I made an example of a peptide-sequence and it would be of great help if you could help me understand this. Lets say I have the following peptide-sequence. Which secondary structure would it get and why? What would stablize it? I have included destabilizing (for alfa-helix-structure) aminoacids just to understand.
https://preview.redd.it/f25vsj1idxy71.png?width=1188&format=png&auto=webp&s=bdf882cf0dd20d41d6dec5b8ae63135d61d5bad0
The given DNA is 3’-T A C T G T C T G A C G A T C-5’
Am I right with my answers?
Complementary DNA sequence: 5’- A T G A C A G A C T G C T A G - 3’
mRNA sequence transcribed from template: 5’-A U G A C A G A C U G C U A G-3’
amino acid sequence of peptide: met – thr – asp – cys - stop
Journal of the American Chemical SocietyDOI: 10.1021/jacs.1c00342
David E. Clarke, Guanglu Wu, Ce Wu, and Oren A. Scherman
https://ift.tt/3sxmxWp
You ever find yourself reading an article but can't remember how you managed to Google yourself there? Yeah, me too.
In this case I ended up reading an article by Tracy Wilson at HowStuffWorks.com [1] wherein she was talking about young-earth creationism and dinosaur tissues. The context was obviously Mary H. Schweitzer and her sensational findings over a decade ago.
Anyhow, I came across a section that puzzled me, but I don't have a black belt in Google-fu so I'm unable to resolve it. In this article Wilson acknowledged that a 2008 paper by Asara et al. [2] "describing protein sequences adds some weight to the idea" that the tissue belonged to a specimen of Tyrannosaurus rex, rather than being a more recent contaminant.
Specifically, these were "endogenous peptide sequences" extracted from this 68-million-year-old fossil, according to Asara et al. But, Wilson notes, "In the minds of many, the presence of peptides in a specimen as old as a T. rex is impossible."
Wilson also pointed to a researcher named Christina Nielsen-Marsh who was quoted by National Geographic News "as saying that the sequences described ‘make no sense at all’." Wilson provided a link to the source material—an article by Scott Norris [3]—but it is unfortunately a dead link. I have tried to find a copy of this article online but to no avail.
Therefore! I am looking for help in either one of two areas:
-
Could someone with better Google-fu locate this 2007 article by Scott Norris? I want to know what Nielsen-Marsh's argument was.
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Could someone explain why Asara et al. did not find the peptide sequences they claimed to have found? Apparently that's "impossible," according to the minds of many (whoever they are).
I really appreciate your enthusiastic help. Thanks, guys.
FOOTNOTES:
[1] Tracy V. Wilson, "How did scientists find soft tissue in dinosaur fossils?" HowStuffWorks.com, August 4, 2008.
[2] John M. Asara, Mary H. Schweitzer, Lewis C. Cantley, John S. Cottrell, "Response to Comment on ‘Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry’," Science, vol. 321, no. 5892 (2008): 1040. doi: 10.1126/science.1157829
[3] Wilson cites the article as: Scott Norris, "Dinosaur soft tissues sequenced: Similar to chicken proteins," *National Geographic Ne
... keep reading on reddit ➡Dear colleagues,
My rather basic question from the looks of it:
I have a short amino acid sequence of the cell-penetrating peptide such as TAT (N-GRKKRRQRRRPQ-C). If I would N-C reverse it to get N-QPRRRQRRKKRG-C, would I expect it to behave and fold in the same manner or not? Should I regard this as a new peptide with potentially different functionality?
I do understand that generally, we would expect that the overall charge, hydrophobicity, hydrophobic moment etc. would be the same (although if it folds differently, the parameters would also change a little?, e.g. some of the parts would not be "poking" out in one protein but nor the other).
I ask this question since I've seen some of the researchers use a reverse sequence as a negative control.
Thank you,
Best wishes
EDIT: The sequence I gave is just an example. My question is regarding any kind of sequence.
Ornithine‐containing peptides are known to be produced by nonribosomal peptide synthetases. We studied a new enzyme family from ribosomally synthesised and posttranslationally modified peptide (RiPP) pathways that installs ornithine residues in ribosomal peptides. Peptide arginases represent a useful synthetic tool to access diverse ornithine peptides through RiPP technology.
Abstract
Ornithine is a component of many bioactive nonribosomal peptides but is challenging to incorporate into ribosomal products. We recently identified OspR, a cyanobacterial arginase‐like enzyme that installs ornithines in the antiviral ribosomally synthesised and posttranslationally modified peptide (RiPP) landornamide A. Here we report that OspR belongs to a larger family of peptide arginases from diverse organisms and RiPP types. In E. coli, seven selected enzymes converted arginine into ornithine with little preference for the leader type. A broad range of peptide sequences was modified, including polyarginine repeats. We also generated analogues of ornithine‐containing nonribosomal peptides using RiPP technology. Five pseudo‐nonribosomal products with ornithines at the correct positions were obtained, including a brevicidine analogue containing ornithine and a d‐amino acid installed by the peptide epimerase OspD. These results suggest new opportunities for peptide bioengineering.
https://ift.tt/3kAJ01O
Journal of the American Chemical SocietyDOI: 10.1021/jacs.9b11617
https://ift.tt/2GibI4E
I hope this doesn't sound stupid 'cause I know that a peptide can take on different configurations based on its environment but I'm assuming this program would just default to the Native State?
Anyways, I'm an undergrad molecular and cellular biology major who is taking biochemistry and think a program like this would help a lot with visualizing what we're covering. I know of pepdraw but that just gives the skeletal structure. Doesn't have to be free, I'd be willing to pay (a reasonable price)!
Thanks!
I made an example of a peptide-sequence and it would be of great help if you could help me understand this. Lets say I have the following peptide-sequence.Which secondary structure would it get and why? What would stablize it? I have included destabilizing (for alfa-helix-structure) aminoacids just to understand.
https://preview.redd.it/p2m5b8xvcxy71.png?width=1188&format=png&auto=webp&s=51371e96465c6320fcb4e1b36842ba8f4d3c808f
Ornithine is a component of many bioactive nonribosomal peptides but has been challenging to incorporate into ribosomal products. We recently identified OspR, a cyanobacterial arginase‐like enzyme that installs ornithines in the antiviral ribosomally synthesised and posttranslationally modified peptide (RiPP) landornamide A. Here we report that OspR belongs to a larger family of peptide arginases from diverse organisms and RiPP types. In E. coli expressions, seven selected enzymes converted arginine residues to ornithines with little preference for the leader type. A diverse range of peptide sequences was modified, including polyarginine repeats. Further exploring the synthetic potential of OspR, we generated analogues of ornithine‐containing nonribosomal peptides using RiPP technology. Five pseudo‐nonribosomal products with ornithines at correct positions were obtained. This included a brevicidine analogue containing ornithine and a d‐amino acid that was installed by the peptide epimerase OspD, suggesting new opportunities for peptide bioengineering.
https://ift.tt/3kAJ01O
