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11

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 ...


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 ...


5

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

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 ...


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

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.



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