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44 votes

How do proteins 'know' where to go?

Even though this animation is very well-known and the narrator says it is "... an accurate representation of the actual DNA replication machine ...", be very careful of its visual appeal. It ...
Domen's user avatar
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11 votes

How do proteins 'know' where to go?

This answer is specific to the "two-legged" proteins from the end of the video (motor proteins). The animation shows identical proteins moving in perfect lockstep, but really there is wide ...
benrg's user avatar
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9 votes
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What determines the direction in which motor proteins go?

While you're entirely correct that the ABABAB sequence is symmetric to a motor protein cruising along, the individual $\alpha$ and $\beta$ monomers themselves are not symmetric along the axis of ...
Dubukay's user avatar
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9 votes
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What is meant by “unique ligand” on the RCSB Protein Data Bank website?

Your understanding is incorrect. A ligand at its most basic is a molecule that binds to another molecule. There is no requirement for metal atoms whatsoever. In the context of RCSB (home of the ...
David's user avatar
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9 votes
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Is there are theoretical limit to the number of proteins possible and their respective structure?

You can certainly estimate a theoretical limit, given some assumptions. Let's say you do not care about any post-transcriptional modifications, you are interested only in the primary sequence. There ...
Domen's user avatar
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9 votes

How do proteins 'know' where to go?

There have been some suggestions that biological molecules may 'know where to go'. Barry Honig's group at Columbia analyzed the electrical charge arrangements in protein and proposed that by placing ...
shigeta's user avatar
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7 votes
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What does a female mosquito need from blood?

According to the Introduction to this paper: Attractiveness to biting insects is important in medical contexts, mostly in the dynamics of transmission of pathogens by mosquitoes that cause diseases ...
Alan Boyd's user avatar
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7 votes

Compatibility between spytag/spycatcher versions

I am currently working with these tags, so going off experience here. The binding efficiency is not 100% even when the correct versions are mixed e.g. version 2 spytag and version 2 spycatcher. I ...
J.E.Bird's user avatar
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7 votes
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Compatibility between spytag/spycatcher versions

I have worked with the coupling of SpyCatchers and SpyTags of different iterations and can confirm that they are all backward compatible. While SpyCatcher003 and SpyTag003 pairs have the quickest ...
dschramm's user avatar
6 votes
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Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

As far as I am aware, there is no known requirement for Cd in mammalian systems, but it is extremely toxic (Waalkes & Goering). It would seem that cadmium is required to get crystals of RBP, and ...
user338907's user avatar
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5 votes
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How much nucleoside triphosphate is required to form one peptide bond during protein synthesis?

Although the question shows considerable effort to achieve clarity, the way it is phrased as: How many molecules of nucleoside triphosphate… [does] it take to release enough energy still allows ...
David's user avatar
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5 votes
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Meaning of ‘motif’ in molecular biology

Meaning of Motif in Molecular Biology In English the word, motif (borrowed from the French), has a variety of meanings in different areas. The one that is borrowed in molecular biology is that of ...
David's user avatar
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4 votes
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Could AI be applied to protein folding?

Yes, and no :-) In the meantime many protein structures can be predicted quite accurately - even those for which no reference fold had been known before. In this case the important buzz word is "...
tsttst's user avatar
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4 votes

Can multiple antibodies bind the same antigen?

Not only is it possible for multiple antibodies to bind a single antigen, when that happens, it's more likely to trigger a full immune response. Here's a description of the concept from a company ...
De Novo's user avatar
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4 votes
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How do anticholinesterase pesticides kill nematodes?

Cholinesterase inhibitors and plant-pathogenic nematodes While it is true that cholinesterase inhibition does not affect gas exchange in nematodes, it does produce other effects by paralysing motor ...
Adhish's user avatar
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4 votes
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What are " temporal kinetics"?

Temporal kinetics does not refer to the kinetics of kinase phosphorylation reactions and, since it is not standard terminology, you likely wouldn’t find its meaning in any textbook. The authors of the ...
canadianer's user avatar
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4 votes

Can mrna spike protein block other proteins entering cells?

Short answer: No. What I am going to do here is some back-of-the-envelope style calculations and a bit of explaining, so bear with me... The way that these vaccines work is by causing the mRNA to ...
bob1's user avatar
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3 votes

How does the body detect irreversible binding to receptors?

The process of downregulating a receptor by internalizing and degrading it in response to (sometimes prolonged) activation or (sometimes prolonged) failure to activate is what pharmacologists call ...
De Novo's user avatar
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3 votes
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Where do the lysines come from during ubiquitination?

The Wikipedia article on Ubiquitin gives a pretty good answer to your questions. Look at the referenced articles if you want to get more detailed answers. Are they just always available for the Ub ...
Ashafix's user avatar
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3 votes
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Does cocaine bind competitively or non competitively to DAT?

Cocaine binds competitively to DAT, though not in precisely the same binding site, rather there is overlap, and many of the same amino acids are involved in binding of each. Amphetamine and ...
Bryan Krause's user avatar
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3 votes

Is there an enzyme that functions without being associated with a complex?

Acetylcholinesterase. Chosen because the esterase seems like a low energy reaction so it wouldn't need energetic co-factors. https://en.wikipedia.org/wiki/Acetylcholinesterase Not sure if I should do ...
Polypipe Wrangler's user avatar
3 votes

What other sites do non-competitive inhibitors bind to apart from allosteric sites?

Here is a helpful excerpt from the lecture notes for Introduction to Molecular and Cellular Biology at Columbia University, taught by Lawrence Chasin and Deborah Mowshowitz (emphasis mine): Re: ...
acvill's user avatar
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3 votes

How does one derive a KD from an equilibrium titration experiment?

The models you are using are based on the Langmuir Isotherm. The classical use of this model is for gas adsorption to a solid. In these experiments, the pressure of the gas is measured against the ...
stords's user avatar
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2 votes
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Pharmacological inhibition of Ras

Protein binding interactions are usually referred to by how easily the binding partner can be displaced by something other than the preferred substrate. Usually, this is in reference to the ...
akaDrHouse's user avatar
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2 votes
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Are the arrows in this diagram of ATP synthase correct?

Yes, the arrows are correct. However, it's not immediately clear what they're trying to show. ATP synthase ATP synthase can act as a generator or a motor. Interactions cause rotation of the F0 subunit ...
James's user avatar
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2 votes

For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?

According to Foyes Principle of Medicinal Chemistry, the significant difference is the crowding of the active site by the cycle next to the lactam ring, which prevent attack on the ester and release ...
Eliane B.'s user avatar
  • 1,145
2 votes

Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?

As Nicolai has mentioned in his answer, change of chirality (L and D) of amino acids will drastically change the way a protein folds. I searched online to find if a solved structure of D only form of ...
Roni Saiba's user avatar
2 votes

Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?

No. One can make no generalization about the effect of the change in chirality in a ligand in the protein to which it normally binds. As the simple diagram below shows, as far as interaction with the ...
David's user avatar
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2 votes
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Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?

There a few things you have to take care of with chirality in biological systems: First note, that for amino acids we usually use L and D instead of r and s nomencalture. In chemistry the ...
Nicolai's user avatar
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