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

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Essential amino acids

Humans and the majority of animal species cannot synthesize essential amino acids (Info: Campbell biology 9th edition). However, meat, eggs, et cetera provide all required essential amino acids. And ...
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“Other” classification for epitopes in the Immune Epitope Database (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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What are “+” and “Ar” in consensus binding sequence of amino acids?

So I was reading this paper and found a figure as below: I understand that [LEAM] means any of LEAM residues, pS is phosphoserine and X means any amino acid residue. What is [+] here ? Is both R and ...
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33 views

Optimum pH of Catalase

I am aware that certain organs in the body have specific pH environments to increase the activity of their enzymes. I'm also aware that enzymes only work at certain pHs due to the configuration of the ...
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1answer
25 views

Rules of motif forming

I want to understand how a motif is present or not, can be deduced from a PDB file. Are there any rule of thumb for forming 3D motifs? Like a series of helices and sheets in some direction will lead ...
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17 views

Kinetics and de novo protein prediction

De novo conformation predictors usually function by producing candidate conformations (decoys) and then choosing amongst them based on their thermodynamic stability and energy state. Most successful ...
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43 views

Why is the protein ubiquitin so ubiquitous?

Ubiquitin is a protein tag that is attached to proteins in order to mark them for destruction/proteolysis by the cell. This system is sometimes used for clearing out harmful viral proteins that infect ...
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77 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 ...
6
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42 views

Optimal pH of protein buffer? Basic principles to adjust buffers according method and analysis

Protein buffers such as PBST, which is used in western blotting, are normally adjusted to pH 7.4. When I try to find why, I find some information about optimal pKa for protein stability. Im not sure I ...
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36 views

Can it be said that proteins determine phenotypic traits?

I am not ignoring the function of genes, or the gene-environment interactions. What I want to know is if behind every "observable characteristic" we can find a protein -or a group of proteins- which ...
1
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1answer
22 views

PBST vs. TBST buffer in western blotting

What is the advantages and disadvantages of using either PBST or TBST in western blotting, or while working with proteins in general? Are there other buffers which are also used for western blotting, ...
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49 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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29 views

How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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Can LC-MS/MS and MRM act as a complementary to RT-PCR, Western blotting and ELISA?

I am working on protein quantification using Liquid Chromatography-tandom Mass Spectrometry with Multiple Reaction Monitoring (LC-MS/MS MRM), I am not sure if it can act as a complementary to RT-PCR, ...
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6 views

Effector protein emission rate in host by pathogen

Is emission of effector protein a one-time process in the host, or does it emit effector multiple times in the same host? If effector proteins are emitted multiple times by the pathogen into the host, ...
2
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60 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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Amino Acid requirement + intake in relation to diet + meat type [closed]

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: It isn't just that the killing is cruel, ...
2
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2answers
46 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 ...
2
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1answer
69 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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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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16 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
18 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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18 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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34 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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30 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
59 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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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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71 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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82 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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65 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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20 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#...
3
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2answers
38 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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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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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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430 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
20 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
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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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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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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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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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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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89 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
57 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
28 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 ...
2
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4answers
446 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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37 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
51 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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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?