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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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What is the fastest way to crystallise lysozyme (for student course)?

High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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How do scientists determine the nature of ions passing through a channel/carrier/pump?

The NCE (Sodium Calcium Exchanger) transports 3 Na+ inside the cell for 1 Ca2+ outside. How did we figure this out, and other mechanisms of this sort? If it were a protein, we could tag it with GFP. ...
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Are there any enzymes without aromatic amino acids?

I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just ...
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39 views

Would this be called a complex?

When an intermediate is formed between a substrate and an enzyme, this is called an enzyme-substrate complex. When a molecule is bound to its respective transfer protein, (the molecule being ...
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Relative densitometry from SDS PAGE

I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software. My questions are ...
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69 views

Proteins folds: relation to splicing and post-translational modification?

Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?
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67 views

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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Plant vs animal protein digestibility?

The protein scoring methodologies ( https://en.wikipedia.org/wiki/Protein_Digestibility_Corrected_Amino_Acid_Score) rate plant proteins of a lower quality than animal proteins. Now I can understand ...
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115 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 ...
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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 ...
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23 views

What is the estimated number of variant surface glycoproteins that trypansomes can express?

In "Vaccination against trypanosomiasis" by Greca and Magez they assert that there are "innumerable" variant surface glycoproteins that the parasite can express. What does innumerable mean here? These ...
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Gene products of recessive/mutated alleles

I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional ...
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How do spiders get silk from their spinnerettes?

I'm 13 and writing a report on spiders. How do they use the silk protein gel from the spinnerets? How does it get from the spinnerets to the web? P.S. I know how silk is created, all the way up until ...
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246 views

Determine secondary structure (per residue pair) from a protein contact map

Given a protein map contact map (which for this particular case is a matrix of all Ca-Ca atoms in protein 1a3a that are less than 8 Angstroms): Question: For each ...
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Is there a cellular mechanism that detects Ribosomal damage?

What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to what happens when a cell sustains damage of some ...
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Can't resolve protein with native PAGE

This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After ...
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Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?

I'm talking about this type of post-translational modifications. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature ...
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Why do BRAF mutations appear more in skin cutaneous melanoma?

When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
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Net electrical load of a peptide

I have to determine the electrical charge of the next peptide chain: C - E - H - P I know that this page is not there to raise doubts about this style, but I have looked for resources on the ...
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How are animal patterns encoded in the dna?

After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this ...
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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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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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31 views

To which SCOP Class corresponds the following secondary structure?

I need to classify this protein into one of the SCOP class (all $\alpha$, all $\beta$, $\alpha +\beta$, $\alpha/\beta$, or small protein). I'm having difficulties understanding the difference ...
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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 ...
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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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When can helices form coiled-coils?

The other day, my teacher suggested we find out whether a chain of the following amino acid sequence would be able to form a coiled-coil: N-KIAEVRAQYEDVANKVRLIVE-C ...
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How to quantify the “stability” of a protein complex?

From experiment we've identified a subset of known mammalian protein complexes as interesting (approximately 50 CORUM complexes). We'd like to do an enrichment-style analysis to know more about them. ...
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Generating all possible conformations of an Intrinsically disordered protein

I want to simulate interaction between the bHLH-LZ domain of c-Myc encoded protein and a test ligand. Since the domain is intrinsically disordered, I want to generate all possible conformations of the ...
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Atomic Force Microscopy Imaging of Proteins

I was reading about various imaging techniques, and I came across Atomic Force Microscopy (AFM). It sounds very interesting, and it also sounds like it is capable of imaging proteins (Page 4) http://...
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Why do Proteins store energy when the body already contains Carbohydrates and Lipids?

We already know that lipids are a source of long term energy and carbohydrates are much faster energy releasing sources. So why do we need specific proteins within the body to store energy? Are ...
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How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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Phase Transitions of Purified Proteins

Why do solutions of purified protein condense into droplet phases? I'm trying to understand the protein phase transitions. Here is the article http://www.cell.com/cell/fulltext/S0092-8674(12)00634-4#...
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Can aptamers be used to identify the terminal amino acid residue of a peptide?

Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal ...
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Lifeforms concentrations of the categories of macromolecules, and Lipids

Lifeforms are formed of large, modular, organic molecules called macromolecules, large organic molecules called Lipids, and simpler molecules such as H2O. Macromolecules are commonly grouped into the ...
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Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
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Multiple transcripts encoding for one protein

Trying to get a better understanding of the process of DNA to proteins. So when we have a gene, it is read from the 5' to 3' end, only translating the exons to mRNAs. A single gene can have multiple ...
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What are all of the currently known variations of the G zipper motif?

The G zipper motif is found in transmembrane proteins at an above random frequency and there are models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly. ...
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Incremental denaturation of protein mixtures

When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time. I assumed that ...
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Are there sterilisation methods that do not denature proteins as heat does?

Context: Most countries require milk to be sterilised through radiation or heat to remove possible harmful bacteria. Both of these processes denature the proteins in the milk (ref). Are there methods ...
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Which method would more accurately help to identify the unknown concentration of a protein sample between the A280 and the Bradford methods?

I quantified my protein using the standard Bradford method and the A280 methods and obtained values that were far off from the theoretical value of the protein of interest, and therefore was wondering ...
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364 views

Can protein sample be made 2% Triton X-100 free?

The protein I am purifying needed an elution buffer with 2% Triton X-100. I formulated the elution buffer not keeping the CMC in mind. My goal is to make my protein sample triton free to check its ...
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How do I get recombinant proteins into the nucleus of mammal cells?

I know that there are Nuclear Localisation Sequencenes (NLS). They can be taken from endogenous or viral proteins and fused to the N or C terminus of my recombinant protein. Which is the best one? ...
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Removal of the Initial Methionine in Venus for FRET

I'm working on building some FRET reporters. In addition to a cleavage site (of varying composition from 15-18AA), a 1 AA linker, I'm using Venus and Cerulean. Initially I was worried that 18AA ...
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Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?

E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
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Endocannabinoid Transporters - which ones are Likely to Exist and what is the Evidence for their Respective Existence?

Endocananbinoid = Endogenous Cannabinoid or CB1 and CB2 ligands. I'm asking which endocannabinoid transporters exist and could the one answering show all the evidence for the existence of the ...
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394 views

What specifically allows alpha-complementation in beta-galactosidase?

I'm familiar with the use of alpha-complementation of beta-galactosidase with the pUC alpha-peptide and the M15 lacZ gene product, and would like to hypothetically apply alpha-complementation in other ...
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How do you interpret the resulting bands of gel zymography?

I would like to clear up some things for gel zymography. I understand that bright bands show proteolytic activity. But which molecular weight do these bands correspond to? Is it the weight of the ...
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protein size range for ultrafiltration or nanofiltration

I am hoping to concentrate mixed proteins in homogenized leafy vegetables such as kale, spinach etc (after removing pulp and fibers) as a first step in further investigations (second step using size ...
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does Trichloroacetic acid remove fats from milk

I am trying to detect melamine in milk. As a part of preprocessing, I add 200 ul of TCA to 1 mL milk,and after filtration I get a clear solution. Does the filtrate contain fat. I feel I am having ...
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Quantify Protein Denaturation with Change in Solubility

I plan to run a lab which compares the impacts of ethanol and methanol, in varying concentrations, on the denaturation of whey protein. Change in water solubility is a good indicator of the degree ...