14
votes
Accepted
Do transcription factors bind to both strands of DNA?
The short summary is that typical TFs bind and read both strands together, as a basepair sequence. Some proteins instead recognise a site on the helix by its shape and flexibility. ssDNA-binding ...
- 766
11
votes
Accepted
How many RNA-binding proteins can simultaneously bind on a single mRNA?
See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq.
Figure 1 of the paper shows ...
- 35.1k
10
votes
Phagemid display
I found article in Nature:
A helper phage to improve single-chain antibody presentation in phage display
Experimental protocol
Standard cloning procedures, determination of colony-forming units and
...
- 5,172
9
votes
Accepted
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
Accepted
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 ...
- 22.4k
7
votes
Accepted
What does units/mg mean for Streptavidin
16 units/mg means 16 units per milligram of protein.
Many companies, including Invitrogen, define 1 unit streptavidin as the amount of streptavidin necessary to bind 1 microgram of biotin.
- 51.1k
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 ...
- 22.7k
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
Accepted
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 ...
6
votes
What does units/mg mean for Streptavidin
Just to add to Chris Stronk's answer:
1 U SAV can bind 1 ug biotin
This tells you that in a 16 U/mg SAV sample, every mg of SAV will bind 16 ug of biotin. You can figure out the molar ratio from ...
- 17.5k
6
votes
Accepted
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 ...
- 1,709
6
votes
How do we know if the folding@home project results are right?
in silico modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally.
From ...
- 17.5k
6
votes
Accepted
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 ...
- 4,638
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 ...
- 22.4k
5
votes
Accepted
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 ...
- 22.4k
4
votes
Accepted
Proteins: Post translational modification
1) Is the attachment of zinc regarded as a type of post-translational
modification?
It is not really considered a post-translational modification because the zinc atom is not covalently bound to ...
- 35.1k
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 ...
- 35.1k
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
Accepted
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 "...
- 1,587
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 ...
- 8,671
4
votes
Accepted
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 ...
- 17.5k
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 ...
- 6,908
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 ...
- 14.7k
3
votes
Accepted
Edman method to identify peptides with Phenylisothiocyanate (PTH)
The short answer is that the Edman degradation is a multi-step process. The Wikipedia page has a decent picture of the mechanism. In practice, the peptide is reacted with phenylisothiocyanate (PTH) ...
- 355
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 ...
- 36k
3
votes
Accepted
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 ...
- 8,671
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 ...
- 1,267
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 ...
- 2,663
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: ...
- 7,564
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