Protein Definition and 159 Threads

What determines protein/biomolecule folding or why it folds in a particular way? For instance, both glucose and fructose have same molecular formula (C6H12O6) with same chemical constituents (CHO) . But glucose has its carbonyl group at the end of the carbon chain, but fructose has its carbonyl...

From this result, the conclusion is that MDCK-siNGT and MDCK-siB4Gal4 resulted in less keratin sulfate, while MDCK-RCA did not produce keratin sulfate at all. Looking at the gel, the band look very smeared, as if nothing was purified prior to blotting. I have noticed a similar looking gel in...

Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in that file. How can I do that? Sometimes people suggest using the `CONECT` field for that purpose. However, some PDB files do not have this field. Example: 4OSK.pdb (Crystal...

Kurzesagt in a Nutshell said that the number of possible protein combinations the human body can have is 6.8 x 10^495. I asked GPT to multiple it by 20 million (which is the hypothetical number of possible alien civilizations in the Milky Way galaxy give or take). The chatbot gave me 1.36 x...

In their (AlphaFold) words: The value of this as a news story is directly proportional to the accuracy of the predictions. The AlphaFold Database includes information about their confidence for each protein segment, but I have not found an overall quantitativ assessment of its accuracy.

While researching S protein interactions I stumbled across a couple of recent papers studying the increased risk of developing Parkinson's after a Covid infection and the possible mechanism that plays a role there. https://pubmed.ncbi.nlm.nih.gov/34860005/ here is the full version of the study...

So I'll try to be brief. There is a recent study that is titled "Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination" https://www.sciencedirect.com/science/article/pii/S0092867422000769 Among other stuff it has measured...

@Bystander @fresh_42 pasta is normally made from tetraploid wheat ( 4n = 4 sets of chromosomes, humans are diploid with 2 sets. ) Semolina and durum are names you will encounter for 4n wheat cultivars. 6n (hexaploid) wheat is so-called bread wheat or sometimes modern wheat. 4n wheat crops...

Before I say something I want to kindly ask any possible participants to refrain from attacking the personal symptom explanation as untrustworthy or made up as some have done before in another thread. Although I will express my personal side in the thread as such, I am looking for answers from...

I have been reading about protein thermodynamics and found different types and models for entropy calculation before and after protein folding. I understand Vibrational, conformational, configurational entropy are some of the most studied "types" of protein folding entropy. My questions is...

This is cool - AI is the future of biology, humans just arent smart enough https://deepmind.com/research/case-studies/alphafold https://predictioncenter.org/casp14/doc/presentations/2020_12_01_TS_predictor_AlphaFold2.pdf Deepmind trained on 100K proteins and is now in the second iteration of...

I am learning about protein purification in my Biochemistry class, and I have a question about protein elution in antibody affinity chromatography. My understanding of the mechanism for the technique is that proteins that do not bind to the antibody will be separated first as it runs down the...

Google’s deep-learning program for determining the 3D shapes of proteins stands to transform biology, say scientists...

Hi, I tend to write down questions/thoughts that come to me as I read articles that are interestsing. I'm reading the intro to solution state NMR in a biophysics textbook. Any there any purely theoretical approaches to determine protein structure / dynamics ? The 1 dimensional digital code...

Many researchers have mentioned in their researches that protein phosphorylation take a decisive position to regulate various physiological activity, from prokaryote to eukaryote. So did anyone has taken the research on control the protein phosphorylation in wildtype microorganisms with...

I think this is important not just for the extraterrestrial part but it can help explain how life starts on planets through Panspermia. https://www.sciencealert.com/scientists-claim-to-have-found-the-first-known-extraterrestrial-protein-in-a-meteorite This could really be groundbreaking. If...

Please give me clues as to how to solve this question. The answer provided is (c).

My understanding: A) As in RTK signalling in which Raf-MEK-ERK are bound to KSR, they are close enough and in proper orientations to transduce the signal faster than when they are not in a complex. So A is correct. B) Correct. Because to cross-link with other signalling pathways the kinases have...

My lecturer said it means: "3rd residue, C-terminal to Helix 'H'" but that makes no sense. If it's the 3rd residue then it can't be on the C-terminal, because the C-terminal is at the end of a massively long sequence of residues. Visa versa if it's on the C-terminal then it can't be the 3rd...

A Harvard teams believe they have found a protein series they call "Hemolithin" in an asteroid. Isotopes and other evidence indicates that it is not from a terrestrial source."Astrobiology Web" link arxiv pdf link

https://phys.org/news/2020-02-green-technology-electricity-thin-air.html I am not competent to judge this (what seems very edgy to me) article. Basically it says: a ten micron thick protein layer with Geobacter on the surface and protein nanowires arranged in a mesh, when exposed to...

hello i came across an old article about crystalline shape of AEC2 receptor that is been some how associated with covid-19 my question dose knowing the crystalline profile of protein receptors some how can help with finding a better aid against this kind of outbreaks and how crystalline...

Answer: (d) My understanding: 1. At pH 6.4 i.e. less than 6.5, protonation or deprotonation will just begin (if we imagine that we are adding an acid to the protein soln), so not many protein molecules will be there in the supernatant 2. Glycerol interacts through H-bond with surface polar...

I'm looking to understand how protein folding has been shown to be NP-complete, but from the computational side rather than the biological side (if this is possible). Is there an analogous NP-complete problem that is similar? I read that self avoiding random walks might have something to do with...

Dear Forum Members, I am a molecular biologist. One of my projects is focused on the identification of a protein that interacts with a known organic molecule. Namely, I try to chase a transmembrane protein that is known to transport one organic acid. If possible, I would like to get an idea on...

Good day! :oldsmile: Imagine the mRNA with some nucleotide sequence that (after translation) will give us such polypeptide chain: L-Alanine (first, in the beginning of translation) - L-Arginine - L-Asparagine - L-Aspartic acid - L-Cysteine - L-Glutamic acid - L-Glutamine - Glycine (last, in...

Hello, I was wondering whether one same protein can assume different foldings that can do different functions in the organism? (each folding still having the usual active/inactive state) And if the is a specific example for this? Many thanks for any thoughts!

Do we know roughly what the surface of a protein channel looks like? In most of the diagrams they are depicted as a sort of cylindrical tube with a smooth surface, but I'm curious if there are some more detailed documentations somewhere? For example I know they aren't rigid objects and may be...

I was wondering whether it can ever happen that only a certain "length" of the same gene gets expressed in different species? Or perhaps even within the same species? (Without it being a random mutation) Basically, can a part of a gene be expressed, and still have some functionality in the...

Here is an NY Times article by Carl Zimmer, describing recent advances in predicting protein design. This involves going from an amino acid sequence to a predict a protein 3D structure or going from what you want in a protein to the amino acid sequence that can generate it. This has long been...

https://www.quantamagazine.org/lifes-first-molecule-was-protein-not-rna-new-model-suggests-20171102/

Is anyone familiar with a way to determine the half-life of a protein from its melt temperature (Tm)? It seems like there ought to be some sort of correlation, be it theoretical or empirical.

Hello there, Situation I got a research position at my university in studying amyloidogenic proteins, which are associated with many different neuro-degenerative diseases. The professor has a NovoControl Dielectric Spectrometer in the lab, which will be the main equipment used to gather data...

Homework Statement Suppose you were told you had a protein with molecular mass of 65,000 g/mol. Show how you would estimate the number of amino acids present in this protein. Keep in mind that you cannot calculate the exact number, the point of this is to approximate how many amino acids are...

I have a few questions on energy from foods. Do we have any other macronutrients that contribute energy to the body other than carbohydrates, proteins and fats in our body? What is the role of Hydrochloric acid (HCL) in our stomach? Is the HCL involved in all three above macronutrient digestion?

Our text says that ionic bonds are much weaker in aqueous solutions than covalent bonds, due to the dissociative properties of most ionic compounds in water. I read elsewhere though, that in general, ionic bonds are stronger due to the increased polarity. So, in protein folding, when different...

Hello again! Is there a common word/term for a gene and the protein that it codes for? I know there is signal transduction, but that would be for a whole set of genes and proteins doing a stream of functions. But would there be a name for the specific gene/protein "bundle"?

I'm undergrad physics student and I have read some statistical physics like equilibrium statistical physics, Langevin model and Fokker-Planck equation. I have developed interest in application of statistical physics in biology like protein folding. So what are the other research topics that lie...

For some reason, I can't seem to be able to find this answer easily on the internet. Or it is there and I somehow I can't see the wood for the trees. I know that in transcription (when DNA is read for protein production), "RNA polymerase" is the protein that creates the mRNA by creating the new...

1. A substrate molecule may be bound to the active site of an enzyme by all of the following EXCEPT A. Hydrogen Bonds B. Peptide Bonds C. Ionic Bonds D. Van der Waals Interactions E. Hydrophobic Interactions 2. Which of the following components is the most important in determining the 3-D...

Homework Statement Hi! So I'm trying to write a lab report about testing BSA solutions for protein concentrations using a Biuret reagent and a spectrophotometer. There is a portion that asks you to give some practical applications for this test and how it applies to biology. The only thing I...

Does anyone know how many times would an average protein fold in its lifetime? And how long do proteins live on average? Also, another quick question, somewhat related, any knowledge on how many "cascades" of different proteins making a conformational change on different new proteins can there...

My understanding is that genes code for proteins that then do a certain function. Apart from mitosis in an organism, I heard that cells (in forms of stem cells) are also produced and released into the body. I guess these would be all the floating around the body cells? Or the nerve cells that...

Hello everyone, I'm a graduate student in a biophysics lab. I'm trying to run a QM/MM simulation with a protein that binds 3 Ca2+ ions, and as such I am having a devil of a time getting the SCF to converge. I've tried DIIS, KDIIS, damping, and a few other methods to try to get convergence with...

I am taking a protein supplement that has far too much sodium in it. If I took the amount I need every day, I would far surpass the safe upper limit of daily sodium intake. I had the idea of dissolving the pea protein powder in water, filtering out the sodium, and then evaporating the water...

I got a question, consuming amino acid and consuming protein is the same thing right? Protein is a chain of amino acids but it does not really change their properties by becoming protein right?

I was wondering if anyone knew what happens to a protein that gets wrongly assembled due to a mutated RNA? Does it just do a slightly different or very destructive action in the organism, or does the organism catch it and kick it out? Also an extra side question: Speaking of mutations of RNA...

If the gene is smaller, is the protein that it codes for smaller too? Vice versa?

Homework Statement UV Rays is said to induce point mutations which get incorporated during the DNA replication process. These mutations are corrected by the excision repair mechanism of the DNA polymerase but sometimes they might be left out. In one of such cases, point insertions were...

I have been looking into different methods of regulating protein activity for a project. I think it is pretty interesting and I want to learn more about this. I want to learn about the different methods out there, if you know of any cool or helpful regulation techniques I would certainly...