43
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 ...
- 1,554
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 ...
- 211
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 ...
- 808
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 ...
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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 ...
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8
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 ...
- 1,554
7
votes
Accepted
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 ...
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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 ...
- 316
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 ...
- 86
6
votes
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Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?
The answer is here, but depending on your level of comfort with the math I'm not sure how enlightening it will be. I think that the reason people tend to stick to one ligand/one receptor models is ...
- 1,719
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 ...
- 4,668
5
votes
Accepted
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 ...
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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 ...
- 23.8k
4
votes
Accepted
Are multi-chain proteins synthesized as one biological unit?
Are multi-chain proteins synthesized as one biological unit?
Sometimes yes but mostly not.
Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to ...
- 35.2k
4
votes
Accepted
In protein-protein interactions what is the difference between a binding site and an interface?
A protein-protein interaction (PPI) binding site is a type of interface. If it has been established that the interface is a PPI binding site, then the terms can from that point forward be used ...
- 369
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 "...
- 1,597
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 ...
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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 ...
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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 ...
- 9,508
3
votes
Accepted
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 ...
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3
votes
Accepted
Does urea at different concentrations (5 or 0.5M) have different effects on proteins?
What you need to do is compare the relative amounts of the protein in the insoluble (pellet) fraction to the soluble (supernatant) one. This way you can determine how soluble the RMAS has become ...
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 ...
- 695
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 ...
- 8,741
3
votes
Accepted
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 ...
- 1,287
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 ...
- 2,838
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: ...
- 8,216
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 ...
- 957
2
votes
Accepted
How is protein cavity centre related to binding?
As you can find under the table with cavity centers in pdf version of this article:
The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are ...
- 293
2
votes
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What is the significance in an alpha-helix being right-handed or left-handed?
Some experimental and modelling observations suggests, folding energy for right handed in more favorable. You can find more detailed answer to this question here.
- 2,396
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 ...
- 1,309
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