Reports

Budapest Biostruct Course 2013: Basics in Protein Crystallization and Crystallography

August 30 – September 3, 2013, Budapest (Hungary)

The first BioStruct-X supported course at the Hungarian BioStruct-X TID centre took place from August 30th to September 3rd 2013 at the Budapest University of Technology and Economics CH building (Biostruct Laboratory). The course was attended by 22 students from the following countries: Slovenia, Croatia, Romania, Czech Republic, Lithuania. Poland, Hungary, France, Spain and Portugal.

The aims of the course were to cover basics in macromolecular crystallization and crystallography, facilitate the initiation and success of X-ray structural biology projects and inform the scientific community about current potentials in structural biology in Europe
 

INSTRUCT and BioStruct-X Training Course “Structure and function of membrane proteins - a multidisciplinary approach”

MembStruct2013, Oeiras (Portugal) – 5th to 8th November, 2013

The Masterclass “MembStruct2013” addressed several techniques within a multidisciplinary approach to the structural and functional characterization of membrane proteins and membrane protein complexes. Organized by Margarida Archer and José Artur Brito (from ITQB-UNL), and Carlos Cordeiro and Ricardo Gomes (FC-UL), “MembStruct2013” trained the participants in the different approaches to membrane proteins characterization and analysis.

Aimed primarily at PhD students and young Post-Doctoral researchers, 20 out of 30 applications were selected to attend the Masterclass. Participants came from Austria (1), Belgium (2), France (1), Germany (2), Ireland (1), The Netherlands (1), Norway (1), Portugal (2), Spain (2), Sweden (1), UK (5), and USA (1). The course was organized with lectures in the morning and tutorials in the afternoon and we think that this format was a surplus for the quality and success of the Masterclass. The lectures took place in the ITQB auditorium, were widely divulged within the scientific community and were also attended by other researchers.

 

The tutors/lecturers were selected by their recognized expertise in the field of research. We had the privilege of having Professor Werner Küelhbrandt (Max-Planck-Institut für Biophysik, Frankfurt, Germany), Professor Marc Baldus (Bijvoet Center for Biomolecular Reseacrh, Utrecht University, The Netherlands), Doctor Jens Preben Morth (Centre for Molecular Medicine, Norway - Nordic EMBL Partnership Molecular), Doctor Julian Langer (Max-Planck-Institut für Biophysik, Frankfurt, Germany), and Professor Pedro Fernandes (Instituto Gulbenkian de Ciência, Oeiras, Portugal), giving excellent lectures and orienting the tutorials on Electron Microscopy, Nuclear Magnetic Resonance, Macromolecular Crystallography,Mass Spectrometry and Bioinformatics, respectively. Besides these main speakers, which made a significant effort and contributed to the high-level quality of the course, we also had the talks of four portuguese researchers presenting their work related to the Masterclass topic (check the attached program for details). The students made flash presentations on the afternoon of the first day, where they had the chance to present their work briefly and discuss it.

Both speakers and students stayed in the same hotel, thus providing time to mingle and have informal discussions about specific questions of their work. There was also time for poster discussion during lunch break and sometimes coffee-breaks. We also had a social dinner with folk dancing, where participants were defied to join the dancing, and all did it very well.

 

Second Course held at TID Centre OULU: “Practical X-ray course on Protein Crystallographic Methods: Data collection, Data Processing, and Phasing”

Oulu, 16th - 20th September 2013

The second Oulu BioStruct-X course on X-ray data collection methods was organized by Rik Wierenga, Tiila Kiema, Kristian Koski, Evangelia Kapetaniou and Lari Lehtiö on September 16-20, 2013, together with Biocenter Oulu.

The course focused on data collection and data processing, using both in-house equipment as well as synchrotron radiation. The course was attended by 16 active students from Finland, Sweden, Germany, Spain, The Netherlands and Russia. The external teachers of the course were Severine Freisz (Bruker), George Sheldrick (Göttingen), Andrey Lebedev (CCP4), and Pierre Aller (Diamond). The course consisted of lectures, practicals in the linux computer class room, as well as practicals on crystal handling, crystal freezing and data collection using our Microstar Proteum X8 data collection unit.  All students collected data from lysozyme crystals and several students collected data from their own crystals.  All students were subsequently able to process their data in our linux class room with the Proteum2 package. One lecture on basic concepts of the protein crystallographic methods was included in the program. The data collection and data processing activities were complemented by lectures and tutorials on phasing methods, either by experimental phasing (SHELXD of the SHELX suite) as well as by molecular replacement (Phaser, Molrep, Ample of the CCP4 suite)

On the last day of the course there was a demonstration of the in-house developed xtalPiMS software for viewing of crystallization results and for preparing shipments to Diamond. Also a very successful remote data collection session at Diamond was organized for the students.
Altogether the course provided an excellent opportunity for the 16 students to get to know more about the state of the art of the methods in protein crystallography. There was much time for working in the linux class room and for discussions between the students and the tutors.  The feedback provided by the students confirmed the continuous importance of such courses for providing opportunities for better understanding of the basic aspects as well as for learning more about the latest developments in protein crystallographic methods.
 

Sixth BioCrys Course held at the ITQB

Oeiras, 20th - 27th October 2012

The sixth BioCrys Course on 'Fundamentals of modern methods in biocrystallography, organised by Maria Arménia Carrondo (ITQB Oeiras, Portugal) and Thomas Schneider (EMBL Hamburg, Germany) took place at the Instituto de Tecnologia Química e Biológica in Oeiras (Portugal) from 20-27 October 2012. The course was supported by FEBS, IUCR, Biostruct-X and IUBMB. It brought together 38 students from 19 different countries and 20 tutors from 9 different countries. Subtitled 'What you always wanted to know about crystallography but never dared to ask', the course aimed at teaching the fundamental concepts of macromolecular crystallography to scientists in the early stage of their crystallographic career. This is particularly important as the field is developing very rapidly and because many young researchers do not receive a formal education in Crystallography. In fact, while learning the efficient use of automated tools in crystallography, it is also critical to understand the underlying concepts for tackling difficult problems of structural biology that are not amenable to the current generation of these tools. Lectures and tutorials covered topics all the way from the cooling of crystals to the validation of the final structural model. A typical day began at 9:00h with a 15 min. recapitulation of the concepts discussed during the previous day given by Thomas Schneider. Lectures ran from 9:15h to 13:00h and interactive practicals and tutorials from 14:00h to 17:30h.

Although the program was extensive, there was plenty of opportunity for all participants to interact outside the formal program of the course. In particular, the fact that all participants were staying in the same hotel provided a good environment to mix and to talk to each other, not necessarily always about crystallographic subjects. We thank our sponsors for the support that made possible to organize the sixth edition of this course on the fundamentals of crystallography. All speakers/tutors are thanked for their dedication and their continuous commitment to this course.

 

Computational Tools Workshop held at the Weizmann Institute of Science

Rehovot, 2nd - 6th September 2012

Course participants on a tour of Jerusalem

The Weizmann Institute of Science held a ‘hands-on’ workshop on “The use of Computational tools for Modeling of Multi-molecular Assemblies and protein design” from 2-6 Sep-2012 at the Weizmann Institute of Science, Israel, where 18 students from 8 different countries took part.

The course consisted of a series of lectures followed by hands-on tutorials where the participants could learn in depth the use of various new computational methods (algorithms) and programs that they were learning. The worship was organized by Prof. Gideon Schreiber, of the Weizmann Institute of Science, and the lecturers were Prof. Haim Wolfson (Tel-Aviv University), Dr. Sarel Fleishman, Dr. Jaime Prilusky and Prof. Joel L. Sussman (Weizmann Institute of Science).

The goal of the workshop was to introduce the participants to state of the art computational methods (algorithms) for the following tasks; 1) Modeling of macromolecular assemblies based on experimental information obtained from various sources. This includes docking and the assembly of large macromolecular structures, 2) Learning to use the Rosetta macromolecular modeling suite with a focus on the design of molecular recognition, 3) Learn how to use Proteopedia to create WEB pages of macromolecular structures and their functions.

 

First course held at the BioStruct-X TID centre in Oulu

Oulu, 30 January - 3 February 2012

20 students from across the world took part in the Data to Structures course held at the Department of Biochemistry at the University of Oulu in Finland from the 30th January to 3rd February 2012. The 5 day course included lectures, demos and hand-on tutorials. The stimulating atmosphere made for lively discussions and a very successful course.

The course program began with lectures on key aspects of protein crystallographic methods before moving onto topcis of data collection, including a data collection demonstration using the institute’s new Bruker microstar setup as well as a demonstration of remote data collection at Diamond Light Source (UK). The data processing lectures and tutorials were on XDS, iMOSFLM and PROTEUM2. The program also included a lecture on solving the heavy atom substructure, with the SHELX suite of programs, as well as CCP4MG and PiMS/XtalPiMS. These topics were also covered by lectures and tutorials.

The participants were very active and the feedback given reflected their enthusiasm. Several students bought their own data with them to work on with the tutors, and would have liked even more time to discuss their work. Rik Wierenga and his team at Oulu were satisfied with the event and have collected food for thought on how to make future events even more successful.  

 

 

 

 

 

 

 

 

 

 

 
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BioStruct-X is part of the Capacities Specific Programme Research Infrastructures, Project Number 283570
BioStruct-X contact: biostructx(at)embl-hamburg.de, I. Custic, ph: +49 - 40 89902 124, fax: +49 - 40 89902 149

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