Sandbox 323: Difference between revisions

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There have been previous studies conducted on the 3DS8 protein concluding that it is an alpha-beta hydrolase and originates from the Lin2722 gene in ''Listeria innocua'', a species of Gram-positive bacteria. Studies included database searches and the measurement of enzymatic activity by UV-Vis colorimetric assays using p-nitrophenyl analogs to form p-nitrophenol.[1]
There have been previous studies conducted on the 3DS8 protein concluding that it is an alpha-beta hydrolase and originates from the Lin2722 gene in ''Listeria innocua'', a species of Gram-positive bacteria. Studies included database searches and the measurement of enzymatic activity by UV-Vis colorimetric assays using p-nitrophenyl analogs to form p-nitrophenol.[1]
The αβ-hydrolases found in plants have many functions, including ligand receptors and catalytic activity. They are also adaptable and malleable regarding the fold of the protein secondary structure, which makes them an ideal target for research. [2]


</StructureSection>
</StructureSection>


== Experimental and Results ==
== Experimental and Results ==
The beginning experiments were conducted on molecular docking sites to compare the structure of the 3DS8 active site with known proteins. Using the SPRITE database [2], the 3DS8 protein was matched with a few proteases through right-handed superpositions with RMSD values ranging from 1.20-1.40, indicating relative similarities.
The beginning experiments were conducted on molecular docking sites to compare the structure of the 3DS8 active site with known proteins. Using the SPRITE database [3], the 3DS8 protein was matched with a few proteases through right-handed superpositions with RMSD values ranging from 1.20-1.40, indicating relative similarities.
The left-handed superpositions matched with more trypsins and displayed better RMSD values ranging from 0.93-1.11.
The left-handed superpositions matched with more trypsins and displayed better RMSD values ranging from 0.93-1.11.


The 3DS8 protein did not have many very specific active site matches with known proteins on the Chimera software [3], however, it was very similar to trypsin,
The 3DS8 protein did not have many very specific active site matches with known proteins on the Chimera software [4], however, it was very similar to trypsin,
alpha-chymotrypsin, and proteinase B. The function of 3DS8 is most likely very similar to those since the active sites have the same amino acids and structures that differ within <4 angstroms.
alpha-chymotrypsin, and proteinase B. The function of 3DS8 is most likely very similar to those since the active sites have the same amino acids and structures that differ within <4 angstroms.




The Dali database [4] was used to determine the conserved sequences within the 3DS8 protein. The majority of the hits were lipases with Z-scores up to 31.8, meaning the proteins are homologous
The Dali database [5] was used to determine the conserved sequences within the 3DS8 protein. The majority of the hits were lipases with Z-scores up to 31.8, meaning the proteins are homologous
to the 3ds8 structure because they are higher than 20. Some hits had high LALI numbers that indicate matching residues in the structure. The active site residues are G104, S102, H222, D188. Each of
to the 3ds8 structure because they are higher than 20. Some hits had high LALI numbers that indicate matching residues in the structure. The active site residues are G104, S102, H222, D188. Each of
these is conserved in the 4 selected protein matches, which means that the active site is conserved. The 3ds8 active site is conserved in many other proteins with similar functions, many of which
these is conserved in the 4 selected protein matches, which means that the active site is conserved. The 3ds8 active site is conserved in many other proteins with similar functions, many of which
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The BLAST database [5] was utilized to search for similar gene sequences and corresponding residue patterns. Using the FASTA sequence, the 3DS8 sequence is matched with similar proteins in an
The BLAST database [6] was utilized to search for similar gene sequences and corresponding residue patterns. Using the FASTA sequence, the 3DS8 sequence is matched with similar proteins in an
alignment that shows similar positions of matching residues. The superfamily of 3DS8 is an αβ-hydrolase. Function and cellular position are unknown, but it is hydrolase-like and exists in bacteria.
alignment that shows similar positions of matching residues. The superfamily of 3DS8 is an αβ-hydrolase. Function and cellular position are unknown, but it is hydrolase-like and exists in bacteria.
The 3DS8 protein is part of the superfamily of alpha-beta hydrolases, so it most likely has the same function. Many structural and sequential similarities are conserved between 3DS8
The 3DS8 protein is part of the superfamily of alpha-beta hydrolases, so it most likely has the same function. Many structural and sequential similarities are conserved between 3DS8
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InterPro Scan [6] searched for structure and taxonomy relations. The results have information about the domains and families of the protein. At the bottom, there are biological processes,
InterPro Scan [7] searched for structure and taxonomy relations. The results have information about the domains and families of the protein. At the bottom, there are biological processes,
molecular functions, and cellular components to learn more about the protein and where it originates from. InterPro confirmed that 3DS8 is most likely a hydrolase. Since 3DS8 is part of
molecular functions, and cellular components to learn more about the protein and where it originates from. InterPro confirmed that 3DS8 is most likely a hydrolase. Since 3DS8 is part of
the hydrolase superfamily, its structure and function are likely to be that of some sort of hydrolase.  
the hydrolase superfamily, its structure and function are likely to be that of some sort of hydrolase.  
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Listeria innocua using Computational and In-Vitro Techniques. https://www.cell.com/biophysj/pdf/S0006-3495(18)31671-0.pdf
Listeria innocua using Computational and In-Vitro Techniques. https://www.cell.com/biophysj/pdf/S0006-3495(18)31671-0.pdf


2. http://211.25.251.163/sprite/
2. Mindrebo, J. T.; Nartey, C. M.; Seto, Y.; Burkart, M. D.; Noel, J. P. Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Science Direct. 2016, 41, 233-246. DOI: 10.1016/j.sbi.2016.08.005.
 
3. http://211.25.251.163/sprite/


3. https://www.cgl.ucsf.edu/chimera/download.html
4. https://www.cgl.ucsf.edu/chimera/download.html


4. http://ekhidna2.biocenter.helsinki.fi/dali/
5. http://ekhidna2.biocenter.helsinki.fi/dali/


5. https://blast.ncbi.nlm.nih.gov/Blast.cgi
6. https://blast.ncbi.nlm.nih.gov/Blast.cgi


6. https://www.ebi.ac.uk/interpro/
7. https://www.ebi.ac.uk/interpro/
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