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12

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 ...


8

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 ...


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.


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 ...


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

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 ...


3

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 ...


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

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 ...


2

The sRNA mediated regulation in bacteria operates via diverse mechanisms. This case of sRNA competing with a mRNA for a protein is a passive kind of regulation. This might be good for finetuning but may not be very efficient. It is much better to actively regulate a mRNA by direct binding. Also, it will work only if the concerned protein is in limiting ...


2

Addition to the answer provided by Teige. Transcription factors bind to both the strands however your question also included proteins in general. DNA remains double stranded and twisted as helix most of the times; most proteins bind to both the strands as mentioned in the previous answer. However some proteins such as SSB (Single-strand binding protein) ...


1

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 similar to hexoses in shape and/or size. The cavity center is the centroid of the reported PDB atom numbers. And a little later: The binding-site center is ...


1

I will try answer your question directly. How do we know if we fold it right? A. If you're interested in only the end product pf folding -- the 3D structure, then this is the subset of the folding problem called the structure prediction (from sequence alone). a. We can verify the structure experimentally by determining the 3D structures by NMR or ...


1

A certain fold of a peptide string can be validated or ruled out if other experimental data is available. Some other techniques to infer protein structure are X-ray crystallography (requires pure protein that will crystallize) and single particle analysis.


1

Katsamba PS, Park S, Laird-Offringa IA. 2002. Kinetic studies of RNA–protein interactions using surface plasmon resonance. Methods 26(2):95-104 There are many methods for studying kinetics, I only mention this one because the lab I'm in has used it for studying protein-ligand interactions. That article has a good explanation of SPR and how it works, so I ...


1

Ridgeway and coworkers designed a really neat microfluidic device for making these kinds of kinetic binding measurements on RNA and protein (Ridgeway et al. 2009). Their device works sort of like a stop-flow, and they used a FRET based scheme to detect binding and unbinding events. They took measurements for one particular rRNA/ribosomal protein pair and got ...



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