hcs research 2009 in bioinformatics

Mentor: Dr. Yuying Gosser

Briani George

Class of 2009

According to NCBI: “Bioinformatics is the field of science

in which biology, computer science, and information technology merge to form a single discipline.”

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 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.

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-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

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.

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.

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

Lin Wang, Sankar Surendran, Kimberlee Michals-Matalon, Gita Bhatia, Susan Tanskley, Richard Koch, James Grady, Stephen K. Tyring, Raymond C. Stevens, Flemming Guttler, 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>

DR. Sat Battcharaya

HCS & Staff

Dr. Yuying Gosser

Mc Cuallay Honors Program @ CCNY