BASIL2022GV3HDT

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Revision as of 01:33, 20 April 2022

Characterizing Putative Kinase 3HDT

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue. This protein (3HDT) is a putative kinase with possibly cytidylate kinase function utilizing ATP and dCMP as ligands.

1 Introduction
2 Online Resources (bioinformatic software)
- 2.1 BLASTp
- 2.2 Pfam
- 2.3 DALI
- 2.4 PANZ
3 Docking
4 Laboratory Experiments
- 4.1 Coupled kinase assay
- 4.2 SDS-PAGE
5 Conclusion/Future Experiments

Introduction

Online Resources (bioinformatic software)

We used a variety of in silico databases with our protein, 3HDT to find similarities with other amino acid sequences, protein family matches, and structural comparisons to known proteins in the PDB. Below are the recorded results and information from each database. From this information, a hypothesized function was created for 3HDT and potential substrates were selected such as dCMP.

BLASTp

Pfam

DALI

PANZ

Docking

Laboratory Experiments

Coupled kinase assay

SDS-PAGE

SDS-PAGE results for the purified protein 3HDT. The total weight of this protein is around 25.79 kD. The first lane (left) contains a size standard. The band in the second lane (right) at ~70kD is not the protein of interest (3HDT) but contains a binding metal protein. There is also a faint band around ~26kD, indicating our protein of interest was present.

Results from running an SDS-PAGE with the purified 3HDT

Conclusion/Future Experiments

Our protein was confirmed to be 3HDT using SDS-PAGE and showed activity during coupled kinase assays. While this confirms that 3HDT is a kinase, the true substrate, however, was likely not dCMP. Further research should be done with molecules such as TMP and GMP in the future to narrow down potential nucleotide substrates or elucidate other types of compounds to be considered as ligands for 3HDT.

References

↑ 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:http://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

Proteopedia Page Contributors and Editors (what is this?)

Jesse D. Rothfus, Autumn Forrester, Bonnie Hall, Jaime Prilusky

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 == Conclusion/Future Experiments ==
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">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.
+Our protein was confirmed to be 3HDT using SDS-PAGE and showed activity during coupled kinase assays. While this confirms that 3HDT is a kinase, the true substrate, however, was likely not dCMP. Further research should be done with molecules such as TMP and GMP in the future to narrow down potential nucleotide substrates or elucidate other types of compounds to be considered as ligands for 3HDT.
 </StructureSection>
 == References ==
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