The Seeds of Knowledge Come to Bloom

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Anyone notice the sparkly new building on the corner of University and Main? How about the hyperbolic sail at Bertner and Bates? Maybe the twisty spire on Moursund and Bertner? I know not everyone goes to the Texas Medical Center everyday, but as a Houstonian you should be proud of these new buildings and what’s going on in them. They are the cutting age research centers that will push the TMC further into the spotlight with this country’s other great leaders of Medical Research.
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Bioscience Research Collaborative Center (University Blvd and Main). The BRC is a 477,000 gross sq. ft. building that houses a collaborative effort with Rice scientists and others in the Medical Center to drive beneficial research for human medicine and health. The current scientists are from such areas as Bioinformatics, Bioengineering, Biochemistry, Cell Biology, and Chemistry. The BRC also houses scientists from the Gulf Coast Consortia and the Cancer Prevention and Research Institute of Texas (CPRIT). CPRIT recently endowed BRC researcher John McDevitt with $3.7 million dollars to expand his research on Bio-Nano-Chip diagnostics (I call it Spit-on-a-Chip!) research. Here is a link for a Virtual Tour of the BRCC.

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The Methodist Hospital Research Institute (near Bertner and Bates). Relative newcomers in the TMC research game, TMHRI is by no means lagging behind. Due for occupancy in late 2010, this 500,000 sq. ft. building will house some of the nations leaders in clinical and laboratory research. The main focus at TMHRI is what’s called Translational Research, where research results from the lab bench translate directly the bedside. TMHRI’s Dr. Stephen Wong recently received a $5 million dollar donation to study neurodegenerative diseases as well as Dr. Baxter’s NEJM publication of a new cholesterol lowering drug passing FDA Phase II trials.
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Perhaps the coolest looking new building is Texas Children’s Jan and Dan Duncan Neurological Research Institute with it’s unique DNA-esque tower. The JDNRI is also scheduled to open in 2010. This 344,000 sq. ft., 13-floor facility is Directed by Dr. Huda Zoghbi with a focus on using “a multidisciplinary research approach to understand the unique issues of a child’s brain structure, development patterns and related diseases.” Here is a great video explaining the many groundbreaking research areas the JDNRI will be pursuing.

Putting It All Together

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Tertiary Structure
Like any parent knows from a long car trip, the order of the family members in the car dictates their behavior during the trip. Similarly, the order of amino acids in the chain of a protein dictates how the entire protein behaves. For example, since our bodies are mostly water, the water loving (hydrophilic) amino acids naturally swim happily on the outside of the protein while the water shy (hydrophobic) amino acids cower mostly in the center. The interactions of the side chains of the helices and strands with each other give the overall 3-D shape (also called the fold) of the protein. The tertiary form of the protein seen in the figure below has many alpha helices (red) and a few beta strands (yellow), with the amino acid side chains shown. The yellow strands and orange helix are the same ones shown in previous entries.

 

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This movie(sorry for the crappy resolution!) shows a 360 degree rotation of the protein model without the amino acid side chains.

This model is of a protein I work with call PPAR gamma (pronounced Pee-Par gamma) and one of its main functions is the metabolic regulation of fat. Some of you with type 2 diabetes may have taken a drug such as Avandia (hopefully not anymore!), or Actos, both which bind to PPAR gamma. In later entries I’ll explain how that works!

If you are interested in seeing the many types of shapes and sizes proteins come in, try this site!

Stranded

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It was recently brought to my attention that I never finished my Protein Structure 101 entry. Sorry I left you stranded…here is the next to the last entry:
In contrast to the curly fry looking helix, protein strands look more like, well, strands. The strand also forms by making hydrogen bonds, but does so in a linear fashion. On the far top left in the figure below, you can see the peptide backbone with the O’s in red and the NH’s in blue and with the lines connecting those representing hydrogen bonds. The picture on the top right shows the same peptide backbone but with the side chains shown. On the bottom right is the arrow cartoon of the strand with the side chains, and on the bottom left without. A group of strands is called a sheet.
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Here’s a different view of the same strand with the side chains shown. See the strand’s flat appearance compared to the helix on the left?

In the next and final structure entry, I’ll show how all these elements come together to form a protein. Then I’ll begin to describe what they do…