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

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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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0answers
11 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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1answer
22 views

Amino Acid requirement + intake in relation to diet + meat type

I was arguing with a friend: I said: the Yulin festivals cannot be condemned by western culture, as we also kill animals in equally cruel ways. She said: not only is it cruel, but the dogs (and ...
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1answer
27 views

“Other” peptides in IEDB

I used the immune epitope database (IEDB) to search for epitopes. I found some epitopes derived from antigens called " other" by IEDB. When I asked about it, the answer was "We use the "other" ...
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1answer
17 views

Why is nitrogen isotopic labelling required for protein NMR?

Why is labelling required for Nitrogen (by 15N) for studying structure of a protein using NMR?
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1answer
54 views

What is membrane-partitioning free energy? Can it be simulated?

Firstly, is there a strict definition of the "membrane-partitioning free energy"? It is banded around in membrane biology, but I have never seen it strictly defined. The only non-scholarly site that ...
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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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1answer
30 views

How does 2-mercaptoethanol lead to shift of the band to a higher molecular weight?

I have a project to isolate a protein with biological properties from a plant. The purified protein forms four bands with similar molecular weight on SDS-PAGE (30–35 kDa) in the presence of 5 % 2-...
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2answers
26 views

Techniques for detecting phosphorylation sites in proteins?

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 ...
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1answer
51 views

Beta Sheets vs Alpha Helix - Strength

Is there a hard and fast rule of which one is stronger than the other, or does it depend on their context in a protein?
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1answer
63 views

What was the precursor of testosterone? [closed]

Testosterone evolved about 500 million years ago (says 8fact.com). What was the precursor of testosterone (if any)? If possible, what caused the 'precursor' to evolve?
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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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42 views

Motifs, Tertiary Structure, and Domains [closed]

I really don't understand these three terms. If somebody could explain — with illustrations — it would be of great help. Given this definition: 'The overall 3D structure of the polypeptide chain ...
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2answers
65 views

Relationship between DNA strands and mRNA

Does the sense strand or antisense strand of DNA code for the polypeptide product? I'm confused because I know the antisense strand is the template for mRNA but it has anti codons so I do not know how ...
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1answer
79 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 ...
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2answers
61 views

Can a small polypeptide fold over itself and have a tertiary structure?

What I want to know is if polypeptides (those which are not considered as proteins) can also "exhibit" a tertiary structure.
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0answers
19 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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1answer
69 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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2answers
32 views

difference between motifs, domains, patterns, signatures and profiles

I can't get clear the difference between those terms, I see them a lot while browsing on Prosite, Pfam, Expasy e.t.c. However, I can find documentation about them, but It still not clear what the ...
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2answers
43 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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66 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
2
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1answer
97 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 ...
6
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1answer
410 views

Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that lactose permease...transports lactose into the cell and When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor ...
3
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1answer
19 views

How would one determine whether a chemical will upregulate a certain class of proteins?

I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity.  How would I go about this experiment? I'm assuming I would use some ...
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1answer
34 views

Can a human being live without any carbohydrates? [duplicate]

Nowadays low-carb is in fashion, but what I recently wondered is whether a human can live without any carbohydrates at all? Of course this would be hard to do in reality, as most food will contain ...
3
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1answer
31 views

Why does BLAST reduce word size for short proteins?

I'm using BLAST to identify a short protein (BLASTp). If I check the short query then the word size reduces from 3 to 2. However the search will then be less ...
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2answers
203 views

Can two protein secondary structures “overlap” in the PDB?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
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1answer
41 views

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?
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1answer
56 views

Difference between the P4 and P5 subtypes of P-type ATPases in plants

In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?
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2answers
39 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 ...
4
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0answers
23 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 ...
3
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2answers
35 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 ...
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2answers
69 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 ...
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1answer
50 views

Coordinates of amino acids in a protein sequence [closed]

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 MKL......
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1answer
27 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 ...
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4answers
430 views

Bacterial cell lysis buffer used in proteomics procedures

What kinds of detergent-free bacterial lysis buffers exist? The proteins we're extracting will be later analyzed by LC-MS/MS, and we're looking for a lysis buffer that won't interfere with this ...
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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 ...
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, ...
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35 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
36 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 ...
11
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1answer
358 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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12 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. Bence-...
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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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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 ...
4
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1answer
189 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 ...
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0answers
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 ...
12
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2answers
209 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 ...
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1answer
57 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
205 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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1answer
41 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 ...