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 are the secondary structure requirements for cell-penetrating peptides AKA protein transduction domains

Cell penetrating peptides. Cell penetrating peptides (CPPs) are a class of short amino acid sequences which are sufficient for crossing cell membranes and delivering themselves along with any ...
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20 views

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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57 views

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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26 views

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 ...
3
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436 views

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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38 views

Structure of proteins

Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a ...
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28 views

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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45 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 ...
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17 views

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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92 views

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 ...
2
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32 views

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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24 views

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 ...
2
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139 views

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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77 views

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 ...
2
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165 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 ...
2
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44 views

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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57 views

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 ...
2
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55 views

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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39 views

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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269 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 ...
2
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66 views

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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10 views

How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.) How can I use MODELLER to make a theoretical ...
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36 views

Proteins in water vs proteins in crystal

I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays ...
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41 views

What is the most stable globular protein?

What is the most thermodynamically stable globular protein? I am looking for a small (ideally less than 50kDa) soluble globular protein motif which folds easily/reliably and is known to be extremely ...
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29 views

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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26 views

mRNA extraction from mice ears.

I am trying to extract RNA from mice ears and for some reason I don't have RNA when I perform the electrophoresis. I directly cut the ears and I put it in a tube with a bead and trizol. then I place ...
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63 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 ...
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11 views

Which fractions are enriched for siRNA cleavage activity by comparing electrophoresis?

Size exclusion column chromatography was used to separate the proteins in a Drosophila cell lysate to attempt to identify the protein complex responsible for processing long dsRNA into siRNAs. SDS-...
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34 views

Wash adsorbed protein without destroying Biotin-Avidin-Mechanism

I am looking for reliable protocols to wash protein (e.g. Fibronectin) adsorbed onto glass surfaces. According to Protein immobilization literature, people usually use 1% SDS and some incubation time. ...
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26 views

How do molecular recognition features work?

The occurrence of relatively short (10–70 residues), loosely structured protein regions bind within longer, largely disordered sequences that were characterized as bound to larger proteins. These ...
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47 views

Protein modification and ATP consumption

According to wikipedia there exists a lot of ways to modify a protein (post-translationally). Just to mention few: phosphorylation, dephosphorylation, glycosylation... While phosphorylation requires ...
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15 views

How are split inteins joined?

Do they form a peptide bond? Or is it just some affinity/van der Waals interaction? Is the mechanism enzyme catalized? Are the residues/moieties at the join site known? Could they be introduced to ...
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63 views

aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel. I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about ...
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53 views

Question about cytoskeleton coordination

I am trying to study for a biology and I am having some confusion over the following topic. Can anyone help explain/ shed some light on the concepts of Rho family GTPases. Is it true that we have Rho ...
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90 views

How do BCAA's promote faster muscle recovery?

I am aware that ingesting Branched chain amino acids (BCAA's) prior, during, and after workouts has an effect on muscle recovery due to their difficulty of metabolism. However, how much more ...
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52 views

Nutritious protein substance for vitamin enhanced crop?

I am not a bio or science major, but we have a subject, like an elective on biotechnology and we were tasked to think of a product that hasn't been invented yet. My groupmates and I thought of a ...
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263 views

negatively charged albumin as major carrier of acidic/negative charged drugs in blood

I reading that orsomucoid (alpha-1-acid glycoprotein) is the major carrier of positively charged (basic) drugs in the blood, while albumin carries negatively charged (acidic) and drugs with neutral ...
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30 views

Is this description of etiology of celiac disease correct?

There is a detailed and, to my inexpert eyes, plausible description of the etiology of celiac disease and other autoimmune disorders posted here: http://no-gluten.org/CeliacDisease.htm Is it is at ...
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50 views

How do PER/CRY complexes accumulate in the cytoplasm?

The Period/Cryptochrome (PER/CRY) complex is a heterodimer that transcriptionally regulates circadian rhythm. When it is phosphorylated, it is transported to the nucleus and it inhibits a ...
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17 views

histamine inter-cellular and cytoplasmic binding site

I noticed that HRH (histamine receptor) has an inter-cellular and cytoplasmic binding site of anti-histamines which are equal in binding energy. Does anyone know what is the function of the well ...
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8 views

Batch convert gene numbers (“ordered locus names”) to protein IDs

I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to ...
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7 views

Phase separation of FIB1 Protein in NaCl solution

What is the mechanism of phase separation that causes droplets to form in a solution of proteins and NaCl, given the concentration of NaCl that allows this to happen?
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13 views

How is the acetone method different from QB buffer for extraction of plant protein?

I primarily work on animal tissue but I thought of running an SDS-PAGE for plant tissue just for fun. I searched for some protein extraction protocols online and I don't know which one to choose. One ...
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17 views

High intensity background on western blot membrane?

I did western blot and I got the high intensity background only in the upper part of the membrane and there is a horizontal line around 50-70kDa (this line separate the upper part and lower part of ...
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12 views

optimization of density gradient centrifugation

I'm trying to isolate a ~320kD protein (in oligomeric form) using density gradient ultra centrifugation technique. Can any one tell me that what gradient (sucrose or glycerol or trehalose or etc) I ...
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23 views

Which proteins cross the blood brain barrier?

Are there any known globular proteins which naturally cross the blood brain barrier as part of their function, i.e., without modification? I'm thinking not just human proteins, but also viral ...
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21 views

Best protocol to optimize solubilization of bacterial fusion proteins?

I'm trying to produce an His-tagged protein in E.coli. Before performing the Ni-NTA column I need to figure out how to extract most of the protein from the cell pellet but I'm getting lost with a ...
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21 views

How does Ultra-pasteurized milk compare with pasteurized milk?

I am specifically interested in whether all proteins and nutrients lose their structure permanently because of the very high temperature of ultra-pasteurization. What is the case for pasteurized milk?...
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31 views

How hydrophilic is human mucus?

I am interested in the stability of virus particles in human mucus, and how this may bias the evolution of surface amino acids in respiratory viruses. For instance if the mucus environment were more ...