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1

Every amino acid has a different isoelectric point: a pH where they do not carry electric charge. This isoelectric point depends on the side chains: By glycine the side chain $-H$ is neutral (while the amino and carbonic acid groups are not) so the IEP is 5.97. By lysine the side chain $-(CH_2)_4\mbox{-}NH_2$ is alkaline $[R\mbox-NH_2 + H^+ ...


2

First, when asking about a specific small term, it's best to check your spelling. If you actually look at the sentience, you will note that you left out a very important hyphen: Pellequer compared several propensity scale methods using a dataset of 14 epitope-annotated proteins. [emphasis added] The phrase means that the protein sequences (amino ...


1

Here a solution that does not require you to upload the files to the servers: You can graphically visualize DSSP and Stride at the Sequence Page at RCSB PDB: http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=5P21&bionumber=1 "add annotation" -> Stride and look at the graphical comparison between DSSP and Stride.


3

Are you taking in an in vitro context for preventing protein denaturation after protein isolation from for example E. coli or are you more worried about proteins in the context of the whole cell? I'm no expert in the protein folding/conformation studies but from laboratory based prospective if you want to achieve denaturation for experimental purposes, you ...


3

Really the question how does protein folding work? But let me answer your questions... 1) Very few proteins have disulfide bonds (usually secreted proteins) or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself. Denaturation is only reversible in relatively few cases in fact. A few proteins, ...


1

You can find examples by using the "drilldown" function at the RCSB PDB homepage: Click on the number 103921 at the top of the page at http://www.rcsb.org then find the "SCOP Classification" section and then e.g. select "All alpha proteins".


4

You may consider taking a look at the SCOP structural classification of proteins to check all beta proteins and all alpha proteins. As per specific examples and though not belonging to the SCOP classes mentioned above, Porin for a beta protein (PDB:1A0S), and Rhodopsin for an alpha protein (PDB:1F88) are two nice structures to look at.


2

In my opinion you should use this formula: $\huge \frac{log_2(Iso_1/Iso_2)}{log_2(GAPDH)} $ This will normalize the relative fold differences between the isoforms with the loading control- GAPDH. Since both numerator and denominator are log transformed they are in comparable domains unlike the formula-2 that you mention in your question. This is just a ...


3

If you have a man in a box scenario where you only look at numbers, the answer is, no, he won't last 14 days.[1] The difficulty with this question for me is that the body doesn't always behave the way it's supposed to. The 3-3-3 rule (3 minutes without air, 3 days without water, three weeks without food) and the "100 hour rule" (4.166 days) aren't ...


2

There is no evidence that one is better than the other, most likely because it differs from case to case. Neither you, nor your critics, are right. There is a tiny bit of science in a paper on digitizing blots, generalizing from blots of a specific protein (PMID: 19517440), and they use grayscale for no given reason. Come to think, that is the best paper in ...



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