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G changes the codon specificity from that of T to A. It’s important to realize that in the codon world T is the amino acid threonine not the nucleoside thymidine, while A is alanine, not adenosine. Using proteins framework databases like Uniprot and interactive modeling sites like Protein Model Portal, we can punch in the alanine variant at position 112 and find out where it is situated among the various loops and folds of the proteins. Searching the dbSNP Short Nucleotide Variations data source exposed that several MT-CYB variations are associated with hypertrophic cardiomyopathy, so I wanted to do some more in-depth analysis there. G version in their study provides an excellent recipe.
The authors of this 2013 research used PolyPhen to investigate mutations close to the conserved function heme-binding redox centers of MT-CYB. Although Polyphen offers feelings-based metrics that rating various mutations as “possibly very harmful,” it can also attribute these subjective explanations to actual practical variables like overtaking at buried sites in the protein.
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Depending on whether or not crystal structures of human proteins are available at sufficiently high resolution, you can use prediction software like I-TASSER and Swiss-PDB Viewer to present amino acid changes and evaluate all possible rotamers. Changes in hydrogen bonding, macromolecular relationships, and energy minimization can be performed using GROMOS drive field.
Full-molecular dynamics simulations are still not for the faint of center. The NAMD and CHARMM22 programs, for example, need a lot of computing power generally. The MT-Cyb subunit interacts with several of the 11 subunits within complex III. Packages like the STRIDE simulator can determine secondary framework at successive time points disclose where interacting alpha helices changeover and alternately changeover to random coils to disrupt the framework of the organic.