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HCS Research 2009 in Bioinformatics. Mentor: Dr. Yuying Gosser Briani George Class of 2009. What is Bioinformatics?. According to NCBI: “ Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline.”.

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Hcs research 2009 in bioinformatics

HCS Research 2009 in Bioinformatics

Mentor: Dr. YuyingGosser

Briani George

Class of 2009


What is bioinformatics
What is Bioinformatics?

According to NCBI:

  • “Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline.”


Lets put these databases into use
Lets put these databases into use

  • While doing research on a protein called PAH or phenylalanine hydroxylase I was able to gather useful information on this protein using the PDB database and the NCBI database


Pdb database
PDB Database

  • PDB or Protein Data Bank archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.


What we can gain from pdb
What we can gain from PDB

  • Specifically for 1tg2:

  • Mutation-A313t

  • It is most commonly found in humans

  • It is located on chromosome 12

  • It was crystallized using a form of vapor diffusion called hanging drop

  • It has 308 residues

  • FASTA sequence


Ncbi database
NCBI Database

  • NCBI-National Center for Biotechnology Information- is a national resource for molecular biology information

  • NCBI itself has a few databases from which you can receive information for example pub med, entrez,, nucleotide databases ie. Gen Bank

  • Using the FASTA squence and BLAST you can see the similarity between proteins



Research paperCorrection of Kinetic and stability defects by tetrahydrobiopterin in phenylketonuria patients with certain phenylalineHydroxylase mutations

  • In this particular research paper scientist were testing the affects of tetrahydrobiopetrin (BH4) on this form of PAH in an attempt to regulate the L-Phe level.

  • They tested 15 mutants. The only mutant that crystallized was A313t.



In conclusion
In conclusion

  • The researchers found that “the molecular mechanisms for BH4 responsiveness potentially increase the amount of active enzyme in vivo as well as mutant PAH activity.

  • The BH4-responsive patients would therefore reach the lower-limit value of the L-Phe hydroxylation, allowing the catabolism of the L-Phe amounts present in normal diets.”

  • Using bioinformatics I was able to understand how using databases and knowledge of biology could aid in the investigation as to how certain proteins work and their comparison with other proteins.


Reference page
Reference page

  • Heidi Earlandsen, Angel L. Pey, Alejandra Gamez et al. "Correction of Kinetic and stability defects by tetrahydrobiopterin in phenylketonuria patients with certain phenylalinehydroxylase mutations." PNAS (2004): 16903-16908 <www.pnas.org/cgi/doi/10.1073/pnas.0407256101>

  • Lin Wang, SankarSurendran, KimberleeMichals-Matalon, Gita Bhatia, Susan Tanskley, Richard Koch, James Grady, Stephen K. Tyring, Raymond C. Stevens, FlemmingGuttler, Reuben Matalon. Genetic Testing. June 2007, 11(2): 174-178. doi:10.1089/gte.2006.0520 <http://www.liebertonline.com/doi/abs/10.1089/gte.2006.0520>

  • pdb.org <http://www.pdb.org/pdb/explore/explore.do?structureId=1tg2>

  • ncbi.gov <http://www.ncbi.nlm.nih.gov/protein/56966068>


Acknowledgements
Acknowledgements

  • DR. Sat Battcharaya

  • HCS & Staff

  • Dr. Yuying Gosser

  • Mc Cuallay Honors Program @ CCNY



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