Open configuration options Second Workshop on Structural Molecular Biology (SMB) at SESAME

8. PERFORMANCE OF SESAME FOR STRUCTURAL MOLECULAR BIOLOGY

Herman Winick SSRL/SLAC/Stanford University

In the upgrade of BESSY I (0.8 GeV, 2 straight sections for insertion devices) to SESAME (1.0 GeV, 4 straight sections for insertion devices) particular attention was paid to optimizing source performance for structural molecular biology (SMB) and other applications using hard x-rays up to about 20 to 25 keV, while preserving performance for SMB and other applications at longer wavelengths including soft x-rays, VUV, and infrared (IR). A favorite photon energy for protein crystallography is the K-absorption edge of selenium at 12.66 keV, easily within the reach of the SESAME wigglers.
The resultant performance, including comparisons with higher energy storage rings, is described in the October 1999 Conceptual Design Report; the so-called Green Book. These show, for example, that in the hard x-ray range up to about 20-25 keV the performance of the SESAME wigglers is comparable to the best wiggler beam lines now operating on SPEAR (3 GeV) and DORIS (4.5 Gev), and to bending magnets on the NSLS 2.5 GeV ring. The basic parameters of SESAME responsible for this performance are summarized in the table below. More details are given in the Green Book.
Hard x-rays are provided by 7.5 T, 13 pole superconducting wigglers. Two of these are planned for initial implementation and each can provide hard x-rays to at least three experimental stations; one on the beam axis and at least two side stations. With a total of four straight sections available for insertion devices, one or two more such wigglers could be installed in the future as user demand requires.
For protein crystallography the relevant performance figure of merit is the number of hard x-ray photons that can be delivered to a small sample (typically about 200 microns in transverse dimensions) within a few milliradians of angular divergence (i.e., less than the mosaic spread of most protein crystals). By making the electron beam transverse size small (see table) it becomes possible to collect radiation with several milliradians of horizontal divergence and focus it (usually with 1:1 x-ray optics or with some demagnification) onto a protein crystal, delivering very high useful flux to small protein crystals. It is in this respect that SESAME compares so well with higher energy sources. This performance is available on the center experimental station of each superconducting wiggler. The other stations served by each wiggler produce very large total hard x-ray flux, but lower flux density due to the fact that the one meter long wiggler is viewed at an angle thereby increasing the apparent source size. These stations can be effectively used for biological studies using EXAFS and small angle scattering techniques.
Due largely to the high stored current and small electron beam source size, the SESAME bending magnets offer excellent performance for SMB applications with infrared radiation and with VUV and soft x-rays up to about 5 keV, comparable to or exceeding that produced by the bending magnets of other low energy rings such as the original BESSY I and the NSLS 750 MeV ring. Thus SESAME is a potent source of radiation that can support a world-class SMB program with radiation over a broad spectral range extending from infrared radiation with wavelengths as long as about 100 microns to hard x-rays with wavelengths down to about 0.5 Å .

SESAME PARAMETERS

1. Establishing a scientific program in structural molecular biology
   • Collaboration and cooperation amongst participants
   • A lot of work !!!!!
2. Focus on the scientific case
   • Identify global goals and perspectives
   • Identify scientific strength
   • Identify scientific needs
   • Identify key collaborations amongst members and internationally
   • Identify key personnel and champions
3. Establish the operational backend
   • SMB today is following a business model
   • SMB is the entry point into many related disciplines from basic molecular biology to structural genomics and structure-aided drug design
   • Establishing and operating a successful SMB center is not a cake walk
   • Planning and preparation of framework will eliminate large scale problems in the future
   • Champions will move forward and be ahead of the game
   • Champions are the ones who have the vision of the project in recognition of the importance SMB research using synchrotron radiation
   • With it has to come the realization that the operations of a SMB center is an operation that is very different from running an independent laboratory which can afford to mostly follow the needs and wishes of the Principle Investigator
   • in structural molecular biology

Appendix B; Workshop Announcement and Application Form top

SECOND WORKSHOP ON STRUCTURAL MOLECULAR BIOLOGY (SMB) AT SESAME
Sponsored by:

The University of Cyprus
The Cyprus Institute of Neurology and Genetics
The Planning Bureau of the Government of Cyprus
UNESCO
Date: December 6-7, 2000
Place: University of Cyprus, Nicosia Cyprus
Date of this announcement: October 28, 2000

Organized by:

Georgios Archontis, Univ. of Cyprus [archonti@ucy.ac.cy]
Spyros Skourtis, Univ. of Cyprus [skourtis@elgreco.ns.ucy.ac.cy]
Anastassis Perrakis, EMBL [perrakis@embl-grenoble.fr]
Peter Kuhn, Stanford Univ./SSRL [pkuhn@stanford.edu]
Ercan Alp, Cochair, SESAME Sci. Comm. & APS/Argon [eea@aps.anl.gov]
Herman Winick, Cochair, SESAME Sci. Comm. & SSRL/Stanford Univ. [winick@slac.stanford.edu]

Structural Molecular Biology (SMB) is expected to be the major scientific program pursued at the SESAME synchrotron radiation research facility. This is based on the experience at other facilities around the world and also the enthusiasm and interest expressed by scientists from SESAME member countries at the first workshop on SMB research at SESAME on April 6-7, 2000 in Athens. Optimizing the facility for SMB was a major objective in the design of the upgrade of BESSY I to SESAME. Equipped with 7.5 T multipole wigglers (critical energy = 5 keV), the new source has a spectral range which extends from the infra-red to hard x-rays. It also features high stored current (0.7A) and small electron beam source size (0.45mm x 0.03mm horiz./vert. 1 sigma values at the wiggler locations) which result in flux density on small samples such as protein crystals that are comparable to that provided by many higher energy rings. The SMB community in the Middle-East and Mediterranean Region (the Region) is now gearing up to fully utilize SESAME for SMB research as soon as the facility is completed in its new location in Allaan, close to Amman, Jordan. Exciting research opportunities will exist for SMB research mainly in four focus areas:

• Macromolecular Crystallography (PX)
• X-ray Absorption Spectroscopy (XAS).
• Use of Infra-red Radiation for Biology (IR).
• Small Angle X-ray Scattering (SAXS).

The report on the first workshop of the SESAME SMB Workshop in Athens summarizes the present level of SMB activity in SESAME member countries and the prospects for the future when SESAME is operational. It also contains a description of an SMB Institute to support this work, with equipment and staff support for SESAME users. The report of this workshop is available on the SESAME web site (www.sesame.org.jo). The first workshop concentrated on PX. In this second workshop we will include the other SMB focus areas and establish the details of a directed path enabling the research programs in the Region to fully utilize SESAME. In addition to planning for the four SMB focus areas, we will consider a visitor program and funding sources to establish an SMB Institute. We will also begin to identify scientists from SESAME member countries to play leadership roles.
We seek to have participation in the workshop by at least one scientist from each of the SESAME member countries. The total number of participants is limited to 25, including those invited from outside the Middle East region. Those interested in participating should fill out the form below and send it to all five of the workshop organizers. Future announcements will provide a tentative agenda and list of participants. Local expenses will be provided by the Planning Bureau of the government of Cyprus, the Cyprus Institute of Neurology and Genetics, the University of Cyprus, and UNESCO. Participants from SESAME member countries must provide their own air fare.

Application Form for SESAME SMB Workshop in Cyprus; December 6-7, 2000

Personal Data

Family Name:
Given Name:
Date of birth:
Nationality at birth:
Present Nationality:
Highest Degree Obtained:

Present or Most Recent Position Held

Title:
Department:
Institution:
Country:

Correspondence Address

Address:
City:
Country:
Zip Code:
Phone (office):
Phone (home):
Fax:
E-mail:

Curriculum Vitae, including a brief statement of activities relevant to SMB research

Appendix C: Workshop Agenda (as distributed prior to the Workshop) top

draft; November 21, 2000
Second SESAME Workshop on Structural Molecular Biology
To be held at: University of Cyprus, Nicosia Cyprus; December 6-7, 2000

Tuesday, December 5, 2000

19:00 Informal Dinner for participants who have arrived by this time

Wednesday, December 6, 2000

Session Chair:Spyros Skourtis, University of Cyprus

09:00-09:10 Welcome Remarks
09:10-09:30 Introduction of the Participants
09:30-10:00 Status of SESAME and its performance for SMB, Hernman Winick
10:00-10:15 The Role of UNESCO, Representative from UNESCO
10:15-10:30 Charge to the Workshop, Peter Kuhn
10:30-11:00 Break

Session Chair: Georgios Archontis, University of Cyprus

11:00-11:15 Samuel G. Haroutiunian, Yervan State University (Armenia)
11:15-11:30 Georgios Archontis, Spyros Skourtis, Univ of Cyprus (Cyprus)
11:30-11:45 Zein El-abidin Kamel Heiba, Ein Shams University (Egypt)
Karimat El-abidin kamel Heiba, (Ein Shams Univ.)
11:45-12:00 Metaxia Vlassi, N.C.S.R "Demokritos" (Greece)
12:00-12:15 Nazarin Moazami, IROST (Iran)
12:15-12:30 Irit Sagi, Joel Sussman, Weizmann Inst. (Israel)
12:30-14:00 Break
14:00-14:15 Sami Mahmood, Yarmouk University (Jordan)
14:15-14:30 Abdel-aziz Soukari, Hassan II University (Morocco)
14:30-14:45 Elsadig Eltayeb, Sultan Qaboos University (Oman)
14:45-15:00 Nael Hasan, Birzeit Univ.
Said Assaf, Arafat National Scientific Center for Applied Research
(Palestinian Authority)
15:00-15:15 Zehra Sayers, Sabanci University (Turkey)
15:15-15:45 Lunch Break

Session Chair: Keith Watenpaugh, Pharmacia Corporation

15:45-16:15 Infra-red, Irit Sagi
16:15-16:45 Small Angle X-ray Scattering (SAXS),
Bob Batterman and Zehra Sayers
16:45-17:15 BreaProtein Crystallography-State of the Art and What is Next,
Peter Kuhn
17:15-17:45 Macromolecular Crystallography in a Multi-National Environment, Tassos Perrakis
17:45-18:15 EXAFS, James Penner-Hahn
19:00 Dinner Break

Thursday, December 7,2000

Session Chair: Herman Winick, SSRL

09:00-9:30 An SMB Institute at SESAME,
Pierre Rizkallah and Metaxia Vlassi
9:30-10:00 Discussion
10:00-10:45 Parallel Sessions [Group Leaders] on
PX, Keith Watenpaugh and Pierre Rizkallah
EXAFS, James Penner-Hahn
IR, Irit Sagi
SAXS, Bob Batterman and Zehra Sayers
10:45-11:15 Break
11:15-12:30 Parallel Sessions Continue
12:30-14:00 Lunch Break

Session Chair: Peter Kuhn

Appendix D: FIRST ANNOUNCEMENT - SESAME WORKSHOP

Bioinformatics and Structural Modelling

Dates: September 3-9, 2001
Location: Sabanci University, Istanbul Turkey
Organizers: Z. Sayers (Turkey), I. Sagi (Israel) and M. Vlassi (Greece)
Sponsored by: Sabanci University, UNESCO

Background and Objectives

In its broadest sense bioinformatics deals with the creation and development of information and computational technologies for problems in molecular biology, biochemistry and biophysics. Availability and rapid accumulation of DNA sequence data have resulted in coordinated efforts to enhance the capacity to critically evaluate and utilize this data. Effective use of sequence-based information would reveal previously unknown relationships - ranging from the identification of unknown genes to the prediction of protein structures. Currently, parallel to improvements in experimental methodologies for faster structural data collection and analysis, computational tools are being developed with the aim of predicting structures and elucidation of structure-function relationships as well as drug design. Particular emphasis is given to computational tools for determining sequence homologies, phylogenetic trees and prediction of 3-D structure of biological molecules.

Following the Sesame Workshop on Structural Molecular Biology (Cyprus December 6-8, 2000) on experimental techniques of structure determination using synchrotron radiation, the present workshop aims to focus on a complementary area, namely computational tools that are used in structure analysis. It is planned as lectures and practical sessions where students from SESAME member countries will have the opportunity to gain hands-on experience in using web-based tools for sequence and structural analysis and modelling.

Specific topics for practical sessions

• Introduction to primary, secondary and tertiary structure and related databases
• Introduction to graphics programs for sualization of 3D structure of proteins
• Secondary structure prediction and related tabases and software
• Homology searches and alignment strategies
• Homology modeling of 3D structure of proteins and related databases and software

Tentative partial list of lecturers/working group leaders (some not confirmed)

C. Baysal (Turkey), M. Edelman (Israel), E. Eliopolos (Greece), D. Lancet (Israel), S. Mobashery (USA), I. Sagi (Israel), Z. Sayers (Turkey), U. Sezerman (Turkey), M. Vlassi (Greece), A. Yonath (Israel), P. Zielenkiewicz (Poland)

For application forms and details of financial support please contact

Professor Zehra Sayers, Email address: zehra@sabanciuniv.edu 2/28/01