This Sandbox is Reserved from March 18 through September 1, 2025 for use in the course CH462 Biochemistry II taught by R. Jeremy Johnson and Mark Macbeth at the Butler University, Indianapolis, USA. This reservation includes Sandbox Reserved 1828 through Sandbox Reserved 1846.
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The original side chain is phenylalanine side chain, is located 3.6 Angstroms from the ligand. There are two main mutations isoleucine and tryptophan. Isoleucine is a smaller molecule and makes a tighter bond in the ligand, with the distance being 3.0 Angstrom. This allows for more efficient interactions with the ligand, likely improving substrate binding and catalytic efficiency. The other is tryptophan, which is a bulkier side chain, which does have a slightly shorter difference of 3.2 Angstroms, while being a larger side chain. The effect that is has is more based on that tryptophan is a nitrogen-containing aromatic ring, which offers new interactions with the substrate, which could also affect enzyme's binding and catalytic properties.
These two mutations both lead to an increase in catalytic activity from the mutation, F243I had a 27.5% increase and F243W had an 17.5% increase, when compared to the wild-type variant.
The original side chain is threonine and is mutated with a methionine. This is really a mutation that increases thermostability. The wild-type variant has a melting point of 84.7 degree Celsius. The mutation of methionine, is a larger, more hydrophobic side chain, and would contribute to stabilization of the protein's core by increasing hydrophobic interactions. The stronger internal interactions help the enzyme to maintain its folded structure more efficiently at elevated temperatures. Which is shown by the M96 mutation having a melting point of 87.4 degree Celsius.
The original side chain is tyrosine, and is has a mutation to glycine. Like the T96M mutation, it also increases thermostability of the protein, with this mutation Y127G having a melting point of 87.0 degree Celsius. The mutation replaces tyrosine, a bulky, rigid aromatic side chain to glycine, which is the smallest amino acid. This mutation leads to allowing greater flexibility for the protein. By reducing steric hindrance and releasing some strain in the protein structure, allowing for it to be more flexible and more stable at higher temperatures.
The original side chain of asparagine, with two options of mutations with aspartic acid and methionine. These mutations are also to increase thermostability. With the wild-type having a melting point of 84.7 degree Celsius. The mutation to aspartic acid, which replaces a polar and neutral side chain with a negatively charged side chain. This likely introduces more electrostatic interactions or salt bridges that help stabilize the protein structure. Taking the N246D mutation with a melting point of 87.9 degree Celsius. While the mutation replaces the original with a hydrophobic amino acid side chain. This introduces a bulkier and hydrophobic side chain, which will strengthen the internal packing of the core of the protein. This leads for the N246M had a melting point of 88.0 degree Celsius.
These are two mutations that are linked one being a serine and aspartic acid. These mutations were meant to replace calcium ions which are very common in these experiments, in an attempt to replace them with a disulfide bond. As their distances between the alpha and beta atoms suggesting that it could be engineered. With the mutation, of both to a cystine, allowing for disulfide bonds, found improved thermostability. Wild-type having a melting point of 84.7 degree Celsius. While the mutation was highly successful in increased thermostability, with the mutation having a melting point of 94.5 degree Celsius, which is a 9.8 degree Celsius increase, which is higher than the rest of the mutations. However, this was also shown to have a result of a decrease in enzymatic activity of 28% compared to wild type.
This is likely why many mutations are all used at once, in order to increase thermostability and maintain or increase catalytic activity. Since they are all for different sites that are mutated, they can be done in combination, depending on what you are looking for. It will also be very important for expanding the look into other substrates and enzymes.
This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
↑Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:https://dx.doi.org/10.1002/ijch.201300024
↑Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
↑Tournier V, Topham CM, Gilles A, David B, Folgoas C, Moya-Leclair E, Kamionka E, Desrousseaux ML, Texier H, Gavalda S, Cot M, Guemard E, Dalibey M, Nomme J, Cioci G, Barbe S, Chateau M, Andre I, Duquesne S, Marty A. An engineered PET depolymerase to break down and recycle plastic bottles. Nature. 2020 Apr;580(7802):216-219. doi: 10.1038/s41586-020-2149-4. Epub 2020 Apr, 8. PMID:32269349 doi:https://dx.doi.org/10.1038/s41586-020-2149-4
