________________________________________________________________________
________________________________________________________________________
PROTEIN DATA BANK
QUARTERLY NEWSLETTER
Release #75
January 1996
________________________________________________________________________
________________________________________________________________________
NEW PHONE/FAX NUMBERS
Telephone..........516-344-3629
Fax................516-344-5751
------------------------------------------------------------------------
INTERNET SITES
WWW................http://www.pdb.bnl.gov
FTP................ftp.pdb.bnl.gov
Gopher.............gopher.pdb.bnl.gov
------------------------------------------------------------------------
JANUARY 1996 CD-ROM RELEASE
4162 full-release atomic coordinate entries
Molecule Type
3777 proteins, peptides, and viruses
88 protein/nucleic acid complexes
285 nucleic acids
12 carbohydrates
Experimental Technique
126 theoretical modeling
566 NMR
3470 diffraction and other
The total size of the atomic coordinate entry database
is 1566 Mbytes uncompressed.
------------------------------------------------------------------------
TABLE OF CONTENTS
What's New at the PDB
Revised Entry Format Description
Letter to the Editor on Crystallographic Data Deposition
Change in Policy for Deposition of Nucleic Acid Structures
Determined by X-ray Crystallography
Current PDB Submission Procedures and Requirements
Replacement Data Procedure
O! O! Oops!
Rasmol's New Home Page
New Server at Weizmann's Bioinformatics Unit: Blocks
Internet Course in Principles of Protein Structure
Training Courses in Parallel Programming and High
Performance Computing
The International School-cum-Seminar on Macromolecular
Crystallographic Data
Targets for Protein Structure Prediction Results Now
Available on WWW
Notes of a Protein Crystallographer
- The Ballad of the 2.8 � Structure of SBMV
Personnel Changes
New Telephone Number Exchange
New PDB Handout
Order Form
Affiliated Centers
-----------------------------------------------------------------------
WHAT'S NEW AT THE PDB
Over the past two years we at the PDB have heard numerous
reports of X-ray structure factors being lost, misplaced, or on
some kind of tape or even punch cards that could not be read
anymore. Frequently the crystallographers who actually collected
the data or other members of their lab turn to the PDB for
this data. As the structure factors are directly derived from the
raw data measured in a crystallographic experiment, we feel that
it is of the utmost importance that this data be deposited along
with the coordinates in the PDB archive.
A great deal of discussion on this matter took place at the
November 1995 International Seminar-cum-School on Macromolecular
Crystallographic Data in Calcutta, India, sponsored by the
International Union of Crystallography (IUCr). Virtually all
participants felt that the deposition of the structure factors
along with the coordinates is essential for the following
reasons:
- Rigorous validation of the structure determination results
can only be carried out using both atomic parameters and
experimental structure factor amplitudes.
- Archiving of this data will ensure their preservation
and continued accessibility (see article in our
October 1995 Newsletter entitled PDB Structure Factor
Files in CIF - A Proposal).
Some participants at this Seminar-cum-School felt that a number
of crystallographers would be reluctant to submit their structure
factors as they may want to continue their refinement before
letting another group work on their data. This should not be a
problem because the current policy of both the IUCr and the
PDB provides crystallographers with the option of delaying the
release of atomic parameters for up to one year and structure
amplitudes for up to four years from the date of publication.
A short `Letter to the Editor' was composed by several participants
which has now been sent to journals in which three-dimensional
structural studies of macromolecules are published (see article
entitled Letter to the Editor on Crystallographic Data Deposition).
This letter urges journals to require deposition of not only atomic
coordinates but also structure factors. The PDB feels that this is
a very important development and urges members of the
crystallographic community to encourage journals to follow this
policy. One way in particular that this can be accomplished is
that referees of journal articles should insist that the journal
require deposition of coordinates and structure factors by the
authors as a requirement for publication. We would welcome any
thought you may have in this regard and would be pleased to
publish these thoughts in future Newsletters.
� Joel L. Sussman
------------------------------------------------------------------------
Revised Entry Format Description
The draft revision of the PDB Format Description has been
finalized and is now available as Protein Data Bank Contents
Guide: Atomic Coordinate Entry Format Description Version,
Version 2.0. The full text is over one hundred pages and is
accessible through PDB's home page on the WWW and via FTP
in the /pub directory.
The PDB wishes to thank all those who made comments and suggestions
about the draft document which has been available on the WWW.
Entries released after April 15, 1996 will comply with
Version 2.0 of the Contents Guide. Conversion of older entries
to this format will begin in the fall of 1996.
-----------------------------------------------------------------------
Letter to the Editor on Crystallographic Data Deposition
The following `Letter to the Editor' has been sent to
journals in which X-ray crystallographic structure
determinations of macromolecules are published.
A formal discussion of the archival journal requirements for data
deposition was held at the November 1995 International
Seminar-cum-School on Macromolecular Crystallographic Data in
Calcutta, India.
The current policy of the International Union of Crystallography
(IUCr) is that upon publication of a crystal structure determination
of a macromolecule, the atomic parameters used or represented in
the publication must be deposited in the Brookhaven Protein
Data Bank. The deposition of structure amplitudes is recommended
but not required. The policy provides crystallographers with
the option of delaying the release of atomic parameters for one
year and of structure amplitudes for up to four years from
the date of publication. Participants strongly supported this
policy and felt it should be strictly applied by the journals
(referees).
Recent developments in X-ray crystallographic experimental and
refinement techniques and the huge expansion in computing power
and networking, however, necessitate the review of deposition
arrangements.
It was noted that the new validation procedures are much more
effective but require the experimental structure amplitudes as
well as the atomic parameters. In addition, the technical
arrangements for deposition, analysis, and validation of
macromolecular crystal structures are now much easier.
The undersigned consider it vital for the macromolecular
crystallographers to respond to these developments in their
deposition practices. We recommend, therefore, that publication
of macromolecular crystal structures should be accompanied by
deposition of atomic parameters and also structure amplitudes.
Amongst the many reasons identified for this practice, the
following two are critical:
- Rigorous validation of the structure determination results
can only be carried out using both atomic parameters and
experimental structure amplitudes. It is important that
journals ensure that referees have sufficient information
to prevent incorrect structures being published.
- Archiving of this data will ensure they are not lost.
There were numerous reports at this Meeting of data being
lost. This most probably reflects a general problem in the
crystallographic community.
Edward N. Baker - Member of IUCr Executive Committee and
Member of the IUCr Commission on Biological Molecules
Department of Chemistry and Biochemistry
Massey University
Palmerston North
New Zealand
Tom L. Blundell
ICRF Unit of Structural Molecular Biology
Department of Crystallography
Birkbeck College
Malet Street
London, WC1E 7HX
England
Mamannamana Vijayan - Chairman of IUCr Commission
on Biological Molecules
Molecular Biophysics Unit
Indian Institute of Science
Bangalore 560012
India
Eleanor Dodson - Member of IUCr Electronic Publishing Committee
Department of Chemistry
University of York
York, YO1 5DD
England
Guy Dodson - Previous Chairman of IUCr Commission on
Biological Molecules
Department of Chemistry
University of York
York, YO1 5DD
England
Gary L. Gilliland, Associate Director
Center for Advanced Research in Biotechnology
9600 Gudelsky Drive
Rockville, MD 20850
USA
Joel L. Sussman - Head, Protein Data Bank
Departments of Biology and Chemistry
Brookhaven National Laboratory
Upton, NY 11973
USA
and
Department of Structural Biology
Weizmann Institute of Science
Rehovot 76100
Israel
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Change in Policy for Deposition of Nucleic Acid Structures Determined
by X-ray Crystallography
This article was written by Helen M. Berman,
Head, Nucleic Acid Data Base, Rutgers University,
Piscataway, NJ, USA (berman@dnarna.rutgers.edu) and
Joel L. Sussman, Head, Protein Data Bank, Brookhaven
National Laboratory, Upton, NY, USA (jls@bnl.gov).
Starting January 1, 1996 data for crystal structures of
oligonucleotides should be deposited directly with the Nucleic Acid
Database (NDB). Once the data are processed they will be forwarded
to the PDB for deposit in the central single archive. This will
simplify current procedures and make the data on nucleic acids
available more quickly. Protein/nucleic acid complexes and all
NMR structures should continue to be deposited at the PDB. All
crystal structure data for DNA and RNA will continue to be available
from both the NDB and the PDB.
To deposit the data, submit the coordinates, structure factors, and
current PDB deposition form to: deposit@ndbserver.rutgers.edu.
A preprint of the related manuscript should be sent by fax to
908-445-5958 or by postal mail to Dr. Anke Gelbin, The Nucleic
Acid Database, Department of Chemistry, Rutgers University,
POB 939, Piscataway, NJ 08855, USA.
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Current PDB Submission Procedures and Requirements
There are three essential elements of a complete PDB deposition:
- PDB-formatted coordinate data.
- A completed up-to-date version of our Electronic Deposition
Form which you can pick up off of the PDB WWW home page
(http://www.pdb.bnl.gov), download from our FTP server
(ftp.pdb.bnl.gov), or request via e-mail from the PDB.
Please fill out this Deposition Form using an on-line
editor rather than by hand, as we run a program on the
form to generate a preliminary header for your final PDB
entry. As our older, non-electronic Deposition Forms are
more difficult to fill out and because those forms are not
as complete, we request that you no longer send the old
forms to us. Our new Form has been available for about
one and a half years, and we prefer that you use it.
- Copies of all relevant preprints and reprints OR a copy
(print-out) of your submitted manuscript with the PDB
Tracking Number it relates to prominently noted. As
questions frequently arise about this, we would like to
stress that IF YOUR PAPER IS NOT AT THE PREPRINT STAGE
YET, a regular xerox or print-out of the submitted manuscript
fulfills this requirement. If there is no manuscript in
progress, please indicate so in the Journal (JRNL) section
of the Deposition Form and the print requirement will be
waived.
Referenced papers can be sent electronically using FTP or
e-mail, by fax to 516-344-5751, or by postal mail to:
Protein Data Bank Depositions
Chemistry Department, Bldg. 555
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000
USA
FOR DEPOSITORS NEEDING TO OBTAIN AN ID CODE AS QUICKLY AS
POSSIBLE, WE SUGGEST YOU E-MAIL OR FAX YOUR MANUSCRIPT.
References are kept completely confidential and are used
only to aid us with the processing of your entries and to
ensure that we reference related papers correctly in the
entries themselves.
The PDB now issues ID codes to depositors as soon as we
receive the above three items. For more information on PDB
submissions, please contact Minette Cummings at pdb@bnl.gov.
-----------------------------------------------------------------------
Replacement Data Procedure
When sending replacement data to the PDB, please send an
accompanying e-mail to pdb@bnl.gov indicating the related
Tracking Number or ID code as well as a listing of all files sent.
-----------------------------------------------------------------------
O! O! Oops!
This article was written by Gerard J. Kleywegt, Department
of Molecular Biology, Biomedical Centre, Uppsala
University, Uppsala, Sweden (gerard@xray.bmc.uu.se).
OOPS is a little utility program for people who use O to rebuild
their crystallographic protein models. Although the program
itself is absolutely trivial, it offers two major benefits:
1. It focuses the crystallographer's attention on the
trouble spots in the current model.
2. It can be instructed to skip residues which appear
to be perfectly in order, thereby saving much
rebuilding time.
Basically, OOPS is a simple filter. As input it takes a number of
files produced by O (or other programs) which contain information
about the quality of the current model on a per-residue basis.
The major output is a set of rebuilding macros for O which
will take the crystallographer on a journey past all residues
which may need attention because they scored poorly in one or
more of the quality tests. The macros are `chained', which
means that when one has finished rebuilding a suspicious residue,
a click of the mouse will take the crystallographer to the next
suspect.
At present, OOPS can check the following quality indicators
(amongst others):
- Bad pep-flips (a measure for the distance between a peptide
oxygen orientation and those encountered in the database).
- Bad real-space-fit values (the correlation or R-factor
between calculated and 2Fo-Fc density for any or all atoms
in a residue).
- Bad rotamer side chain (RSC) fit values (a measure of how
well the side chain conformation resembles that of a rotamer).
- Too high and too low temperature factors and occupancies.
- Bad phi, psi angle combinations.
- Poor peptide planarity.
- Poor C(alpha) chirality.
In addition, the current model can be compared to the previous one
(in terms of displacements, temperature factor, and occupancy
changes, as well as changes in the main and side chain torsion
angles). Moreover, up to ten user-defined criteria can be used
(e.g., quality of the geometry from X-PLOR, or the number of bad
contacts from Procheck).
The output of OOPS consists of:
- Statistics for most of the used quality indicators.
- Plot files for some of the criteria (as a function of
residue number).
- A list of potentially bad residues, plus their faults.
- A list of the violation counts for each quality criterion.
- A set of O rebuilding macros.
- A small file with PDB REMARK records pertaining to the
quality of the current model. If the current model is the
final one, these records can be included in the PDB
Deposition Form.
Using OOPS requires some O datablocks to be prepared in
advance (however, there is an O macro available to do most of
that work for the user as well). Running the program takes only
a few minutes. The result in terms of speed-up of the rebuilding
process is well worth this small effort. Also, OOPS makes it
less likely that residues with serious errors in them are
overlooked and may therefore help improve the quality of the
model.
OOPS is one in a series of `O-dalisques', i.e., programs that
work in conjunction with O. The OOPS program runs on SGI, ESV,
and DEC ALPHA/OSF1 workstations. For more information,
contact Gerard Kleywegt via e-mail (gerard@xray.bmc.uu.se).
-----------------------------------------------------------------------
Rasmol's New Home Page (http://www.umass.edu/microbio/rasmol)
This article was written by Eric Martz, Department of
Microbiology, University of Massachusetts, Amherst,
MA, USA (emartz@microbio.umass.edu).
RasMol has a new home page dedicated to its popularization and
distribution, educational uses of RasMol, and access to atomic
coordinate (PDB) data files for macromolecules and other
free molecular visualization resources. The introductory
documents on this home page are written for the scientific
public (biologists not specializing in protein structure,
high school teachers, etc.). Don't miss the personal history of
the origin of RasMol by Roger Sayle (author of RasMol)! An
e-mail list has also been set up for announcement of new
releases of RasMol and discussion of its use (details on the
home page).
RasMol is a highly capable and amazingly fast program for
molecular visualization. It runs on Windows, MacIntoshes,
and unix systems via X-windows. The University of California,
Berkeley MultiChem Facility offers an enhanced version of
RasMol (now available for the MacIntosh; Windows version
under development). This can display several molecules at
once and move them relative to each other. RasMol is the
generous gift to the scientific public from Roger Sayle, the
University of Edinburgh, and Glaxo Research and Development
(Sayle's employer, Greenford, UK), who are continuing to
upgrade and distribute it free.
The RasMol page offers the first publicly available PDB
formatted file for an intact antibody molecule, provided by
Eduardo Padlan of the National Institutes of Health. Other
contributions of wide interest would be welcomed (lipid
bilayers, T-cell antigen receptor complexes with MHC:peptide,
etc.). Several RasMol scripts are provided. One, designed
to introduce RasMol to general biological science
audiences/classes, shows the power and glory of RasMol by
illustrating several aspects of the structure of the DNA double
helix. Scripts for more specialized audiences/classes treat the
structure of antibody and antibody interaction with antigen, as
well as the structure of the major histocompatibilty complex
and its binding to peptide antigens. Links are offered to class
WWW pages at various universities which make extensive
use of RasMol. These include New York University's `Mathematics
& Molecules' aimed at K-12 groups, organic chemistry (Virginia
Polytechnic Institute and State University), biochemistry
(University of California, Santa Barbara and Carnegie-Mellon
University), immunology (University of Massachusetts, Amherst),
and chemotherapy and drug design (Leeds University, UK).
As this issue went to press, the RasMol home page was receiving
visits from nearly one thousand people per week, from over
thirty countries.
The RasMol home page and e-mail list were set up by
Eric Martz, a professor at the University of Massachusetts,
Amherst, MA, USA (emartz@microbio.umass.edu). Eric welcomes
suggestions of additional resources/improvements for the RasMol
page.
-----------------------------------------------------------------------
New Server at Weizmann's Bioinformatics Unit: Blocks
This article was written by Jaime Prilusky, Bioinformatics
Unit, Biological Services, Weizmann Institute of Science,
Rehovot, Israel (lsprilus@inherit1.weizmann.ac.il).
Detection and verification of protein sequence homology is now
available at the BLOCKS WWW Server at the Bioinformatics
Unit, Biological Services, Weizmann Institute of Science,
Rehovot, Israel at URL http://bioinformatics.weizmann.ac.il/blocks.
This Server is provided in collaboration with Jorja Henikoff
(jorja@howard.fhcrc.org) from the Fred Hutchinson Cancer
Research Center, Seattle, Washington, USA.
Blocks are multiply-aligned, ungapped segments corresponding
to the most highly conserved regions of proteins.
Block Searcher, Get Blocks, and Block Maker are aids to
detection and verification of protein sequence homology. They
compare a protein or DNA sequence to a database of protein
blocks, retrieve blocks, and create new blocks, respectively.
- The Blocks Database
The blocks for the BLOCKS database are made automatically
by looking for the most highly conserved regions in groups of
proteins represented in the PROSITE database. These blocks
are then calibrated against the SWISS-PROT database to
obtain a measure of the chance distribution of matches. It is
these calibrated blocks that make up the BLOCKS database.
The WWW versions of the PROSITE and SWISS-PROT databases
that are used on this Server are located at the ExPASy
WWW Molecular Biology Server of the Geneva University
Hospital and the University of Geneva (http://expasy.hcuge.ch).
The blocks created by Block Maker are created in the same
manner as the blocks in the BLOCKS database but with
sequences provided by the user. Results are reported in a
multiple sequence alignment format without calibration and
in the standard BLOCK format for searching.
-----------------------------------------------------------------------
Internet Course in Principles of Protein Structure
This article was written by John Walshaw, Jacky Turner,
and David Moss, Crystallography Department,
Birkbeck College, University of London, London
WC1E 7HX, UK (pps2@mail.cryst.bbk.ac.uk).
The pilot year of an undergraduate level course in Principles of
Protein Structure, the first international multimedia science-
education course to be taught entirely via the Internet, finished
in June 1995. Over 150 students, teachers, and advisors from
twenty-seven countries were involved, and about seventy students
finally `graduated'. The course, a collaboration with the
Texas-based Virtual School of Natural Sciences, was pioneered
at Birkbeck by Peter Murray-Rust of Glaxo-Wellcome
and Alan Mills now of Venus Internet Ltd.
Beginning on January 15, 1996 an updated PPS course will
run - this time as a one-year, part-time Advanced Certificate
course accredited by Birkbeck College (University of London)
and available worldwide to those with access to a suitable
networked computer. The course comprises three units
(approximately one per term): bioinformatics, protein structure,
and a dissertation. Students will be familiarized with the biological
Internet, including some technical issues behind the genomic,
protein sequence, and structural databases.
The core is the study of protein structure, progressing from
fundamentals to recent developments and current research. The
course material on the WWW is public to all, whether they are
involved in the course or not. In the second half of the course,
students will produce a hypertext dissertation to be mounted
on the WWW.
An equally important component is the interaction between
students, teachers, and an international network of volunteer
consultants with a range of specialist interests. We have had
a fantastic response from these volunteers.
Students are divided into small e-mail discussion groups,
each with a tutor from the Crystallography Department who
holds discussions and tutorials on the week's work. Students
are to spend approximately six hours per week on the course.
We are very fortunate in having several rooms in the BioMOO
at the Weizmann Institute for `virtual' tutorials and the
enthusiastic cooperation of both Brookhaven National Laboratory
(http://www.pdb.bnl.gov/PPS2/index.html) and Daresbury
Laboratory (http://www.dl.ac.uk/PPS/index.html) who are
providing mirror services.
The academic level is formally that of the final year of an
undergraduate degree, but inevitably more specialized. The Internet
medium allows us to tailor the course to the interests, needs,
and talents of individual students. There is a wide range of
backgrounds among the students currently enrolled. Many are
professional research scientists or Ph.D. students, who will
enrich the course by sharing their expertise. (Unfortunately
the regulations do not allow current undergraduate students to
register for the course, except in the case where the student's
university decides to incorporate it as one credit unit in the
undergraduate degree.)
The Advanced Certificate course consists of three 11-week terms
beginning on January 15, 1996 and ending in October 1996. The
cost is 186 pounds sterling for EU students and 500 pounds
sterling worldwide. Enrollment is now taking place.
Anyone interested in the course, either as a student or a consultant,
please refer to http://www.cryst.bbk.ac.uk/PPS2/ or send e-mail to
j.mcgill@mail.cryst.bbk.ac.uk.
-----------------------------------------------------------------------
Training Courses in Parallel Programming and High Performance Computing
As part of the Supercomputing Resource for Molecular Biology (SRMB)
programme, the European Molecular Biology Laboratory in Heidelberg,
Germany is offering training courses in Parallel Programming and
High Performance Computing to European researchers in molecular
biology.
Participants will receive instruction in writing message passing
and data parallel programs using PVM, MPI, and Fortran90/
HPF. General tuning and performance optimization techniques,
suitable for today's high performance RISC microprocessors,
will also be covered. All topics are complemented by hands-on
training sessions, using the parallel supercomputer facilities at
EMBL-Heidelberg.
This course is open to European Molecular Biologists at the
advanced post-graduate level with research interests in
sequence analysis, image processing, structural refinement,
protein design, and molecular dynamics.
Visitors from EU and associated countries will have travel and
accommodation expenses funded by an EU HCM/ALSI grant.
Visitors from other EMBL member states will be supported by
funds from EMBL.
The next course is scheduled for February 19-23, 1996. Please see
http://www.embl-heidelberg.de/Services/srmb/pphpc_course/ for
information from EMBL.
For additional information on the SRMB programme, visit URL
http://www.embl-heidelberg.de/Services/srmb/ or write to:
SRMB Secretary
Biological Structures and Biocomputing Programme
European Molecular Biology Laboratory
Postfach 10.2209
D-69012 Heidelberg
Germany
Phone: +49 6221 387 271
Fax: +49 6221 387 306
E-mail: SRMBadmin@EMBL-Heidelberg.de
-----------------------------------------------------------------------
The International School-cum-Seminar on Macromolecular
Crystallographic Data
This article was written by Geoffrey B. Jameson,
Department of Chemistry and Biochemistry, Massey
University, Palmerston North, New Zealand
(G.B.Jameson@massey.ac.nz).
The International School-cum-Seminar on Macromolecular
Crystallographic Data (ISMCD) was held at the Saha Institute
of Nuclear Physics in Calcutta, India, from November 16-20, 1995.
Over 150 participants were present from fourteen countries,
and included representatives from the Protein Data Bank
(Joel Sussman and S. Swaminathan), the Nucleic Acid Database
(John Westbrook), the Biological Macromolecule Crystallization
Database (Gary Gilliland), the International Union of
Crystallography Editorial Office (Brian McMahon), and the
mmCIF project (Philip Bourne).
Three broad themes relating to macromolecular crystallographic
data were interwoven throughout the ISMCD. The first related
directly to databases of macromolecular structure. The current
status and future plans of the PDB and the NDB were presented.
The PDB, in particular, is growing exponentially and very
rapidly. Ease of deposition, efficient validation of data, and
improved and more sophisticated access were addressed. The
Crystallographic Information File (CIF, now widely accepted and
used in the small molecule community) and the macromolecular
version (mmCIF) provide a standardized format and content
for data deposition that, in cooperation with the community of
programmers, should facilitate data deposition and data
validation. Eleanor Dodson described the overall CCP4 structure
and then focused on refinement strategies and indicators for
reliability and precision of refined structures. A lively
discussion, chaired by Guy Dodson, ensued on data deposition and
withholding of deposited data, especially structure factors.
Even with a one-year hold on coordinates and a four-year
hold on structure factors, concerns were expressed about
both the loss of intellectual property, especially to entities not
prone to releasing their own data, and the consequences
resulting from detection of major errors. Others stressed the
importance of depositing data in the PDB as a guard against loss
of data as well as the responsibility of scientists (and of
journals) to make available raw data ensuring that (re)analysis
of and comparisons among known structures and the development
of new insights are not stifled or restricted by non-availability
of data.
The importance of having available at least the coordinate
data from the PDB was underscored by the second theme of
the conference - the mining of databases for deeper insight
into macromolecular structure and function. Tom Blundell
described superfamilies containing proteins of weak sequence
homology but similar structure and general function, a topic
examined in detail by Ted Baker for the four-helix bundle
structure of cytochromes c' and by M. Vijayan for quaternary
association of lectins. A complementary perspective was
offered by Guy Dodson of the diverse and unrelated structure
types of the hydrolases in which catalytic triads share a
common mechanism of nucleophilic attack on amides, esters, and
related substrates. Databases underpin molecular modelling for
structure prediction (Tom Blundell and an alphabet soup of
programs for proteins, M. Bansal and N. Yathindra for
oligonucleotides); for structure solution by molecular
replacement (Jorge Navaza, M.R.N. Murthy, and K. Suguna);
for structure refinement and drug design (T. Bhat and
Jose Varghese); for virtual reality approaches (N. Seshagiri);
and for designer mutants (R. Varadarajan and P. Balaram).
Importantly, databases house information which in an individual
structure lacks statistical significance, but which when
repeated in many structures acquires validity, as exemplified
by the C(alpha)-H..O=C(main chain) hydrogen bonds found in beta
sheets (V. Pattahbi) and by the rarity of `unusual'
conformations (P. Balaram). In a series of hemoglobin structures,
the use of a common database of restraints and refinement
protocols revealed small but systematic and significant
structural effects of pH, with implications for the mechanism
of cooperativity (Guy Dodson).
The final theme involved additions of new structures to
macromolecular databases. Recent oligonucleotide structures were
presented by M. Sundaralingam (a novel U-U C-H..O hydrogen
bond), C. Betzel, and N. Gautham. Recent protein structures,
additional to the ones mentioned above, included bovine
cytochrome c oxidase - a monumental crystallographic achievement
(T. Tsukihara), beta-lactoglobulin revisited (Maria Bewley),
a Kunitz-type chymotrypsin inhibitor (J.K. Dattagupta), two new
species of lactoferrin (T.P. Singh), a double mutant of D-xylose
isomerase for which quantum chemical analysis provided insight
into the origins of metal specificity for effective catalysis
(Monica Fuxreiter), and the complex of acetylcholinesterase
with the snake neurotoxin fasciculin (Joel Sussman).
The scientific content was outstanding, from which only a
selection has been presented above. Location in India and
generous sponsorship from the IUCr provided opportunities
for attendance at an international conference by students
and post-doctoral fellows for whom attendance otherwise
would have been difficult. The strength, depth, and vitality of
structural biology in India was evident. Finally, the success
of the Conference was ensured by the organizing team
headed by J.K. Dattagupta (Saha Institute of Nuclear Physics
in Calcutta) and M. Vijayan (Indian Institute of Science
in Bangalore) through their meticulous attention to logistical
detail and an extraordinary level of hospitality extended to
all participants.
-----------------------------------------------------------------------
Targets for Protein Structure Prediction Results Now Available on WWW
This article was written by Tim Hubbard, Centre
for Protein Engineering, MRC Centre, Cambridge,
UK and Anna Tramontano, Istituto di Ricereche di
Biologia Molecolare, Pomezia, Rome, Italy
(th@mrc-cpe.cam.ac.uk).
Between July and September 1995, announcements were sent
to the PDB's Listserver mailing list inviting the submission of
protein sequences of unknown structure as prediction targets
for the IRBM practical course entitled Frontiers of Protein
Structure Prediction.
This Workshop was held from October 8-17, 1995 at the Istituto
di Ricereche di Biologia Molecolare (IRBM). One hundred thirteen
target submissions had been received by then and these were
automatically analyzed to screen for homologies to known
structures and provide raw material for the course. Of these,
twelve were predicted during the Workshop, at different levels
of detail.
The results of the analysis carried out on each of the 113 target
proteins, the detailed reports on the twelve predictions, a
short description of all the methods used, and the documentation
provided by each teacher are all now publicly available at the
URL http://www.mrc-cpe.cam.ac.uk/irbm-course95/. A large
amount of general documentation written for the course is also
available at this URL.
Our sincere thanks to all those who took the time to fill in the
forms to submit their sequences and apologies to those whose
sequences were not worked on during the course due to the
limited time available.
-----------------------------------------------------------------------
Notes of a Protein Crystallographer
- The Ballad of the 2.8 � Structure of SBMV
This article was written by Cele Abad-Zapatero, Abbott
Laboratories, Abbott Park, IL, USA (abad@abbott.com).
Most people would associate the term `ballad' with past
achievements which could go back as far as the origins of story
telling. It is certainly unusual to read or even hear this word
associated with contemporary scientific events. Even more so
for the solution of the three-dimensional structure of a
macromolecule: they are so commonplace nowadays. The scientific
journals are inundated with beautiful color pictures
advertising on their cover the solution of yet another protein
structure.
However, in the early nineteen seventies a modern research
project in structural biology reminded me of the mighty feats of
medieval heros. For nine long years, several generations of
valiant postdocs led by Professor M.G.R. struggled to adapt
the methodology of protein crystallography to the solution of
the atomic structure of the first icosahedral virus particle.
There were two other groups working on a similar endeavor.
One at Harvard led by Professor Steve Harrison, focused on
Tomato Bushy Stunt Virus (TBSV) - at the time the best
structurally characterized virus. A second in Uppsala, Sweden,
trying to solve the structure of Satellite Tobacco Necrosis Virus
(STNV), a very small satellite virus, under the aegis of
Professor Bror Strandberg.
The achievement established new methodology which is currently
used; and the results obtained opened intriguing lines
of research on the structure, function, and evolution of
viruses. As I worked on the project, the stanzas of a ballad
came to my mind as the most natural way to express my
admiration for the feat of all the participants. If you do not hear
from the other groups, it is not because their achievement
was less significant. Absolutely not; they simply did not have
their balladeer.
The virus of our story is Southern Bean Mosaic Virus (SBMV),
a humble RNA-containing plant virus which infects bean plants
in the South of the United States. Neither SMBV nor its
relative TBSV were ever as famous as the animal viruses that
are fashionable today as human pathogens. However, small
(approximately 300 � in diameter), nonenveloped, single-stranded,
RNA plant viruses like they, were easy to obtain in gram
quantities from a few infected plants. In addition, they were easy
to crystallize and consequently they were the object of a
concerted effort to obtain their atomic structure by X-ray
diffraction methods.
The icosahedral symmetry of small spherical viruses had been
proposed by Watson and Crick in the early fifties, and the
detailed arrangement of the proteins in the capsid on the
surface was described by Caspar and Klug in their classic
1962 paper. Nonetheless, there was yet no atomic model for
an icosahedral virus particle. As initially proposed by M.G.R.,
the crucial factor in the determination of the structure was the
presence of several identical copies of the polypeptide chain in
the asymmetric unit. In those days the major hurdle was to devise
algorithms and programs which would allow averaging of enormous
electron density maps, containing many millions of grid points,
over the redundant copies in the asymmetric unit.
One of the most striking results of the structure determination
of SBMV was the similarity of folds between the protein
capsids of SBMV and TBSV, and later STNV. This unifying
principle has had an enormous impact in understanding the
structure, function, evolution, and diversity of a wide spectrum
of viruses.
Someday I may have the time and space to print the entire ballad,
including the music. For this occasion, I would like to include
only a few stanzas to give the reader a sense of the innuendoes
of the text and of its rhythm and flow.
M.G.R. began to work on small viruses soon after the structure
of LDH had been published by taking a sabbatical leave in
Uppsala, in the laboratory of Bror Strandberg.
LDH has now been solved
I must find something to do
Rossmann fold has been proposed
I'll take a sabbatical leave (repeat)
And I'll look at the STNV.
Soon after the sabbatical leave, he started to work on SMBV.
Afternoon tea was a ritual at that time in the lab where the work
progress was discussed.
Shall we start by growing some crystals?
It's only a matter of weeks
After that we can write some proposals
For the future of SBMV (repeat)
You should drink your afternoon tea.
Although M.G.R.'s dream was to solve viruses ab initio, he soon
realized that heavy atom derivatives were a safer route at the
time. Of course, he continued to sail in Lake Freeman, Indiana.
Heavy-atoms must now be found
Playing chemists is all we must do
One alone will be safer ground
For the structure of SBMV (repeat)
I'm sailing the Indiana sea.
After eight years of work, the atomic model of SBMV slowly
grew as a metallic sculpture made up of Kendrew parts in a
forest of rods within a Richard's Box. M.G.R. kept bumping
his head against the top of the box, so he purchased a hard
hat which he rigorously wore for his building sessions with
me.
Eight years have already passed
Many people have done their best
I won't say the struggle has finished
For the structure of SBMV (repeat)
I'll buy a helmet for me.
The fold of SBMV turned out to be a beta-barrel almost identical
to the one already described by Steve Harrison for the structure
of TBSV.
After so many years of labor
All we have is a barrel of sheet
Steve H. did us a favor
With the structure of TBSV (repeat)
We can trace our SBMV.
The entire original text of the ballad was sung at a party at
the Rossmann's residence to celebrate the structure solution of
SBMV. The melody was adapted from a song by Pete Seeger that I
heard on the radio one beautiful autumn morning on my way to
the lab. The entire ballad was meant to be an homage to all
participants in the project of the three-dimensional
structure of SBMV. Many of them I have met through the years
at meetings and conferences. I shared with others hours of effort,
frustration, and excitement in the basement of the Lilly Hall
of Life Sciences at Purdue University, a unique laboratory whose
day-to-day routine is still masterly orchestrated by Sharon Wilder.
To all of them (the unsung heros of this ballad) and to many
others who participated in less visible ways, I would like to
express my deep appreciation: Sherin Abdel-Meguid,
Toshio Akimoto, J.E. (Jack) Johnson, Andrew G.W. Leslie,
Ivan Rayment, Michael Rossmann, Ira Smiley, Dietrich Suck,
Tomitake Tsukihara, and Mary Ann Wagner. I am just a modest
minstrel, the troubadour of this epic feat.
-----------------------------------------------------------------------
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