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
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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?

Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?
0
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1answer
13 views

Techniques for phosphosite detection?

I would like to know how phosphorylated sites in proteins are detected in practice. I read some papers where the authors were talking about mass spectrometry techniques. But my question is that why ...
3
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2answers
26 views

How to find PDB id of an amino acid sequence

Suppose I have an amino acid sequence whose PDB id is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence? is there any site that will find the pdb ...
0
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2answers
51 views

Multiple start and stop codons in mRNA and pre-mRNA [duplicate]

I have a main question that will lead to further questions depending upon the answer. In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA? If ...
1
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1answer
43 views

Coordinates of amino acids in a protein sequence [on hold]

In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids ...
0
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1answer
25 views

What are the binding sites (or receptors) of cortisol?

I am in the process of a OCR GCSE Case Study, and my question is "Do the benefits of anabolic steroids outweigh the risks, which has an obvious conclusion. I need to know the scientific name, or a ...
1
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0answers
33 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 ...
1
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0answers
34 views

Similarity with protein sequence [closed]

I have chosen a protein sequence and I want to record the sequences having similarity more than 85% of the chosen sequence. How can I find it using FASTA?
2
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0answers
35 views

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 ...
0
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0answers
11 views

Bence-Jones proteins in urine on heat

The preliminary test for proteinuria is precipitation/turbidity on heat due to denaturation. This turbidity should not disappear when 10% acetic acid is added - to differentiate from phosphates. ...
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2answers
38 views

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

Why is it impossible for proteins to make copies of themselves?
2
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1answer
62 views

Why don't membrane proteins move?

I understand that based on their tertiary structure, intrinsic proteins have hydrophobic non-polar R-groups on their surface and that they 'interact with the hydrophobic core of the cell membrane to ...
2
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2answers
38 views

How do prions transmit their conformation to other proteins?

I was reading about prions and many sources say something to this effect: "Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces ...
0
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0answers
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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0answers
38 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 ...
1
vote
1answer
49 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 ...
4
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0answers
21 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 ...
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
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 ...
2
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0answers
36 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 ...
1
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1answer
25 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 ...
0
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1answer
112 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?
6
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4answers
187 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?
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0answers
27 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 ...
2
votes
2answers
36 views

How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
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0answers
24 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
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 ...
4
votes
1answer
83 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. ...
2
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2answers
50 views

Server for protein structure prediction for multiple sequences

Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, ...
3
votes
1answer
149 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
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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: ...
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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?
4
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1answer
86 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 ...
3
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1answer
63 views

What is the lower temperature limit for ion channels function?

What is the cold-block temperature of ion channels? (not of nerves or axons)
0
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1answer
44 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 ...
5
votes
1answer
65 views

Electrophoresis of hemoglobin from a carrier for sickle cell anemia shows two bands - why not three?

Electrophoresis of hemoglobin from a carrier for sickle cell anemia shows two bands - why not three? Since there are two beta chains in each hemoglobin, it seems to me they should have three types of ...
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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 ...
10
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2answers
143 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 ...
0
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1answer
59 views

Predicting 3D structure of a protein?

While predicting 3D structure of a protein through homology modeling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
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0answers
11 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?
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0answers
25 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 ...
0
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1answer
36 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
49 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?
2
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1answer
65 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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0answers
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
57 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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1answer
60 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
23 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 ...
2
votes
1answer
51 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 ...