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?
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Are proteins a different shape in space?

Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth? If the structure and shape is in fact affected, then would it be enough of a ...
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What attaches plant cells to the cell wall?

In animal cells integrins span the plasma membrane and attach the cell membrane to the extracellular matrix. I was wondering how are plant cells attached to the cell wall? Is it just the middle ...
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The insulin protein of apes & chimpanzees [closed]

How many amino acids do the insulin protein of apes and chimanpzees compose of?!
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Can you say “screening for a” in English?

I know this is not a "Correct Use of English Forum" but I'm afraid that people from outside the field won't be able to properly answer my question. Would it be correct to say "screening for a long ...
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Do GPCRs have 7TMHs?

I've screened a non-redundant set of GPCRs acquired from UniProt. I found a handful of examples of record IDs that contain more than the 7 TMHs. For example Q89609 and P20905, both of which have been ...
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1answer
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How big is the change in proteins due to alternative splicing?

How different can the proteins be that are coded from the same DNA-sequence but undergoe alternative splicing? What I am trying to wrap my head around is why we are so fixated with the DNA-sequences ...
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Indicators of Ras binding domain (RBD) activity in Ras effector proteins?

Ras family based small GTPase proteins usually have a Ras binding domain (RBD) in their effector downstream proteins like Raf. Roughly Ras proteins cycle between active(GTP-bound situation) and ...
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Visual maps of the neuronal membrane

There are lots of visual maps of the brain as a whole, especially the cortex, that show the distribution of "features" over a two-dimensional map, e.g. the Brodman areas (their morphology and their ...
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Can one refer to pieces of proteins produced by enzymatic digestion as “enzymatic lysates”?

A Russian text I'm translating says this: The location of post-translational modification (PTM) sites was determined using the “bottom-up” approach commonly used in this field. In accordance with ...
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Will a polyclonal antibody attach to proteins of different kDA?

If I have a GST 26kDa polyclonal antibody, will it bind to the GST 28kDa protein as well?
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580 views

What is the function of cystine, cysteine, and cysteine protease?

I am not a biologist, and I have a probably dumb biological question. For some purpose, I need to understand the function of the CTNS gene, and here is the definition of it: "This gene encodes a ...
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1answer
849 views

Effect of mutation on phenotype

Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?
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Multi-protein drug treatments

Apologies if this an obvious question - I am very new to this. I am, as of now, under the impression that multiple SNP variations interact to create multiple mutated proteins, which ultimately results ...

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