BASIL2023GV1ZBS

2023-04-19T17:52:46Z

Danielle Selover:

BASIL2023GV1ZBS

2023-04-19T17:51:58Z

Danielle Selover:

File:1ZBS CHART.png

2023-04-19T17:51:02Z

Danielle Selover:

BASIL2023GV1ZBS

2023-04-19T17:46:54Z

Danielle Selover:

File:1ZBS Concentration.png

2023-04-19T17:45:54Z

2023-04-11T19:16:55Z

Danielle Selover: Two Chains of 2CH5 shown here, so that reader can visualize the protein that 1ZBS is similar to.

<scene name='95/957643/2ch5/1'>Text To Be Displayed</scene>=='''''Inquiry of the Possible Function of Protein 1ZBS'''''==
==''' Abstract'''==
ZBS is a novel protein whose structure is solved but the function is unknown. This research was designed to attempt to uncover the function. Computational research indicated that N-acetylglucosamine (NAG) may be the potential substrate, and that the protein may phosphorylate NAG. This was determined using multiple computational tools, such as BLAST-P, DALI, SPRITE, InterPro. Molecular docking using NAG as a substrate was done with PyMol and Vina docking. After the computational research was completed, the protein was over-expressed and purified. The protein was used to test for activity with the substrate NAG. The kinase assay concluded that NAG is most likely not the substrate for 1ZBS due to a lack of specific activity.
== '''Introduction''' ==
<StructureSection load='1zbs' size='340' side='right' caption='1ZBS dimer as in its original state' scene=''>
1ZBS is a protein with unknown function discovered through a genomics project of predictive folding. The goal of this project was to determine what the function of protein 1ZBS was using a combination of computational analysis and physical lab work.
[[Image: FlowChart.png ]]
For this project, we started by doing our computational work, which includes BLAST, DALI, SPRITE, Net-GO, and the Docking analysis, while we started transforming our bacteria, and over-expressing and purifying our protein for the kinase assays. From the computational analysis, it was believed that 1ZBS could be a NAGK protein. Further analysis into the kinase activity did not fully support this conclusion, as the specific activity was too low.
== '''Sequence Alignments''' ==

=== BLAST-P ===

The first type of analysis that was done was using Protein Blast from NCBI. The analysis was first done as it only gave very broad information about the potential function of the protein, by matching domains across other proteins with known functions.
[[Image:BLASTP.png]]
These results for 1ZBS showed that it was a match to the superfamily BADF. BADF is the superfamily that NAGK proteins also belong in so this was one of the reasons that we believed that 1ZBS may potentially be a NAGK protein.
== '''Structural Alignments''' ==
=== DALI ===
DALI is a global alignment software that is used to match proteins up to possible structural matches within the Protein Data Bank (PDB).

[[Image:DALI_alignment.png]]

This is the DALI alignment of 1ZBS and 2CH5, where 1ZBS is colored in green and <scene name='95/957643/2ch5/1'>2CH5</scene> is colored in yellow. The best results from the DALI alignment were mainly proteins with unknown functions, which makes it difficult to deduce a possible function off of. Because of these results, 2CH5, while only matching parts of the sequence was the best result for this analysis as it's function is known. The function of 2CH5 is a NAG kinase, which would further support the thought that 1ZBS could also be a NAG kinase.
==''' Substrate Possibilities '''==

== '''Kinase Assays''' ==

== '''Conclusion''' ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene></scene> by Group, and another to make <scene name='95/957643/1zbs_view_2/1'> a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

BASIL2023GV1ZBS

2023-04-11T19:03:04Z

Danielle Selover:

BASIL2023GV1ZBS

2023-04-11T19:01:45Z

Danielle Selover:

BASIL2023GV1ZBS

2023-04-11T19:01:08Z

Danielle Selover:

BASIL2023GV1ZBS

2023-04-11T18:49:49Z

Danielle Selover:

=='''''Inquiry of the Possible Function of Protein 1ZBS'''''==

== '''Introduction''' ==
<StructureSection load='1zbs' size='340' side='right' caption='1ZBS dimer as in its original state' scene=''>
1ZBS is a protein with unknown function discovered through a genomics project of predictive folding. The goal of this project was to determine what the function of protein 1ZBS was using a combination of computational analysis and physical lab work.
[[Image: FlowChart.png ]]
For this project, we started by doing our computational work, which includes BLAST, DALI, SPRITE, Net-GO, and the Docking analysis, while we started transforming our bacteria, and over-expressing and purifying our protein for the kinase assays.
== '''Sequence Alignments''' ==

=== BLAST-P ===

The first type of analysis that was done was using Protein Blast from NCBI. The analysis was first done as it only gave very broad information about the potential function of the protein, by matching domains across other proteins with known functions.
[[Image:BLASTP.png]]
== '''Structural Alignments''' ==
This is our DALI alignment of 1ZBS and 2CH5. [[Image:DALI_alignment.png]]
==''' Substrate Possibilities '''==

== '''Kinase Assays''' ==

== '''Conclusion''' ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene></scene> by Group, and another to make <scene name='95/957643/1zbs_view_2/1'> a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

2021-04-19T03:40:19Z

Danielle Selover:

{{Sandbox_Reserved_BHall_Sp21}}
==CTX-M Beta-Lactamase==
CTX-M Beta Lactamase is a class A enzyme that creates drug resistance to ampicillin and cefotaxime through a two step process of deacylation and acylation.
== Function of your protein ==
<StructureSection load='7K2X' size='340' side='right' caption='Overall structure of CTX-M Beta-Lactamase without any important ligands. (PDB: 7K2X)' scene=''>
CTX-M Beta-Lactamase is an enzyme made to inhibit Beta-Lactam. It is found within bacteria, specifically the ''E. coli'' bacteria. Beta- Lactamase binds with <scene name='87/873236/Ampicillin/2'>ampicillin</scene> and <scene name='87/873236/Cefotaxime/3'>cefotaxime</scene>, both of which are types of drugs made to fight bacterial infections. Beta-Lactamase specifically attacks the lactam ring within both of these structures using a deacylation.
== Biological relevance and broader implications ==
This enzyme inhibits the drug's function by breaking apart the lactam ring. This is does cause drug resistance within the ''E. coli'' bacteria making it much harder to treat via drug therapies.
== Important amino acids==
The important amino acids within the CTX-M Beta Lactamase are Ser70, Ser130, Lys234, Arg234, and Lys73. This creates the catalytic <scene name='87/873236/Active_site_red/1'>triad</scene> with one proton shuttle. The residue at 234 does undergo a mutation in some cases and therefore can be either a Lys, or an Arg. The catalytic triad are the residues at 70, 130, and 234. The S130 helps to cleave the amide bond and distributes a proton to the nitrogen. S70 attacks the carbonyl carbon on the lactam ring before also protonating to create an alcohol and it breaks off again. K73 does work as a proton shuttle for both parts of the reaction.
== Structural highlights ==
This protein has eight chains. Each <scene name='87/873236/Secondary_structure/1'>chain</scene> has eleven separate alpha helixes, and nine separate beta sheets. Some of the chains do bind to a GOL to help with stability. Within each chain, there are two of the catalytic amino acids within helix three. The last catalytic amino acid is located in helix seven. Both of those helices form important interactions with the ligands because of those catalytic amino acids.
The important<scene name='87/873236/Amino_acid_tert/1'> tertiary structure</scene> is how the protein folds to allow the amino acids in the catalytic triad to be near each other because in the sequence, the amino acids are not near each other. By folding, the protein is able to create the binding pocket that holds the catalytic amino acids that help Beta- Lactamase function normally.
In the <scene name='87/873236/Space_fill/1'>space fill</scene> view of the enzyme, you can see the small binding pocket that is created to hold the substrate better.
== Other important features ==
As previously mentioned, this enzyme does also utilize a <scene name='87/873236/Lysine_73/2'>lysine</scene> at residue 73. This is to help shuttle protons through the reaction. S170 uses it in the first part of the reaction and Glu166 is activated by this as well, and completes the reaction, as well as recreates the S170, by donating more protons. This can allow the enzyme to work multiple times and retain it's function overtime which is not good in regards to drug resistance.
Another interesting feature is the K234 as it doesn't actually bond with the substrate like the S130, but instead works to lower the pKa of the S130, so that it is more likely to donate a proton.
</StructureSection>
== References ==
<ref>PMID:33109613</ref>
<references/>