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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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1answer
39 views

How does the body detect irreversible binding to receptors?

I have read an article on Wikipedia about irreversible agonists and antagonists. These permanently bind to a target receptor on a cell. However, the receptor protein is then internalized and recycled ...
1
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1answer
628 views

What's the difference between physical (direct) and functional (indirect) protein interaction?

I read that the Protein-Protein interactions one can consider are generally of two types, namely physical and functional, but I cannot get the difference between the two. I was just thinking that if ...
2
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0answers
21 views

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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1answer
87 views

What is the difference between a signal peptide and a transit peptide?

From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal ...
20
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2answers
2k views

What inactivates pepsin in infants?

In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach. Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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1answer
148 views

Plasma Membrane Proteins and Cytoskeletal Attachment

Regarding membrane protein functions, which of the following statements is CORRECT? a. Membrane proteins are responsible for both cell to cell recognition and cell anchoring and are ...
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0answers
27 views

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 ...
2
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2answers
58 views

Why do dietary recommendations for methionine consumption combine methionine and cysteine?

I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids (source: wikipedia). I don’t understand why they pair Methionine + Cysteine: ...
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1answer
30 views

Where do the lysines come from during ubiquitination?

I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from? Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine ...
0
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1answer
113 views

Is it possible for human body to convert carbohydrates to protein? [closed]

Is it possible for human body to convert carbohydrates to protein to build muscle for example? EDIT: I read in many articles that you should eat more than 1.5 gram protein for each 1 kg weight of ...
5
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0answers
47 views

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/...
5
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2answers
230 views

How can one create images like those in the PDB ‘Molecule of the month’?

I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create ...
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1answer
186 views

Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
2
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1answer
16 views

Can someone help me interpret these charts on fluorescent polarization?

I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a:...
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2answers
84 views

Etymology of PAX proteins

What is the reasoning behind naming proteins first found in Drosophila as paired box? All I could find on internet is that it was first found in Drosophila as a protein with paired domain, but I ...
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0answers
9 views

How to use VMD command line to assgin color to atoms based on index?

I know how to use the GUI "Graphical Representations" to assign different colors to different atoms: But how can I do this using a command line?
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0answers
20 views

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. ...
0
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1answer
29 views

Obtaining protein atomic co-ordinates from dihedral angles

https://en.wikipedia.org/wiki/Dihedral_angle#/media/File:Protein_backbone_PhiPsiOmega_drawing.svg I've been reading on Protein Amino Acid Sequences and their 3D structure. It seems that the 3D ...
2
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1answer
64 views

What is the importance of alkaline condition in biuret test?

Biuret test aims to quantify the amount of protein in a given unknown sample. Biuret agent contains copper sulphate, sodium potassium tartrate and Sodium hydroxide. Coppper ions form the complex of ...
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1answer
41 views

What does “PDPN+ cells” means?

Are they podoplanin positive cells (cells that tested positive for podoplanin)? "...though it has been shown that podoplanin (PDPN+) cells analogous to mouse FRCs are found in human secondary ...
2
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2answers
74 views

When does protein folding begin?

I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds ...
1
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1answer
33 views

What are the different types of helices in protein secondary structures and how do they differ?

What are the different types of helices in protein secondary structures and how are they differentiated? In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5. In the ...
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0answers
116 views

How does DNA code for the actual *shape* of individual body parts/areas (NOT segments or Hox genes)?

Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and ...
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0answers
23 views

How many proteins are common to all species? [duplicate]

Are there any proteins that are common to every Species in Earth's biosphere? If so, how many? If not, are there any proteins common to every species of an entire Kingdom? If so, how many? If not, ...
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1answer
57 views

How does DNA determine all of our hereditary traits?

It's my understanding that DNA codes only for protein synthesis. Does that mean that hereditary traits, like the shape of our nose, are determined only by the proportions in which various proteins are ...
4
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2answers
176 views

Will new proteins incorporating new amino acids trigger an immune response?

This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done ...
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2answers
10k views

Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?

I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express. Depending on the ...
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1answer
45 views

What created the first ribosome

If a ribosome is made of protein, yet is used in protein sysnthesis, what created the first ribosome? What created the ribosomal RNA?
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1answer
35 views

How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

I have two datasets, from different sources, that I need to compare. The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
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0answers
14 views

What does ubiquitination between 2 genes mean?

I have come across the Hedgehog signaling pathway. In this pathway, the genes Cul3 and ptc have an interaction of ubiquitination (The information is available from the KGML file). What does this ...
0
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1answer
28 views

Amino acid substitutions near the receptor binding site HA protein in type A H3N2 influenza strains?

I have read the scientific paper, "Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution" by Björn F. Koel et al (http://science.sciencemag.org/...
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1answer
25 views

How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has?

I know that some amino acid substitutions are more effective in causing antigenic drift than other substitutions based on their location in the 3d structure of the HA protein (proximity to the ...
5
votes
1answer
164 views

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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0answers
19 views

How to take precise/low number of cells from cell lysate? [closed]

I would like to know that how can we take low or precise number of cells from a cell lysate? (without using any protein quantification assay). Let say, If I have a cell line having cell density 5x10^...
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0answers
15 views

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 ...
0
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1answer
34 views

is a-keratin a fully functional protein?

is a-keratin before it coils with another polypeptide, makes chains, and build intermediate fillaments a fully functioal protein? I mean, is the single monomer of a-keratin a protein or it has to ...
3
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3answers
382 views

Are all enzymes proteins?

So throughout my education and research career I have been taught that all enzymes are proteins. This makes sense when you consider enzyme denaturing and folding/shape etc. However, I was recently ...
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1answer
40 views

What's a good reference for learning about recombinant proteins?

I'm looking for books and articles that can bring me up to speed on the design, expression, and purification of mammalian proteins in recombinant systems, both in E. coli and in more complex systems ...
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1answer
44 views

How do people measure how many calories or proteins/fats/сarbohydrates are in some food?

How is the composition (in fats, proteins or carbohydrates) of a certain food estimated and how is the amount of calories provided by the food calculated?
2
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1answer
34 views

How is the activation energy lowered in an enzyme by just orientating the reactants closer to one another?

If the activation energy is lowered, bond strength has decreased. How does purely orientating the reactants closer to one another lower the activation energy in a protein? The only thing I can think ...
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0answers
44 views

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 ...
50
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4answers
8k views

What is the longest-lasting protein in a human body?

Protein life times are, on average, not particularly long, on a human life timescale. I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/...
1
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1answer
34 views

False positives in TAP - MS experiments

Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments? Particularly the Acs1 protein (Acetyl-...
1
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1answer
41 views

Centrifuge after sonication

I follow a protocol to get protein from E.coli cells after sonication. I used to grow 6 litres of large cultures and add IPTG to express the protein. I centrifuge for 10 mins at 8,000 rpm and get the ...
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2answers
2k views

Is tyrosine hydrophobic or hydrophilic?

I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does tyrosine actually ...
4
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0answers
77 views

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 ...
2
votes
1answer
81 views

How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations. The idea is that ligands which bind more ...
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0answers
11 views

How can we quantify the effect of pancreatin (biological enzyme) on the clarification of milk powder

Alright so I'm trying to quantify the rate at which casein (protein constituent of milk powder) is converted into a product (I am unaware of) by pancreatin (a biological enzyme that speeds up the ...
4
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2answers
450 views

Which server to use for volume and accessible surface area calculation of proteins

I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving ...
0
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1answer
81 views

Why is gel used in electrophoresis?

In analysing amino acids content in a protein through gel electrophoresis, What's the purpose of the gel? Wouldn't putting the amino acid in the gel prohibit the amino acid from dissolving into the ...