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

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Estimated protein size using CDs data [closed]

The number of amino acids in a protein is important to predict their size. I used coding DNA sequence (CDs) to predict the average of the protein size of E.coli k12 from a sample provided by the ...
11
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1answer
380 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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2answers
39 views

Why can't proteins make copies of themselves? [closed]

Why is it impossible for proteins to make copies of themselves?
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0answers
24 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 ...
4
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1answer
191 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
1
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0answers
43 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 ...
12
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2answers
215 views

How can we verify predictions of protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
1
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1answer
63 views

Does the order of amino acids matter in making up a protein?

For instance, if a protein is made of 2 amino acids, that is, AB, would the same protein form if the order of combination of amino acids become BA? If yes, would the behavior of interaction of that ...
6
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4answers
223 views

Do all cells produce the same proteins?

If DNA is more or less the same in all cells, and DNA is used to produce proteins from aminoacids, then do all cells produce the same proteins or are they specialised/controlled by something?
2
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1answer
44 views

Do residue sequence numbers in PDB files correspond to the positions in the backbone?

In other words if two residues have sequence numbers, say, 20 and 21 then are they next to each other in the backbone? If no (or not necessarily) then is there any way to find consecutive residues ...
0
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1answer
39 views

Relative concentration of enzyme vs reaction product

I was reading a paper in which a recombinant protein (His-6 tagged) is expressed in E Coli (BL21 DE3). The yield of the enzyme isolated from the culture is reported as 10-30 mg per L of bacterial ...
0
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0answers
22 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 ...
1
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1answer
27 views

Hydrophobic proteins in the body?

I know that we can get hydrophobic amino acids, but are there any proteins in the body whose surface is hydrophobic? If so what is their typical function and where can they typically be found and if ...
2
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0answers
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 ...
0
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1answer
172 views

If human proteins are synthesized from only 20 different amino acids, then how can there be such variety of proteins in human cells?

I know that human proteins are synthesized using only 20 different amino acids. However, how can there be thousands of different proteins in human cells, if we only use 20 amino acids to make them?
0
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1answer
47 views

A molecular marker for global protein synthesis

I know that protein synthesis is governed by a lot of factors (I'm mostly studying the mTOR pathway), but I'm looking for some kind of marker that will indicate the global protein synthesis rates. I ...
1
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0answers
28 views

How accurate are proteomic-based biomarkers of cancer? [closed]

Currently protein expression is one of the widely used biomarker types. For example, any $i^{th}$ protein could be a selected biomarker. How can a minute change in single protein concentration ($m/...
2
votes
1answer
47 views

Conserved acetylation sites in a given protein

I want to identify potential conserved Acetylation sites in protein X. As it is known, acetylation happens in Lysines (K), thereby I would like to identify conserved K residues for protein X during ...
1
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0answers
30 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 ...
0
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0answers
22 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?...
5
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1answer
65 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 ...
3
votes
1answer
245 views

What is an isolated beta bridge?

DSSP gives the letter B for a "residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)", according to Wikipedias page for secondary structure (and various other proper sources). Can ...
4
votes
1answer
116 views

How to get the correct RefSeq Protein transcript for a given RefSeq Nucleotide transcript?

How to get versioned Protein Accession Number for a Refseq Accession Number? I have some versioned RefSeq Accession numbers and I would like to know their corresponding Protein Accession Numbers. ...
10
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2answers
149 views

Protein tertiary Structure formation

As we know that coils and loops are evolutionary variable regions where mutations,deletions, and insertions frequently occur. So does it mean that they don't have much role in the structure of protein?...
4
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0answers
29 views

Derivation of Michaelis' Equation from Michaelis' Constants [duplicate]

The enzyme reaction condition, $E + S \leftrightarrow ES \rightarrow E + P$ uses $\kappa_{1}$ (forward reaction), $\kappa_{-1}$ and $\kappa_{2}$ as the rate constants. E: Enzyme S: Substrate P: ...
2
votes
1answer
74 views

Why does heating kidney beans at a low temperature potentiate the toxicity of phytohaemagglutinin?

I recently found out that red kidney beans contain a relatively high amount of the toxic lectin, phytohaemagglutinin. An article on phytohaemagglutinin on the FDA website states: Several ...
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1answer
23 views

What are in common between transcription factors?

In terms of their structures (primary to tertiary) and locations? Why do they have these commonalities? Or are any of these commonalities critical to their functions?
3
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1answer
64 views
4
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1answer
97 views

What is the process of degradation of proteins into amino acids inside living cells?

Just like beta oxidation does our cells have a distinct mechanism for degradation of proteins? There are processes for degradation of amino acids but where does these amino acids come from, is it all ...
2
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2answers
70 views

What are some useful physical information of a protein?

Beside energy and heat, I don't know any useful physical information of a protein. Can you help me list some of it. Somethings like Fourier-transform infrared spectroscopy to provide protein structure ...
0
votes
1answer
67 views

Why do raw prawns turn red after sitting in vinegar?

Yesterday morning I put some raw prawns (shell removed) into vinegar (more specific this one), and put them in fridge. When I came back at night all of them turned red, which looks cooked, except ...
0
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0answers
32 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 ...
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0answers
12 views

Are receptors integral membrane proteins or peripheral membrane proteins?

In tegral membranes serve as transporters. Peripheral protiens serve as cell adhesion molecules, antigens and enzymes. So what about receptors? Which protiens carry out the duty of receptors?
1
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1answer
41 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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0answers
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 ...
2
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0answers
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 ...
2
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3answers
575 views

Amplification technique for proteins similar to PCR for DNA?

I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up ...
2
votes
1answer
835 views

Difference between protein channels, protein carriers and protein pumps?

I'm revising for my biology exam and I don't fully comprehend the difference between protein channels, carriers and pumps. I know that: Protein channels do not require ATP (passive transport) The ...
0
votes
1answer
48 views

How does protein enter bloodstream?

If a hemophiliac patient injects his factor 8 through the veins directly into the bloodstream to provide the body with clotting factor... Why don't they just make the drug as a pill and have the liver ...
0
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1answer
82 views

Will dissolved proteins pass through a 0.2 micron filter?

Given that there may be exceptions, can you usually expect protein to pass through?
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8 views

Is there a deblocking aminopeptidase without normal aminopeptidase activity?

The deblocking aminopeptidase is a unique exo-type aminopeptidase that liberates blocking groups (formyl, acetyl, and myristyl) from proteins and peptides. However, according to this paper, it has two ...
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0answers
66 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 ...
0
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0answers
25 views

SDS-Page-Concentration confusion

So I purified some a protein, purified it using two different types of resins (comparing resins for cost efficiency). Ran a Bradford Assay to find concentrations of each. Unsure of SDS-Page protocol ...
3
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1answer
93 views

What is the shortest mRNA the ribosome can read to produce a peptide?

This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome. In general, Glutathione has a "gamma" ...
2
votes
1answer
52 views

How do proteins perform their function [closed]

I have asked a question on physics stackexchange, but was redirected here. I copy the entire question word for word. The original is here. Let's, for example, take a ribosome. It is an enzyme that ...
1
vote
1answer
36 views

A question involving immunoprecipitation to identify interacting proteins?

Using recombinant Flag-tagged Dcr-2 and His-tagged protein X, pull-down assays were performed to determine whether protein X and Dcr-2 interact directly. The recombinant proteins (either alone or in ...
3
votes
1answer
50 views

Resolution of X-ray crystallography

A structure determined by X-ray crystallography has a resolution of 1.5 Å. When I look at the coordinates, I find every backbone C-N distance is 1.32 Å.i.e. Accurately predicted. If resolution is not ...
1
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0answers
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-...
3
votes
1answer
132 views

Does urea at different concentrations (5 or 0.5M) have different effects on proteins?

The problem is to explain why each additive gives rise to the distribution of the protein (RMAS) as shown in the Western blow below: In each case, the homogenates were subjected to high-speed ...
1
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1answer
42 views

Stabilizing forces between the protein sequences?

we know that Protein structures from secondary to Quaternary are maintained by noncovalent or weak interactions including electrostatic interactions,van der Waals forces & hydrogen bonding. What ...