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
21k views

What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?

I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an ...
18
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2answers
3k views

Do gene expression levels necessarily correspond to levels of protein activation?

I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid? My problem ...
14
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4answers
977 views

How many human proteins have a solved 3D structure?

I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
14
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1answer
2k 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 ...
13
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5answers
4k views

Can any protein be phosphorylated?

I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (Skowrya et al., 1997). I have heard of ...
13
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4answers
241 views

Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?

What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them? If none are known, what computational tools might be used to search for such examples?
13
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2answers
565 views

Intrinsically disordered proteins as potential drug targets

Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological ...
13
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1answer
12k views

What effect has changing pH and salt concentration on protein complexes?

I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...
12
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2answers
115 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 ...
12
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1answer
8k views

What is the significance and method behind Ramachandran plots?

My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and ...
10
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2answers
913 views

Why and how does uniprot list ~150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns ~146,000 proteins. I was under the impression that there were only 20-25,000 proteins in ...
10
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2answers
1k views

Why are restriction enzymes not frozen?

We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is ...
10
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1answer
454 views

How would I explain different properties of the same protein in different species?

I recently finished an experiment where I analyzed the rate of ATP hydrolysis of Heat shock protein 104 in three species of fungi. They have shown to all have different rates of ATPase activity. How ...
10
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1answer
160 views

Protein data bank syntax: Can two protein secondary structures “overlap”?

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: ...
9
votes
2answers
160 views

What role does a protein's size have on protein-protein interactions?

Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
9
votes
1answer
149 views

Circular mRNA to produce long proteins

Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I ...
8
votes
1answer
893 views

Is there a protein in the eye that gets kinked by photons and shipped down to the liver to get un-kinked?

My friend made the claim that there exists a protein in your eye responsible for vision. This protein is sensitive to different wavelengths of light, and when it gets hit by the right wavelength, it ...
8
votes
1answer
749 views

Did not understand a small excerpt from a research paper

Was going through this paper, among multiple things that i did not understand, I came across this part: Each amino acid residue of a single window was encoded into a unitary bit string of length ...
8
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2answers
304 views

How many human proteins are very well characterized?

Following up on How many human proteins have a solved 3D structure?,is there a list of very well characterized human proteins / protein complexes? My criteria for "very well characterized" ...
8
votes
2answers
60 views

All UniprotIDs of a cancer pathway

I need to download all uniprotIDs of a cancer pathway, say the AKT Signaling. It may be super easy, but I don't know which resource to look at since it is a new field. How/where do I find these?
8
votes
0answers
546 views

Rosetta ab initio prediction and protein-protein interaction fitness help [closed]

I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to ...
7
votes
2answers
451 views

How to compute properties of peptides ?

I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following : Length ...
7
votes
3answers
446 views

Can protein structure be determined by X-Ray Diffraction in a single image?

I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration ...
7
votes
3answers
12k views

Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
7
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2answers
3k views

Gene & Protein nomenclature: N-Myc, c-Myc, et. al

Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins? I think I know that for genes, we use an italic ...
7
votes
1answer
141 views

How does Yeast-two-hybrid detect interactions between several proteins in one experiment?

I am trying to understand the Y2H screening method. I can understand how we can check if two specific proteins interact with each other. For example, if we want to check whether protein A and protein ...
7
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2answers
69 views

Is there a binding affinity metric for interactions not in equilibria?

I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the ...
7
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3answers
568 views

Protein Biology Cheat Sheet

I'm looking find a cheat sheet for protein biology to stick on my desk to remind of some of the key principles of protein biology. I seem to remember the specific and complex principles in protein ...
7
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2answers
133 views

What are some (bioinformatic) methods to characterize potentially novel gene transcripts?

I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, ...
7
votes
1answer
137 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
7
votes
1answer
132 views

What is peptide mapping?

After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand ...
7
votes
1answer
2k views

Where do lost membrane proteins go after exocytosis?

Exocytotic vesicles take away membrane proteins and glycocalyx on the cell's plasma membrane surface. When those vesicles are released into the interstitial fluid and wherever else, where do they go? ...
7
votes
1answer
265 views

Protein construct design

I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying ...
7
votes
1answer
294 views

Recombinant protein fraction in E. coli

If a protein is heterologously expressed in E. coli under the T7 promoter, what fraction of the total protein concentration in the cell is the heterologously expressed protein? What could be its ...
7
votes
1answer
98 views

Can you get enough water by eating only fish?

Scenario: In a boat in the middle of the sea, no freshwater or food stores, no desalination equipment, no rain, but you can catch fish and eat it raw. Can you get enough water this way to survive, ...
7
votes
2answers
87 views

Exactly which amino acids are phosphorylated in higher plants during state transitions?

I know it is usually stated as the threonine residue near the N-terminus of either light harvesting complex (lhc) b1 or lhcb2, but if this is somehow lost, say in a mutant, is the system flexible ...
7
votes
1answer
139 views

Why is leucine amino acid used the most in proteins and tryptophan the least?

The amino acid leucine, is used in proteins more than others. Leucine with 9.1 percent (its average in more than 1.150 different proteins) is used most and tryptophan with 1.4 percent is used less ...
7
votes
1answer
94 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
7
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0answers
84 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 ...
6
votes
2answers
514 views

What is the purpose of using two layers of gel in SDS- PAGE?

I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about ...
6
votes
3answers
224 views

Proteins folding

Some of us are involved in the folding@home project, spending time, money and resources. I would like to know an answer to two main questions: how do we know we fold it right? I mean these models ...
6
votes
3answers
16k views

Differences Between Protein Motifs and Protein Domains?

I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins. Any suggestions would be much obliged.
6
votes
1answer
85 views

Where do the electrons and protons formed from biological reactions go?

In a reaction like disulphide bond formation protons and electrons are released. These particles are presumably damaging in high levels. What systems are in place to prevent a build up of electrons ...
6
votes
1answer
66 views

What regulates the timing of the motion of molecular machines during DNA Replication?

This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines. I know that those big ...
6
votes
1answer
381 views

Determining if a specific proline is cis or trans in the protein?

While peptide bonds usually adopt the trans conformation, peptide bonds to proline can exist in either cis or trans conformation. The isomerization between cis and trans is slow, and has been shown to ...
6
votes
2answers
549 views

Solvent Accessibility, the 20% cut-off method

I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value. I understand how the RSA is ...
6
votes
1answer
118 views

Determining if a Protein Model Contains a Backbone Clash

I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be ...
6
votes
1answer
501 views

How can I predict DNA binding affinities from a protein sequence?

Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?
6
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1answer
48 views

Has the protein composition (with identification) in honey and other honeybee byproducts been studied?

I am interested in studying honey and other honeybee byproducts. I have not been able to find sequence or structure records for any of the contents of honey. In particular, I want to study the ...
6
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1answer
368 views

Is consuming proteins different vs. consuming amino-acids and how?

Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that ...