14
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 proteins obviously bind one strand but they do this in a non-specific manner.
RNA-binding proteins recognise the sequence on a single strand by inserting ...
11
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 distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression.
They show number of protein protected ...
10
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
plaque-forming units, and immunoblot after PAGE were carried out
according to Sambrook et al.
Construction of the packaging cell line.
DH5alpha/pIII
[...
9
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 movement (or any axis at all, as far as I can tell). This produces a polarity that can be seen in the figure below, from the original 1998 paper describing it.
The ...
9
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 Protein Data Bank) we are only concerned with ligands that bind to macromolecules, the structures of which are presented there — usually proteins. The following ...
7
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.
7
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 such as dengue and malaria. Blood feeding is an essential part of the lifecycle for most mosquito species as it provides females with the proteins necessary ...
7
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 believe this is the original paper (https://pubs.acs.org/doi/pdf/10.1021/ja910795a) it reported 60 % binding efficiency after an hour (I presume for version 1) and ...
7
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 reaction rate, reactions of all pairs (including SpyCatcher and SpyTag version 1) should go to completion under the right conditions.
The SpyCatcher002-SpyTag1 is ...
6
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 that they capture all the intuition without the tedious algebra.
It's interesting that you are asking for the fraction of ligand bound to receptors ($[RL]/[L]_{...
6
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 this:
$16\mu g\ BIO\cdot\frac{1mol\ BIO}{244310000ug\ BIO}\cdot\frac{52800000mg\ SAV}{mol\ SAV}$
Which equals:
$\frac{3.46mol\ BIO}{mol\ SAV}$
Theoretically, ...
6
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 the Folding@Home website:
Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation of our ...
6
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 its presence is an artifact of the crystallization process (ref):
Pig holoRBP crystals were obtained at 277 K by the sitting-drop vapor- diffusion method, ...
5
This is a classical protein purification problem - you have to find ways to fractionate your mixture so that each fraction can be assayed for the activity you are interested in. When you find the active fraction you then subject that to a different type of fractionation.
Salting out
The solubility of proteins is affected by the ionic strength of the buffer....
5
See here.
Histones are basic proteins (cationic, high pI) because they are required to interact with polyanionic DNA at physiological pH. Heparin and dextran are polyanions which form insoluble salts with the cationic histones.(Dextran is a polymer of glucose. In dextran sulphate it is derivatised with sulphonate groups creating a polyanionic material.)
...
5
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 ambiguity, as I would not really regard the NTPs involved in protein synthesis “releasing energy”. So let us consider two reformulations of the question, as the ...
5
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 pattern together with a hint, perhaps, of emblem or badge.
The word pattern indicates both repetition and a master mould from which copies are made. In molecular ...
4
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 the protein. Binding to zinc is adsorption.
2) When carbonic anhydrase is denatured, is the zinc ion released in
the medium?
Yes, but it depends on the ...
4
Telomerases are tightly controlled on all level: Expression, post-translational modifications and by external factors. I think for this the external factors, a protein class called telomeric proteins. They bind to the end of the telomere and regulate the telomerase.
The figure is from this paper, which looks into the topic quite extensively:
Regulation of ...
4
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 yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See ...
4
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 interchangeably. But the word "interface" is very generic and does not have any specific scientific meaning so the nature of the interface must be defined or else the ...
4
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 "big data": co-mutations (of charged amino acids) that can be found when sequencing many independent genomes. (... which indirectly bypasses the emphasis on ...
4
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 that sells antibodies for research. To help understand the quote, you'll need to know that the portion of an antigen that an antibody binds is called an epitope.
...
4
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 paper quoted in the question use the phrase temporal kinetics to describe the phosphorylation state of a proteome-wide selection of kinase substrates (ie ...
4
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 enter the cell, where it is translated into the encoded protein sequence. This is then translocated to the surface of the cell and in some cases into the ...
3
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) under mildly basic conditions to give a thiourea, which is stable. The excess PTH is separated from the thiourea intermediate. The thiourea is then treated with ...
3
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 through the effect of the indicated compound.
DTT breaks disulfide bonds, but does nothing else to solublize the protein, so it's all in the pellet, with none ...
3
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 benztropines also bind in the same region.
Beuming, T., Kniazeff, J., Bergmann, M. L., Shi, L., Gracia, L., Raniszewska, K., ... & Loland, C. J. (2008). The binding ...
3
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 to find to during the ubiquitination process?
Yes, This [Ubiquitination] process most commonly binds the last amino acid of ubiquitin (glycine 76) to a lysine ...
3
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 desensitization (in either context). You can read about this generally in Goodman and Gilman's Pharmacological Basis of Therapeutics, Chapter 3, under the ...
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