Sandbox GGC5: Difference between revisions

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==FABP3 with myristic acid==
=='''Beta Lactamase'''==
<StructureSection load='78/781193/Overall/1'</scene>
<StructureSection load='3ZWF' size='340' side='right' caption='tRNAse Z Metallo-Beta Lactamase (homosapien)' scene=''>
Heart-type Fatty acid-binding proteins (H-FABP/FABP3) are cytoplasmic carrier protein that active fatty acid metabolism in the heart; found in cardiomyocytes.


== Function ==
Beta Lactamase is a highly conserved enzyme in both prokaryotes and eukaryotes. In prokaryotes, it gives bacteria such as ''E.coli'' antibiotic resistance. In eukaryotes, it acts as exo and endonucleases to regulate transcription activity.
Heart-type fatty acid binding protein (H-FABP) found in heart and skeletal muscle tissue. FABP3 involved in fatty acid metabolism by myristic acid.
Myristic acid is long saturated fatty acid chain that found in plant and animal, especially in milk fat. It produced during human metabolism and binds with FAPB3.<br />
Hexaethylene glycol used in crystallized FABP3 with myristic acid.


== Disease ==
=='''Background Information'''==
Pulmonary Embolism is lung disease that occurs when blood clots block the one of the pulmonary arteries. It blocks blood and oxygen flow and can causes pulmonary infarction when it gets severe. <br />
There are several classes of antibiotics, including cephalosporin and penicillin <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. Some common examples of specific drugs in these classes include cefazolin, cefadroxil, penicillin, ampicillin, and methicillin <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. These antibiotics function by preventing bacteria from forming their cell wall, regardless if the bacteria are gram positive or gram negative <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. These antibiotics all contain a beta-lactam ring <ref>https://doi.org/10.1021/cr030102i</ref>.
Acute Myocardial Infarction is heart attack that due to cholesterol, saturated fat, and trans-fat build plaque and block the arteries which causes cardio tissue damage.
Inside of the gram positive or gram negative bacteria, there is a protein called the penicillin binding protein. The penicillin binding proteins (PBPs) are what help the peptidoglycan walls to form by linking NAG and NAM chains together. The beta-lactam ring fits particularly well into the PBP, which is how antibiotics like penicillin prevent bacteria from synthesizing its cell wall.
 
[[Image:beta lactam ring in antibiotics.png]]
Beta Lactam Ring present in Antibiotics
 
[[Image:Penicillin inhibition.svg]]
Penicillin inhibition
 
=='''Mechanism of Antibiotic Beta Lactam Ring Resistance'''==
Bacteria such as ''E. coli'' make and excrete an enzyme called beta lactamase <ref>DOI: 10.1080/10409230701279118</ref>. Bacteria can become resistant to antibiotics that contain lactam rings when the B-lactamase enzyme attacks the beta lactam ring (classified as a hydrolase). Once the beta lactam ring is sliced open, it is no longer functional <ref> DOI 10.2210/pdb3ZWF/pdb </ref>.
=='''Beta Lactamase in Humans (PDB: 3ZWF)'''==
 
In order to make mature tRNAs, first they have to be processed <ref>https://doi.org/10.1101/575373</ref>. The enzyme that does tRNA processing is called TRNase Z. In humans, the form of beta lactamase formed uses a zinc-dependent mechanism, noted as metallo-beta lactamase <ref>DOI: 10.1080/10409230701279118</ref>. These enzymes in humans function to regulate nuclear activity, providing exo and endonuclease activity.
 
=='''Structural highlights'''==
 
Macromolecules:
Two chains (A,B) of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
 
''Unique Ligands''
 
 
- Phosphate (PO4) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
 
<scene name='78/781193/Po4/1'>PO4 Ligand</scene>
 
- Zinc (Zn) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
 
 
<scene name='78/781193/2_zincs/1'>Zinc ions are adjacent to the phosphate to balance the charge</scene>
 
- 2007 hydrophobic amino acid residues <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
<scene name='78/781193/Hydrophobic_amino_acids/1'>hydrophobic amino acid properties </scene>
 
- 1878 polar amino acid residues <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
<scene name='78/781193/Polar_amino_acids/1'>polar amino acids</scene>
 
- Sodium (Na+) ion on chain B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.  
<scene name='78/781193/Sodium_ion_enlarged/1'>Sodium Ion present</scene>


== Structure ==
<scene name='78/781193/Overall/1'>4 amino acids</scene> <br />
<scene name='78/781193/Myr_hydrogen_bonds/2'>Myristic acid</scene> <br />
<scene name='78/781193/P6g_with_lys_and_ser/2'>Hexaethylene glycol</scene>


</StructureSection>
</StructureSection>


=='''Disease'''==
If there are mutations in the tRNase Z metallo-beta lactamases, these enzymes have been implicated in several diseases including prostate cancer <ref>DOI: 10.1080/10409230701279118</ref>. While there is still much to learn about how these lactamases work inter-connectedly with other enzymes, research suggests that metallo-beta lactamases function as cleavage and polyadenylation factors <ref>https://doi.org/10.1101/575373</ref>.
== '''Evolutionary Considerations''' ==
Beta Lactamase protein structure is highly conserved across both prokaryotes and eukaryotes <ref>doi: https://doi.org/10.1101/819797</ref>. Their presence indicates that these proteins are highly adaptable, with a wide range of substrates <ref>https://doi.org/10.1101/575373</ref>. The highly conserved nature of this structure suggests that the genetic material for beta lactamase is ancient in origin <ref>https://doi.org/10.1101/575373</ref>. They have found early beta lactamases in deep sea sediment, before the first antibiotic was ever encountered.
== '''References''' ==
<references/>


== References ==
[1]
<references/Matsuoka, Shigeru, et al. “Water-Mediated Recognition of Simple Alkyl Chains by Heart-Type Fatty-Acid-Binding Protein.” Angewandte Chemie International Edition, vol. 54, no. 5, 2014, pp. 1508–1511., doi:10.1002/anie.201409830.>
[2]
<references/Myristic acid and Lauric acid. https://www.acs.org/content/acs/en/molecule-of-the-week/archive/m/myristic-acid.html (accessed Nov 6, 2019).>
[3]
<references/National Center for Biotechnology Information. PubChem Database. Myristic acid, CID=11005, https://pubchem.ncbi.nlm.nih.gov/compound/Myristic-acid (accessed on Nov. 6, 2019)>
[4]
<references/Mechanic, O. J. (2019, August 15). Acute Myocardial Infarction. Retrieved from
[5]
https://www.ncbi.nlm.nih.gov/books/NBK459269/.>
[6]
<references/Pulmonary embolism. (2018, March 7). Retrieved from https://www.mayoclinic.org/diseases
[7]
conditions/pulmonary-embolism/symptoms-causes/syc-20354647.>
[8]
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