Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

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Protein that exit from the cell - as marker

Searching for some protein, that I could use as extracellular marker for mammalian cells. I need to insert mRNA to cell, and to detect the protein outside the cell (not on membrane) if the mRNA ...
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1answer
20 views

Do the enzymes and compounds in saliva help with stain removal?

Does spitting on stains help with removal? Saliva is high in amylase that should help with the breakdown of protein rich stains like blood and semen. It also contains antimicrobial enzymes and ...
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1answer
23 views

How does the MET gene work and what happens when the promoter region gets mutated?

I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET ...
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1answer
22 views

How does the structure of the pancreatic acinar cell relates to its function?

So the pancreatic acinar cell synthesizes, stores and secretes digestive enzyme precursors called zymogens e.g. pepsinogen. The structure of the acinar cell shows that there is an apical and basal ...
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67 views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
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19 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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0answers
89 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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26 views

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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14 views

What is internal symmetry in membrane proteins?

I have come across the term "internal symmetry" in the context of membrane proteins, but have never found a satisfactory definition. I'm struggling to figure out exactly what this term means... What ...
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24 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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0answers
47 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 ...
2
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0answers
46 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 ...
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66 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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0answers
32 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? ...
2
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0answers
96 views

What keeps resting potential of neurons constant at -70mV?

I know the sodium-potassium pump pumps out 3 Na+ ions and pumps in 2 K+ ions per reaction so the negative charge in the axon increases. However, once the voltage (difference of charge inside and ...
2
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0answers
50 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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0answers
48 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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0answers
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 ...
2
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0answers
229 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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0answers
61 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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0answers
22 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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35 views

Compare Proteins - Structural / Sequence parameters

I have been working on algorithms that extract co evolutionary signatures from protein sequence. As a result of my work I got some evolutionary information which possibly explains cotranslational ...
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22 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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23 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 ...
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34 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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45 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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88 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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25 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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43 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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62 views

Ferredoxin synthesis pathways

I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of ...
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16 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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0answers
11 views

How are membrane and extracellular proteins delivered to the target membrane?

In bacteria, either folded or unfolded proteins can be trafficked to the membrane or the extracellular space provided that they have the appropriate signal sequences. Once the chaperones or Signal ...
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17 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
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13 views

About post translational modifications

A secreted monomeric protein of 132 amino acids, lets say protein XY, has two N-linked glycosylated Asparagine residues, at position 10 and 67, and act as a ligand for a XY-Receptor (XYR). I want to ...
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45 views

Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...
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21 views

Where does the oxygen and water produced from the decomposition of hydrogen peroxide by catalase enzyme go?

How are they disposed of by the body, or are they disposed of at all? Since our body needs water and oxygen anyway, I'm speculating that these "waste product" will be reused/recycled by the body in ...
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29 views

How to do Sliding 80mer Window search against a database with fasta

I know how to do a 80-mer window search against a single protein ...
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67 views

Medical Uses of toxic venom

One interesting thing I recently learned is that venom has medical uses that can actually save lives! But from what I see so far this either applies to venoms from creatures that are not fatal to ...
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33 views

Typical in-vivo protein concentration

I am studying RNA-binding proteins involved in RNA granules. I am searching the literature for an order of magnitude of the absolute global concentration in the cytoplasm. Although I am aware this ...
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53 views

Substrate specificities of GPPS, FPPS and GGPPS (isoprenoid biosynthesis enzymes)

I have some questions related to isoprenoid synthesis enzymes. Does Geranylgeranyl pyrophosphate synthase (GGPPS) contribute in Geranyl-Pyrophosphate (GPP), Farnesyl pyrophosphate (FPP) and ...
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19 views

VMD set molecule as top using script

I have 10 molecules in VMD main screen and I was wondering if there is a script command to change what molecule is the top. For example, molecule ...