To mutate nucleic acids you will have to use the command line. Choose Favorites... Command Line to show the command line. Then you can use the command “swapna”. You can see how to use this command to specify the residue(s) to change and what to mutate them into by choosing Help… Commands Index, and then searching for the link to the “swapna” command on that web page.
Loop modeling is the most immediate technique that could be applied. There are tools in Chimera to do this, but they also require another software, MODELLER, which is freely available to academic researchers, but not to government or commercial entities without a fee. www.cgl.ucsf.edu/chimera/1.5.2/docs/ContributedSoftware/model/model.html If the model is already published, another way to do this would be to use I-TASSER. zhanglab.ccmb.med.umich.edu/I-TASSER/
As shown at the start of the video, an article in the Biophysical Journal shows a variety of experimentally studied mutations. This is an example of the most common motivation for choosing a particular residue to mutate, that is, to scrutinize experimental data that suggests a specific mutation is important and to try to understand or explain it structurally. A mutation may affect a protein's stability, its ability to interact with other proteins, or its ability to bind small molecules. The structure of a mutation may reveal the mechanism for these effects.
The Pubmed Central table was from a paper that was only used to provide a rationale for the example mutation shown in the demo, and does not need to be downloaded. If you are interested in looking at this paper, you can find the publication here: www.sciencedirect.com/science/article/pii/S0006349504736437
A “rotamer” (or “rotational isomer”) is an isomer arising from rotations about bonds in the side chain of an amino acid. It is one kind of “conformational isomerism”. en.wikipedia.org/wiki/Conformational_isomerism The number of rotameric states for amino acids have been computed a variety of ways, notably by Dunbrack, but also by others. See the Chimera reference page (www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html) for more information on the various “rotamer libraries” that have been proposed over the years. The selection of a rotamer in this tutorial is simply to select a starting state for the position of the amino acid such that it will not seriously perturb the structure (note my commentary at time 5:04 in the video). The minimization shown in part 2 of the tutorial modifies this starting state so that it better approximates a more physiological state.
@@AlexKChen The tertiary structure of protein complex shown in the video is derived from X-ray crystallography. The “crystal structure” of the protein is described by a collection of related atomic points in space. It is true that molecular structures have motion, but that is beyond the scope of this kind of modeling. You can see examples and explanations of this kind of “molecular dynamics simulation” here: th-cam.com/video/5JcFgj2gHx8/w-d-xo.html
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thanks a lot for the clip. I enjoyed this. I use Chimera in my lectures, but it is always nice to see how other people do it.
Very helpful. Good presentation, I learned a few (for me) new chimera tricks today. Thanks!
Very helpful, thank you Darrell! This is exactly what I needed for swapping out amino acids in a theoretical protein.
E. No
Thank you very much Dr. Hurt. This video tutorial is very helpful and informative!
Excellent tutorial. Thanks a lot!
thanks you sir, its really imp of us
thanks a lot ...very useful ...
Excellent well-paced tutorial. Will this procedure work with nucleic acids?
To mutate nucleic acids you will have to use the command line. Choose Favorites... Command Line to show the command line. Then you can use the command “swapna”. You can see how to use this command to specify the residue(s) to change and what to mutate them into by choosing Help… Commands Index, and then searching for the link to the “swapna” command on that web page.
very useful - however, I wonder how to model a deletion or insertion? Is there an alternative to the rotamer tool for this purpose?
Loop modeling is the most immediate technique that could be applied. There are tools in Chimera to do this, but they also require another software, MODELLER, which is freely available to academic researchers, but not to government or commercial entities without a fee.
www.cgl.ucsf.edu/chimera/1.5.2/docs/ContributedSoftware/model/model.html
If the model is already published, another way to do this would be to use I-TASSER.
zhanglab.ccmb.med.umich.edu/I-TASSER/
Sir,I wonder how to save the file in pdb format after the mutation... because after saving it remains to be in the same residue as in before mutation.
Barnase -Chain A-and Barstar chainD - Are these multiprotein complex?
Hi... Upload tutorial for MD simulation in chimera
How do we choose the favorable residue, the residue that we are going to change?
As shown at the start of the video, an article in the Biophysical Journal shows a variety of experimentally studied mutations. This is an example of the most common motivation for choosing a particular residue to mutate, that is, to scrutinize experimental data that suggests a specific mutation is important and to try to understand or explain it structurally. A mutation may affect a protein's stability, its ability to interact with other proteins, or its ability to bind small molecules. The structure of a mutation may reveal the mechanism for these effects.
where did u find pubmed central table box??? Do i have to download pubmed central table?
The Pubmed Central table was from a paper that was only used to provide a rationale for the example mutation shown in the demo, and does not need to be downloaded. If you are interested in looking at this paper, you can find the publication here:
www.sciencedirect.com/science/article/pii/S0006349504736437
How did you change the background color in White?
Use the “Actions > Colors” submenu. Click first on “background,” then on “white” (or any other color).
How to mutant amino acid by formylglycine
how do we know there are 9 rotamers for tryptophan?
A “rotamer” (or “rotational isomer”) is an isomer arising from rotations about bonds in the side chain of an amino acid. It is one kind of “conformational isomerism”. en.wikipedia.org/wiki/Conformational_isomerism
The number of rotameric states for amino acids have been computed a variety of ways, notably by Dunbrack, but also by others. See the Chimera reference page (www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html) for more information on the various “rotamer libraries” that have been proposed over the years.
The selection of a rotamer in this tutorial is simply to select a starting state for the position of the amino acid such that it will not seriously perturb the structure (note my commentary at time 5:04 in the video). The minimization shown in part 2 of the tutorial modifies this starting state so that it better approximates a more physiological state.
awesome thanks! also how do we know the tertiary structure of the inputted protein? (can it be changed b/c the tertiary structure evolves over time?)
@@AlexKChen The tertiary structure of protein complex shown in the video is derived from X-ray crystallography. The “crystal structure” of the protein is described by a collection of related atomic points in space. It is true that molecular structures have motion, but that is beyond the scope of this kind of modeling. You can see examples and explanations of this kind of “molecular dynamics simulation” here: th-cam.com/video/5JcFgj2gHx8/w-d-xo.html