RCSB PDB Newsletter
Number 26 --  Summer 2005

Published quarterly by the
Research Collaboratory for Structural Bioinformatics
Protein Data Bank

Weekly RCSB PDB news is available online at
www.rcsb.org/pdb/latest_news.html.

Links to RCSB PDB newsletters are available at
www.rcsb.org/pdb/newsletter.html.

To change your subscription options, please visit
lists.sdsc.edu/mailman/listinfo.cgi/rcsb-news.
-----------------------------------------
TABLE OF CONTENTS

Message from the RCSB PDB

Data Deposition and Processing
     PDB Focus: pdb_extract Makes Deposition Easier
     PDB Deposition Statistics

Data Query, Reporting, and Access
     RCSB Beta Site Features
     PDBML/XML Data Uniformity Files
     PDB Focus: Redundancy Reduction Cluster Data Available
     Website Statistics

Outreach and Education
     RCSB PDB Focus: Help Desks
     Meetings, Exhibits, and Workshops

PDB Community Focus: Robert M. Sweet, Brookhaven National Laboratory

Education Corner: Wisconsin High School Science Olympiad PROTEIN
     MODELING Event by Gary Graper, Event Supervisor

PDB Molecules of the Quarter: Kinesin, Self-splicing RNA, Carotenoid Oxygenase

RCSB PDB Job Listings
Statement of Support
RCSB PDB Leadership Team
Snapshot

--------------------------------------------
MESSAGE FROM THE RCSB PDB

In July 2004, the RCSB PDB released a reengineered website and
database (pdbbeta.rcsb.org) for public beta testing.  The underlying
database consists of curated mmCIF files resulting from the data
uniformity project, which allows for improved query access to the
unified data.

Thanks to feedback sent from users, this website is constantly being
refined and enhanced.  Some of the features of this site are described
in this newsletter, and in previous newsletters.

The beta RCSB PDB website, along with tools for deposition, will be
demonstrated at the wwPDB exhibit stand (Booth number 12) at this
year's XX Congress & General Assembly of the International Union of
Crystallography (IUCr; August 23 - 31 in Florence, Italy).  Our wwPDB
partners MSD-EBI and PDBj will also demonstrate their websites and we
will all be available throughout the exhibition to meet with PDB
users.  A roundtable discussion about data mining from the PDB will be
held on August 27 with presentations from Helen M. Berman, Kim
Henrick, Haruki Nakamura, and Philip E. Bourne.  Other wwPDB-related
activities at this meeting will be announced on the RCSB PDB website.  
We look forward to seeing you there.

The RCSB PDB

--------------------------------------------
DATA DEPOSITION AND PROCESSING

     PDB FOCUS: PDB_EXTRACT MAKES DEPOSITION EASIER

pdb_extract helps depositors automatically prepare crystal structure
depositions. This software tool extracts information about data
collection, phasing, density modification, and the final structure
refinement from the output files produced by many applications used
for structure determination. The collected information is organized
into an mmCIF file that is ready for deposition. Fewer data items have
to be manually entered -- saving time and minimizing errors.

pdb_extract can be downloaded in source and binary versions for Linux,
SGI, SUN, OSF and Mac OSX from sw-tools.pdb.org. Source and Linux
binary versions of ADIT are also available.

pdb_extract is also part of the CCP4i interface (www.ccp4.ac.uk).

     PDB DEPOSITION STATISTICS

In the first half of 2005, 3168 experimentally-determined structures
were deposited to the PDB archive.

The entries were processed by wwPDB team members at RCSB-Rutgers,
MSD-EBI, and PDBj. Of the structures deposited, 67% were deposited
with a release status of HPUB; 17% with HOLD; and 16% with REL.

78% of these entries were determined by X-ray crystallography; 19%
were determined by NMR. 80% were deposited with experimental data. 52%
released the sequence in advance of the structure's release.

--------------------------------------------
DATA QUERY, REPORTING, AND ACCESS

     RCSB PDB BETA SITE FEATURES

In July 2004, the RCSB PDB released a reengineered beta site
(pdbbeta.rcsb.org) for public testing. Some of the features of this
site are described below.

Comments and suggestions about the beta site are welcomed at
betafeedback@rcsb.org.

* Improved Searching and Visualization for Ligands

Beta site searches can use common ligand names or the identification
codes from the Chemical Component Dictionary (formerly called the HET
group dictionary). These queries will search ligand names, some
synonyms, and class specifications using the Chemical Component
Dictionary created by curation efforts of the RCSB PDB team.

Ligand name searching supports partial string matches. For example,
searching for 'benz' will return all structures that contain benzene
as well as those containing benzamidine. For an exact match, the 
complete name of the ligand must be entered. Ligand searches can also 
be performed using the three-character ligand ID in the PDB file (the
"HET" record). For example, searching for 'HEM' returns all structures
that have a heme ligand.

A recently added search feature is the ability to query for ligands
using a SMILES string representation or a 2D structure of the ligand
drawn using the MarvinSketch applet. SMILES (Simplified Molecular
Input Line Entry Specification) is a comprehensive yet simple
nomenclature system for chemicals. A SMILES string represents the
valence model of a molecule.

For example, [Fe+2] or [Fe++] is the SMILES string for iron(II)
cation; C1=CC=CC=C1 or c1ccccc1 is the SMILES string for benzene; and
Nc1ncnc2n(cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O is the
SMILES string for Adenosine-5'-triphosphate.

Exact, substructure, and similarity searches can be performed. An
exact search will retrieve PDB IDs associated with ligands whose
structures match the SMILES/2D structure exactly. A substructure
search will retrieve all PDB IDs associated with ligands that are
superstructures of the query. A similarity search returns PDB IDs
associated with ligands whose topology is similar to that of the
query.

Similarity searches are based on finding molecules similar to the
query based on a dissimilarity coefficient, whose value can be set to
range from 0 to 1. The default value is 0.3. The dissimilarity
coefficient is defined as 1- Tanimoto coefficient. The higher the
value, the greater the hits, since ligands that are only remotely
similar to the query are also returned. A lower threshold returns
fewer hits. It is more stringent in that it returns ligands that have
greater similarity to the query structure.

Both the SMILES string search and the 2D structure search list all the
ligands that match the query and the criteria. The matching ligands
can be viewed and further explored. A 2D ligand viewer can also be
launched from the Structure Explorer page for a single structure.

* Molecular Viewers

The beta site features three third-party molecular viewers for
interactively visualizing structures:

    * KiNG (Kinemage, Next Generation), written by Ian Davis
      (kinemage.biochem.duke.edu/software/king.php)
    * Jmol, an open source molecule viewer (jmol.sourceforge.net)
    * WebMol, written by Dirk Walther
      (www.cmpharm.ucsf.edu/~walther/webmol.html)

Links to all three viewers are found on each entry's Structure Explorer
page. The viewers require a Java-enabled browser, but not any
additional plug-ins or helper installations. However, some applets may
require the user to accept a security certificate upon first download
(click "Yes" or "Always").

All three viewers offer rich functionality for visualizing molecules,
with many options for selecting, rendering, and coloring portions of
or entire PDB structures.

KiNG, by default, presents a colored ribbon diagram of the
structure. The top menu contains many visualization options, along
with additional tools, and the ability to save and later reload the
currently displayed view. The right hand panel contains a list of
check boxes that determine which molecular entities in the structure
file are being displayed. This option extends to the models in NMR
structures, and is therefore particularly convenient for comparing
multiple NMR models in a single PDB file.

Jmol offers a large number of options for selecting portions of a
structure and rendering them in different ways (for example showing a
space filled representation of a ligand and a ribbon diagram of the
main protein chain). This can be accomplished by right clicking on the
applet, and by choosing "Select", "Render", and "Color" from the
cascading menu. Other convenient features include the ability to
continuously spin the structure, or to visualize the crystal axes or
unit cell boundaries.

WebMol presents a stick model of the molecule with several options for
coloring (e.g. by chain or by B-factor). Dotted molecular surfaces can
also be displayed. Distance matrix plots or Ramachandran plots can be
opened in a separate window, which is interactively linked to the
display of the molecule.

For further help, information about these viewers is provided --KiNG
and WebMol help are available from within the applets, Jmol help is
available at the Jmol home page).

     PDBML/XML DATA UNIFORMITY FILES

After an extended period of beta testing, the remediated PDB data
files from the data uniformity project are now available in PDBML/XML
format on the production FTP archive in the following directories:

    * ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/XML/
    * ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/XML-extatom/
    * ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/XML-notatom/ 

The files in the XML directory contain separate XML tags for each item
in the atom-site category. XML-extatom files contain the atom records
only, in an alternate format with only one pair of XML tags for each
atom. XML-noatoms files contain only the metadata for each structure
and no atom records. All files are gzipped (.gz compressed). In each
case, the data files are in the usual hash directories according to
the middle two characters of the PDB ID (e.g. the files for 100d are
in a hash directory 00).

More information on the PDB data uniformity project is available at
www.rcsb.org/pdb/uniformity. Comments are welcome at
info@rcsb.org.

     PDB FOCUS: REDUNDANCY REDUCTION CLUSTER DATA AVAILABLE ON THE PDB
     FTP SITE

The results of the weekly clustering of protein chains in the PDB are
posted at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/. These clusters
are used in the "remove similar sequences" feature on SearchLite and
SearchFields on the PDB web sites.

Files that list the clusters and their rankings at 50%, 70% and 90%
sequence identity are available. Smaller rank numbers indicate higher
(better) ranking. Chains with rank number 1 are the best
representative of their cluster.

The contents of these files and the details of the clustering and
ranking are further described at
ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/README and
www.rcsb.org/pdb/redundancy.html.

     WEBSITE STATISTICS

The PDB is available from several Web and FTP sites located around the
world. Users are also invited to preview new features at the RCSB PDB
beta test site, accessible at pdbbeta.rcsb.org.

Access statistics are given below for the primary RCSB PDB website
at www.pdb.org.

  Daily Average...Monthly Totals
Month...Hits......Files....Sites.....MBytes.......Files.......Hits
Jun 05..258126....188615...115846....223130124....5469838.....7485679
May 05..283870....204733...131339....281893387....6142012.....8516121
Apr 05..320485....234752...143047....356340329....6573056.....8973602

--------------------------------------------
OUTREACH AND EDUCATION

     RCSB PDB FOCUS: HELP DESKS FOR BETA SITE FEEDBACK, DEPOSITION
     INFORMATION, AND MORE

For answers to questions ranging from "how can I deposit my structure"
to "how can I create a report about the structures I've found" to
"what is DNA?", the RCSB PDB actively maintains several e-mail help
desks. Responses are rapidly returned.

* betafeedback@rcsb.org receives bugs and comments about the beta web
  site that is currently undergoing testing (pdbbeta.rcsb.org)

* deposit@rcsb.rutgers.edu answers questions about deposition and
  annotation. A FAQ regarding depositing, updating and releasing files
  is also available (rcsb-deposit.rutgers.edu/depoinfo/depofaq.html)

* info@rcsb.org responds to questions and comments relating to the
  navigation of the RCSB PDB. Questions about searches, reports, and
  using all of the resources available from the RCSB PDB should be
  sent to this address.

     ART OF SCIENCE EXHIBIT AT TEXAS A&M AND RUTGERS

The RCSB PDB's "Art of Science" exhibit was on tour this past spring.
It appeared at Texas A&M University's Visual Arts Gallery in the
Memorial Student Center (April 13 - May 15, 2005).  The show was also
part of the American Chemical Society Mid-Atlantic Regional Meeting
(MARM) held at Rutgers (May 22-25, 2005).

The Art of Science traveling exhibit looks at the beauty inherent in
protein structures.  It displays images of molecules in the PDB,
including the pictures available from Structure Explorer 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 many places, including 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 EDUCATIONAL RESOURCES POSTER

Resources for education available from the RCSB PDB are highlighted on
a poster that is available for download
(www.rcsb.org/pdb/education.html; 8 1/2 by 11 inches).

* The Molecule of the Month feature illustrates important biological
  molecules and how they function through descriptive text, pictures,
  and links to specific PDB entries and other resources.

* The RCSB PDB Newsletter regularly features interviews with members
of the community and descriptions of how the PDB is used in all levels
of education.  

* The Education Page provides resources for learning about Proteins
and Nucleic Acids, protein documentaries, and suggested reading
materials and links.  

* RCSB PDB tools for finding and visualizing proteins are used in the
classroom in a variety of ways, including downloading molecular
images, exploring the links to information found in journals, and
trying different keyword queries to locate specific proteins.

     RCSB MEETINGS:  ACA AND ISMB

Highlights from the Annual Meeting of the American Crystallographic
Association (ACA) held May 28 - June 2, 2005 in Orlando, FL included
exhibiting in "Data Alley", along with CCP4 and CCDC. RCSB PDB staff
were on hand to answer questions and provide demonstrations of
deposition software and the beta site. Annotator Kyle Burkhardt
presented a tutorial on using RCSB PDB validation software at
the "Workshop on Macromolecular Structure Validation."

The RCSB PDB also exhibited at the 13th Annual Meeting of the
International Society for Computational Biology ("Intelligent Systems
for Molecular Biology" June 25 - 29 in Detroit, Michigan).  Wolfgang
Bluhm presented "Structural Bioinformatics Education from the RCSB
Protein Data Bank" as part the Education session.

     RCSB POSTER PRIZE AWARDED AT RECOMB AND ACA

Thanks to the students and judges who participated in the recent RCSB
PDB Poster awards.  Details are available at
www.rcsb.org/pdb/poster_prize.html.  The next award will be presented
at the XX Congress of the International Union of Crystallography
(August 23-31 2005 in Florence, Italy).

* At the Ninth Annual International Conference on Research in
  Computational Molecular Biology (RECOMB, May 14-18, Cambridge, MA),
  the RECOMB & PDB Poster Awards recognizing insight and innovation in
  structural computational biology went to "Comparative Modeling of
  Mainly-Beta Proteins by Profile Wrapping" by Andrew V. McDonnell,
  Matthew Menke, Nathan Palmer, Jonathan King, Lenore Cowen, Bonnie
  Berger (MIT) and "MAPPIS: Multiple Alignment of Protein-Protein
  Interfaces" by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov
  and Haim J. Wolfson (Tel-Aviv University).

* At the ACA, the award for best student presentation went to "Safety
  in Cycling: Novel Redox Proteins from Escherichia coli" by Melanie
  A. Adams (pictured) and Zongchao Jia (Queen's University).

-----------------------------------------
COMMUNITY FOCUS: ROBERT M. SWEET, BROOKHAVEN NATIONAL LABORATORY

Robert (Bob) Sweet is a member of the Biology Department at Brookhaven
National Laboratory (BNL), and group leader of the Macromolecular
Crystallography Research Resource (PXRR) at the National Synchrotron
Light Source (NSLS; funded by BER/DOE and NCRR/NIH).  Raised in rural
midwestern US, he was educated at Caltech and the University of
Wisconsin, Madison.  His first exposure to crystallography was at the
knee of Dick Marsh at Caltech, where in about 1963 he estimated
intensities visually from Weissenberg photographs and calculated his
first Fourier synthesis with Beevers-Lipson strips and a Marchant
calculator.  An automated diffractometer helped to solve a few
cephalosporin structures in the lab of Larry Dahl in Madison that
provided Bob with a PhD at the beginning of 1970.  Then postdoctoral
work with David Blow at the MRC Lab in Cambridge gave him an
introduction to protein crystallography.  Bob also managed to play a
small role in the creation of modern oscillation photography in
cooperation with Uli Arndt and Alan Wonacott.  He spent a decade in
Chemistry at UCLA, and has been at BNL since 1983.  There, the
importance of the NSLS to the PX community has grown steadily: the
PXRR now comprises six beam lines, and has contributed to over 280
publications during the last year.

Q: Its very clear that the PXRR facility will be generating a
tremendous number of macromolecular structures, all of which should
ultimately be deposited in the PDB.  What is your vision for optimal
interactions between facilities such as the PXRR and the PDB?

A: Well, to begin with we can remind our users that you're important to
us.  For six or seven years, our beam-time request form has had a
check box (persuasively pre-checked) followed by the words,
Acknowledge your intent to submit the coordinates of the structure
derived from this work to the Protein Data Bank.  Also, for at least
that long, we've had a dream that our data collection and processing
programs would create a stream of information in mmCIF format that
would represent a major part of the experimental portion of a PDB
entry.  We have fragments of the data-harvesting code available, but
our proudest achievement in this regard is that just a year ago we
released our experiment-tracking database, PXDB.  This system (please
play with it: www.px.nsls.bnl.gov/database/pxdb_intro.html) accepts
the information from the users initial application for beam time, logs
actual visits, records the identities of specimens, and registers
every image taken.  We expect it to be hugely useful as Dieter
Schneider and Alex Soares get our specimen-mounting robots in place.
In summary, we'll grease the rails for you as best we can.

Q: What is the current ratio of "FedEx" data collection to hands-on 
data collection at the PXRR, and how do you see this changing as time 
goes on?

A: This program was started by Mike Becker, brought into regular
practice by Howard Robinson, and now operated also by Annie H roux and
Alex Soares.  (These folks prefer to call it mail-in, but I think the
name you used has a certain ring to it).  At the last attempt to
answer this question we found that, integrated over many months, the
mail-in scientists have been employing 0.8 of our 6.0 beam lines.  It's
a growth industry it has nowhere to go but up; buy stock in it if you
can.  Another interesting question is, What fraction of the users
follow the traditional cycle of trimester proposals vs. those who gain
rapid access?  For five or six years we have had a rapid-access
mechanism for some of our less heavily loaded beam lines.  It started
out as a simple web form, is now an integral part of PXDB, and will
eventually be a part of the NSLS user program.  Rapid access to at
least five of the beam lines is overseen by Anand Saxena, and it can
be really fast.  Essentially, if there's time available and you have
crystals, Anand will get you in.  So the answer to the question is
that something over half of our users come to us this way.  It's quick,
efficient, and more personalized than you might think.  In this
context, the FedEx work can be quick: typically a week elapses from
the time a dewar of cryocooled crystals arrives until data are
reported back to the user and the project is essentially finished.

Q: Rapid on-site data collection, mail-in service, and automatic data
reduction and structure solving packages are having a profound effect
on macromolecular structure determination. How much crystallography
will a researcher need to know to solve structures?  And, as an
educator continually involved in teaching crystallography, what do you
see as the best way to teach the fundamentals of crystallography to
the growing base of scientists producing and using the structural data
stored in the PDB?

A: I think your first question is really, How little may a researcher
know and still be able to solve a structure reliably?  Well, how much
do you know about optics and diffraction gratings when you measure an
UV/Vis absorption spectrum?  Not very much, probably, but you still
get really good spectra because the instrument just works.  I think
that we who devise instruments, software, and methods take this as a
model: eventually for some range of routine structures, macromolecular
crystallography will work about that well.  Of course if there are
half a dozen anomalies that can give a misleading absorption spectrum
(a one-dimensional pattern), then there are at least that many cubed
for a crystal structure.

But I'm not answering your questions.  We've had seven cycles of our
RapiData course www.px.nsls.bnl.gov/RapiData2005/.  We have a
number of the software gods come to teach firstly data reduction, and
then solving of the phase problem.  These descriptions are at a fairly
high level some knowledge of diffraction is really necessary.  We
found fairly quickly that whereas we expected to be judging applicants
to the course based on their preparation, instead we find we're hoping
they know enough to understand!  Four years ago I started teaching a
fundamentals course as an optional extra day at the beginning of
RapiData and at least 3/4 of the students have been coming for the
five-hour series of lectures.  You're welcome to have a look at the
visuals I used during the lectures here:
www.px.nsls.bnl.gov/fundamentals_lecture/.  You'll see that I teach a
bit of diffraction theory as related to lens optics, show how a
repetitive pattern gives spots, and then move on to reciprocal space.
I look briefly at ancient and modern x-ray cameras and diffractometers
(students liked the history).  Then I develop the expressions for the
structure factor and Fourier synthesis.  I do a very brief treatment
of symmetry, including defining a space group or two and showing how
the symmetry of the diffraction pattern comes from the symmetry of the
crystal.  Then I talk about heavy-atom and direct-methods phasing, and
I'm done: all of that in five hours.

I believe this represents the sort of thing the users of our
equipment, software, and methods ought to understand in order to have
any idea what is going on.  The only evidence I have of the usefulness
of the approach is that several students each year will say things
like, So thats what that is all about, or I always wondered how that
worked.  Certainly no one has said (in our anonymous course
evaluations) that it is a waste of time.  It would be better, of
course, if the same material were presented in a more detailed and
leisurely format over ten to twenty lectures back at the university.
I'm not experienced with people using but not producing PDB data, so I
won't comment on that part of your question.

Q: The PDB is growing at a steadily increasing rate. How have your
interactions with the PDB changed over the years and where do you see
them going as both macromolecular crystallography and the PDB continue
to evolve?

A: Well, a big change is that before 1999 I used to be able to walk
across the street to talk with the PDB workers.  That changed, of
course, when the RCSB took over.  Seriously though, the changes are
small and incremental.  We've had the idea in mind of pipelining
information from the data stream to PDB deposition for a long time.
We can see that the increased pace makes this even more important.
The possibility of having a new synchrotron here (NSLS-II;
www.nsls2.bnl.gov) gives us an accelerated mission to be ready for the
increment in productivity that this will engender.  I'm impressed with
the ease with which the PDB is providing interchangeability among its
file formats from PDB to mmCIF to the more modern XML.  This
innovation matches our own migration of information-exchange media.  I
believe well be able to communicate easily, and will continue to grow
in parallel.

-----------------------------------------
PDB EDUCATION CORNER: WISCONSIN HIGH SCHOOL SCIENCE OLYMPIAD PROTEIN
MODELING EVENT BY GARY GRAPER, EVENT SUPERVISOR

Gary Graper is a former biology teacher who taught 35 years at Madison
West High School in Wisconsin before retiring from the classroom 2
years ago. Since retirement, he has been promoting the Wisconsin
Science Olympiad, facilitating University of Wisconsin College of
Engineering outreach to K-12 education, helping teachers develop
constructivist approaches to instruction in their classrooms, and
advising a high school SMART (Students Modeling A Research Topic)
team.

An understanding of 3D molecular structure and function is at the
heart of rapidly expanding fields in the molecular
biosciences. Protein Modeling is a new Wisconsin Science Olympiad
event in which teams first master the use of a molecular visualization
tool to display and analyze a molecular structure, and then create a
physical model of that structure using mini-toobers, a free-form
modeling media especially designed for this purpose. This event has
introduced Science Olympiad competitors in Wisconsin to the value of
3D molecular visualization in understanding protein structure and
function, to the PDB and the wealth of information it contains, and to
the RCSB PDB's Molecule of the Month's informative articles on
relevant and important molecules. The event is an excellent
opportunity for high school students to practice inquiry-based science
using the tools and methods of research scientists.

Science Olympiad tournaments are rigorous academic interscholastic
competitions that consist of over 30 individual and team events which
students prepare for during the year. These challenging and
motivational events are well-balanced between the various disciplines
of biology, earth science, chemistry, physics, computers and
technology. The events require knowledge of science facts, concepts,
processes, skills and science applications.  Students demonstrate an
understanding and mastery of science, mathematics, and technology
concepts that require not only knowledge and problem solving skills
but also the ability to work together as a team. Science Olympiad is
devoted to improving the quality of science education, creating a
passion for learning science and providing recognition for outstanding
achievement in science. One of the major goals of the Science Olympiad
is to elevate science education and learning to a level of enthusiasm
and support that is normally reserved only for varsity sports
programs. At the end of the competition individual medals and team
trophies are awarded to the top competitors.

The Science Olympiad Protein Modeling event was part of the Wisconsin
Division C (High School) 2005 regional and state (April 2)
competitions. For the competition, teams of 1 to 3 students first had
to design and build a model of the potassium channel protein (1bl8)
that told the story of the proteins function. They utilized RasMol and
the Molecule of the Month article, as well as individual research to
explore the potassium channel structure and learn how the protein
functions. The molecular model was constructed in the weeks prior to
the competition using mini-toobers for the backbone and any other
creative materials of the students choice to illustrate the
significant structural features of the protein. The models were
impounded for scoring on the day of the competition. The scoring
rubric was based on accuracy of the physical model, as well as
creativity and originality of design. This first part of the
competition counted for 40% of the final score.

The second part of the competition consisted of a 50 minute time
period during which the teams designed and built a physical model and
answered questions about a protein selected from the Molecule of the
Month. The modeled structure used at the regional competitions was
amino acids #4-31 of the zinc finger molecule (1ZAA), and at the state
competition was chain B of the major histocompatibility complex
molecule (1HSA).  The model was constructed using mini-toobers and
clip-on amino acid side chains provided at the competition. In
addition, students were provided with RasMol, a PDB file, and the
Molecule of the Month feature to guide their model construction and to
help answer questions about the protein's structure, function,
importance, researchers, when and where the research was published,
etc. At the end of the 50 minutes, the model was scored with a rubric
for accuracy which counted 30% of final score, and the multiple-choice
test was scored which counted for 30% of the final score.

The Wisconsin Science Olympiad Protein Modeling event was designed,
organized, and supported by the Center for BioMolecular Modeling (CBM)
at the Milwaukee School of Engineering along with myself, a retired
science teacher who has utilized the services of the CBM for a number
of years to develop curriculum that makes chemistry more interesting
and understandable for high school students as well as to support my
former schools SMART (Students Modeling A Research Topic) team.  The
team of CBM members Director Tim Herman, Co-Director Michael Patrick,
Jennifer Morris and Shannon Colton and myself wrote the event
descriptions and rules, selected molecules to be modeled, planned and
taught 4 workshops around the state of Wisconsin, developed scoring
rubrics, and ran and judged 2 regional and the state competitions. The
mini-toobers and other modeling materials were provided to the fifty
teams registered for the event by 3D Molecular Designs. The event was
a success at both the regional and state competitions with many
competitors expressing enthusiasm and support for continuation of the
event. At the National Science Olympiad held at the University of
Illinois-Champaign on May 21, 2005, the event was presented to
numerous other state directors with a great deal of interest. It is
hoped that arrangements can be made to have other states run the event
in 2006, and that it can be a trial event at the 2007 national
competition and possibly a regular event at state and national
competitions in the future.

     REFERENCES

PDB ID 1bl8. Doyle, D. A., Morais Cabral, J., Pfuetzner, R. A., Kuo,
A., Gulbis, J. M., Cohen, S. L., Chait, B. T., MacKinnon, R.: The
structure of the potassium channel: molecular basis of K+ conduction
and selectivity. Science 280 pp. 69 (1998)

PDB ID 1zaa. Pavletich, N. P., Pabo, C. O.: Zinc finger-DNA
recognition: crystal structure of a Zif268-DNA complex at 2.1
A. Science 252 pp. 809 (1991)

PDB ID 1hsa. Madden, D. R., Gorga, J. C., Strominger, J. L., Wiley,
D. C.: The three-dimensional structure of HLA-B27 at 2.1 A resolution
suggests a general mechanism for tight peptide binding to MHC. Cell 70
pp. 1035 (1992)

     RELATED LINKS
National Science Olympiad 
     www.soinc.org
Wisconsin Science Olympiad  
     wisconsinso.uwstout.edu
Wisconsin Science Olympiad Protein Modeling Event 
     wisconsinso.uwstout.edu/wsoprotein.html
Center for BioMolecular Modeling 
     www.rpc.msoe.edu/cbm
RCSB PDB Molecule of the Month 
     www.rcsb.org/pdb/molecules/molecule_list.html
RasMol 
     www.umass.edu/microbio/rasmol

--------------------------------------------
MOLECULES OF THE QUARTER: PHENYLALANINE HYDROXYLASE, MAJOR
HISTOCOMPATIBILITY COMPLEX, T-CELL RECEPTOR

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

The complete Molecule of the Month features are available at
www.rcsb.org/pdb/molecules/molecule_list.html.

* April: Kinesin.  Kinesins are used for many tasks in cells. Typical
  cells contain an array of microtubules, all pointed from the center
  of the cell outwards to the surface. Kinesins are used to drag large
  objects, like lysozomes or endoplasmic reticulum, outwards away from
  the nucleus and towards the surface. Dyneins are used for the
  opposite function, to pull things inwards. Kinesins drag materials
  down the enormous length of nerve axons--this function is how
  kinesins were discovered. Kinesins are also used to slide
  microtubules next to one another, for instance, during the process
  of creating two separate systems of microtubules to separate
  chromosomes when the cell divides.

* May: Self-splicing RNA.  In plants and animals, most RNA molecules
  are made as long precursors that need to be trimmed and reassembled
  to create the final active molecule. These precursor RNA molecules
  are composed of exons, which are the important parts, separated by
  introns, which must be removed. In most cases, the RNA is cut and
  spliced together by a spliceosome, a molecular machine composed of
  protein and RNA. In a few cases, however, the RNA can perform the
  splicing reaction on its own. The first example, discovered by
  Thomas Cech, was a ribosomal RNA found in a protozoan. Since then,
  hundreds of examples have been identified in genome sequences of
  many organisms.

* June: Carotenoid Oxygenase.  The bright color of carrots and many
  other orange and yellow vegetables is caused by carotenoid molecules
  such as beta-carotene. Carotenoids are long, thin molecules with a
  string of carbon-carbon double bonds in a row. These bonds absorb
  light and give carotenoids their characteristic yellow
  color. Hundreds of different types have been discovered in different
  plants, where they color flowers, leaves, fruits, and even the
  roots. Carotenoids are remarkably useful, both for the plant and for
  the people eating the plant. In plants, carotenoids assist the
  chlorophyll molecules that absorb light in
  photosynthesis. Carotenoids also absorb excess light when it reaches
  dangerous levels. Our retinas contain carotenoids such as lutein
  that protect us from excess light that might damage our
  eyes. Carotenoids also are antioxidants that scavenge reactive forms
  of oxygen, destroying them before they damage our molecular
  machinery.

-----------------------------------------
STATEMENT OF SUPPORT

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-----------------------------------------
SNAPSHOT -- July 1, 2005

31535 released atomic coordinate entries

Molecule Type
 28739 proteins, peptides, and viruses
  1481 nucleic acids
  1302 protein/nucleic acid complexes
    13 carbohydrates

Experimental Technique
 26932 diffraction and other
  4603 NMR

17182 structure factor files
 2552 NMR restraint files