PDB in a Cave: Virtual Reality Environment Highlights PDB Structures

To offer a new way of looking at molecular structure, the RCSB PDB and CalIT2 have released the first version of CAVE (Cave Automatic Virtual Environment) software for visualizing 3D macromolecular structures in an immersive, virtual reality environment. The CAVE offers a room-sized space for users to interact with high-resolution video. Wearing stereoglasses, the viewer can move through and around a structure that is projected in the CAVE.

The new software has an interface that makes a connection to the RCSB PDB web site to download and display files. In addition, the software also supports visualization of structure motions by supporting multiple file loading. For example, users may visualize structure motions from the Database of Molecular Movements. The software, built on the COVISE platform, runs in the CAVE in both single user and collaborative modes.

With over 100 CAVEs around the world, users may now download and visualize any PDB structure while in this unique environment.

Protein Modeling at the NJ Science Olympiad

Several high school teams competed in the protein modeling trial event at the New Jersey Northern Regional and State Science Olympiads.

The first place team Stacy Chu and Reza Parungao from Montville Township and their model of de novo protein 1psv at the Northern NJ Science Olympiad that was held January 12, 2006 at Montclair State University.

At the start of the Olympiad, the student teams submitted a previously prepared model and written description of the TATA-Binding Protein created using resources available from the RCSB PDB. Then, each team built a model at the competition and answered written questions about the structure, function, importance, and history of the protein. In a hushed room, the teams used the Molecule of the Month feature on Designer Proteins, the PDB coordinate file, and the structure's primary citation to complete the challenge at the regional competition. At the state final, the teams built cholera toxins.

The three-dimensional protein models are built using Mini-Toober¹ kits provided by the RCSB PDB.

State Champions Greg Kacprzynski and Justin Leung of East Brunswick High School and their model of cholera toxin 1xtc.

The students all submitted great structures, with awards going to Montville Township High School (First Place), Freehold High School (Second Place), and Alghazly High School (Third Place) at the regional level. In an extremely close competition at the state competition, East Brunswick High School (First Place), The Lawrenceville School (Second Place), and Montgomery High School (Third Place) created very strong models.

Special thanks to our judges from the RCSB PDB (Kyle Burkhardt, Cathy Lawson, Jeramia Ory, Irina Persikova, Massy Rajabzadeh, Monica Sundd, and Jasmine Young), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event. Questions about the NJ Science Olympiad Protein Modeling trial event should be sent to buildmodels@rcsb.rutgers.edu. Information is also available at http://education.pdb.org/olympiad/.

1. Mini-Toobers are products of 3D Molecular Designs www.3dmoleculardesigns.com

Jasmine Young compares the Mini-Toober cholera toxin with a prebuilt model. The models built at the competition had to be quickly judged before the awards ceremony.

The models were judged by annotators from the RCSB PDB. Here, Jeramia Ory scores one of the TATA-binding protein models.

Meetings and Exhibits

• Biophysical Society Annual Meeting
  
  Wolfgang Bluhm and Jeramia Ory met with users and provided demonstrations of the new site at the RCSB PDB's exhibit booth at the 50th Annual Meeting of the Biophysical Society (February 18-22, 2005 in Salt Lake City, Utah).
  
  
• Experimental Biology
  
  Demonstrations were also available at the American Society for Biochemistry and Molecular Biology's (ASBMB) Annual Meeting (April 1-5, San Francisco, CA), which was held in conjunction with the Experimental Biology conference (EB). In addition to exhibiting, Shuchismita Dutta presented "Educational Resources for Structural Biology at the RCSB Protein Data Bank" as a talk and poster.
  
  EB is sponsored by the American Association of Anatomists (AAA), American Physiological Society (APS), ASBMB, American Society for Investigative Pathology (ASIP), American Society for Nutrition, Inc. (ASN), and American Society for Pharmacology and Experimental Therapeutics (ASPET).
  
  
• Virginia Tech Structural Biology Symposium
  
  Images from the RCSB PDB's "Art of Science" exhibit were on display at Virginia Polytechnic Institute and State University as part of their Structural Biology Symposium (March 31 - April 1, Blacksburg, VA). Attendees also explored protein structures in the "PDB-in-a-CAVE" environment.
  
  The Art of Science traveling exhibit displays images of molecules in the PDB, including the pictures available from individual structure pages and from Molecule of the Month features. Since its beginnings at a space dedicated to art exhibits at Rutgers University, the show has traveled to EMBL-Hamburg, Germany; University of Wisconsin- Madison; California State University, Fullerton; Purdue University; and Hyderabad, India. The RCSB PDB would like to see the "Art of Science" travel to other places. If you would be interested in sponsoring this exhibit at your institution, please let us know at info@rcsb.org.

RCSB PDB Focus: Frequently Asked Questions

The Frequently Asked Questions page answers a number of common queries about the new RCSB PDB site, including How do I link to a Structure Summary page for a PDB ID? and What are the URLs to download files?

Questions related to searching, reporting, and using all of the resources available from the RCSB PDB not found on this page should be sent to info@rcsb.org.

For deposition-related queries, please see the Deposition FAQ or contact us at deposit@deposit.pdb.org.

Molecules of the Quarter

The Molecule of the Month series explores the functions and significance of selected biological macromolecules for a general audience.

The molecules featured this quarter were Topoisomerases, Alpha-amylase and Tissue Factor.

The complete Molecule of the Month features are accessible from the RCSB PDB home page.

• January: Topoisomerases.

  Each of your cells contains about 2 meters of DNA, all folded into the tiny space inside the nucleus, which is a million times smaller. As you might imagine, these long, thin strands can get tangled very easily in the busy environment of the nucleus. To make things even more complicated, DNA is a double helix, which must be unwound to access the genetic information. If you have ever tried to unravel the individual fibers in a piece of rope, you will understand the knotty problems that this can cause. To help with these problems, your cells build several different topoisomerase enzymes that untangle and relax DNA strands.

  
  PDB ID 1a36: Stewart, L., Redinbo, M.R., Qiu, X., Hol, W.G., Champoux, J.J. A model for the mechanism of human topoisomerase I. Science v279 pp.1534-1541 (1998)

• February: Alpha-amylase

  Glucose is a major source of energy in your body, but unfortunately, free glucose is relatively rare in our typical diet. Instead, glucose is locked up in many larger forms, including lactose and sucrose, where two small sugars are connected together, and long chains of glucose like starches and glycogen. One of the major jobs of digestion is to break these chains into their individual glucose units, which are then delivered by the blood to hungry cells throughout your body.

  

   

  PDB ID 1ppi: Qian, M., Haser, R., Buisson, G., Duee, E., Payan, F. The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution. Biochemistry v33 pp.6284-6294 (1994)

• March: Tissue Factor

  Blood performs many essential jobs in your body: it transports oxygen and nutrients, it protects your cells from infection, and it carries hormones and other messages from place to place in your body. But since blood is a liquid that is pumped under pressure, we must protect ourselves from leaks. Fortunately, the blood has a built-in repair method that quickly stops up breaks in the blood circulatory system as soon as they happen. You see these repairs in action whenever you cut yourself: the blood thickens and forms a gooey clot, which then dries into a scab that seals and protects the cut until it can heal.

  

   

  PDB ID 2hft: Muller, Y.A., Ultsch, M.H., de Vos, A.M. The crystal structure of the extracellular domain of human tissue factor refined to 1.7 A resolution. J.Mol.Biol. v256 pp.144-159 (1996)