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STRUCTURE AND FUNCTION FROM MACROMOLECULAR CRYSTALLOGRAPHY:
ORGANISATION IN SPACE AND TIME
The Advanced Study Institute “Structure And Function From Macromolecular Crystallography: Organisation In Space And Time" was held in Erice, Italy at the Ettore Majorana Foundation and Centre for Scientific Culture from 3 to 13 of June 2010. The course counted with 137 total participants from various countries. The programme included 39 lectures given by invited speakers and senior participants, and 12 workshops. 92 posters were presented, preceded by short oral presentations by the presenting author.
The main objective of the Institute was to train the younger generation on advanced methods and techniques to discover relevant structural and dynamic aspects of biological macromolecules. The course reviewed the techniques used to study protein assemblies and their dynamics, including X-ray diffraction and scattering, electron cryo-electron microscopy, electro nanospray mass spectrometry, NMR, protein docking and molecular dynamics.
The quality of all lectures was of a very high standard, since the speakers were among the top leaders in the world on the corresponding subject. The scientific programme of the Institute was organized in several blocks according to a main topic: Assemblies, covered by Tom Blundell (UK), Ken Holmes (Germany), Maria Arménia Carrondo (Portugal); Membranes, covered by Bob Stroud (USA), Werner Kuhlbrand (Germany), Ermanno Gherardi (UK/Italy); Imaging, covered by Janos Hadju (Sweden); Ribosomes, covered by the three Nobel Laureates of 2009, Ada Yonath (Israel), Tom Steitz (USA), Venki Ramakrishnann (UK) and also Nenad Ban (Switzerland); Cryo-Electro Microscopy, covered by Helen Saibil (UK), Wolfgang Baumeister (Germany); Mass Spectrometry, covered by Justin Benesch (UK); Dynamic Assemblies, covered by Helen Saibil (UK), Ammon Horovitz (Israel); Viruses-Large Particles, covered by David Stuart (UK), Nuria Verdaguer (Spain); Small Angle Scattering, covered by Dmitri Svergun (Russia) and Signalling covered by Louise Johnson (UK) and John Kuryan (USA).
Twelve workshops on data bases and software developments were an important part of the school: Protein Interactions by Richard Bickerton, CCP4 set of programs by Garib Murshudov, Proteopedia by Eran Hodis, Jaime Prilusky and Joel Sussmann, ARP-WARP by Tassos Perrakis, SHARP/AutoSHARP by Clemens Vonrhein, Large Assemblies by Dima Chirgadze, Cryo-EM images by Carsten Sachse, Crystallisation by Terese Bergfors, MODELLER and IMP by Ben Webb, COOT by Paul Emsley, Molecular Dynamics by Michele Vendruscolo and Virtual Screening by John Irwin.
After the school, a detailed anonymous questionnaire was filled in by most participants to obtain their evaluation and assessment on its importance and success. Overall 54% of the participants considered it very important and 30% even as of essential importance. In terms of success, 62% considered it very successful and 64% as very successful providing an overview of the most recent results in the field. Also 80% of the respondents considered that the selection of the speakers as the best available in the field, while 86% this opportunity as a very successful opportunity for young participants to exchange experience with each other during informal discussion and 78% as a very successful opportunity to meet experts in the field. Finally and on a scale of 0 – 100, the participants gave an overall score of 91 to the meeting.
A complete report of the answers to the questionnaire can be found here.
The Advanced Study Institute “Structure And Function From Macromolecular Crystallography: Organisation In Space And Time" focused on the role of macromolecular crystallography and other complementary techniques in studying spatial and dynamic nature of macromolecular assemblies and their roles in living organisms. The major themes and “take home” messages of the School were as follows:
Macromolecular assemblies are central to the machinery of cell
regulation and growth. They play roles in cell signaling, translocation of
molecules and movement of cells, DNA replication and transcription and translation,
and protein degradation. Indeed it has been estimated that 70% of proteins
form complexes with a composition averaging 5 proteins. Many, particularly
cell surface receptors and signal transduction complexes, are transient with
assembly and disassembly carefully regulated. Others, like polymerases, ribosomes,
exosomes and muscle, are machines, large parts of which are preassembled.
2. EXPERIMENTAL APPROACHES TO DEFINING STRUCTURE AND DYNAMICS
Although the main experimental focus was on crystallographic approaches, the School explored the need to understand both dynamical and spatial aspects of the organisation of macromolecular assemblies.
2.1. X-RAY CRYSTALLOGRAPHY: Remains the most powerful technique for large and complex structures. Low-resolution structures are often obtained due to the inherent flexibility and dynamics of the systems. Low solvent contrast continues to make their analysis a major challenge, especially where molecular replacement in reciprocal space is attempted. There is an urgent need for new approaches to modelling in real space into low-resolution electron density.
2.2. CRYO-ELECTRON MICROSCOPY: Single particle reconstruction methods using cryo-em are playing a major role in defining structures of assemblies and their dynamic nature. Resolution approaches 3Å in the best-ordered structures. Methods for separating different populations of assemblies are central to progress, and fitting of individual structures obtained by NMR and X-ray methods remains an important challenge. Cryo-electron tomography is making huge contributions to understanding the organization of assemblies in their cellular settings. A critical limitation is specimen thickness; only prokaryotic cells or thin regions of eukaryotic cells can be investigated, larger cells or tissues must be sectioned before EM. The ultimate goal is a pseudo-atomic atlas of the inner space of cells. Now alternative micromachinery for frozen-hydrated material is developing, and first encouraging results using this technology are being reported.
2.3. SAXS: SAXS is not limited by the need of crystals or the molecular mass of the protein sample and permits quantitative analysis of complex large systems and processes. The dynamics of many complex and transient assemblies, for example in DNA double-strand break repair are being studied.
2.4. IMAGING: Free Electron Lasers will enter a new stage, in the near future, with 1 Å X-rays shots at LCLS.
2.5. BIOPHYSCICAL METHODS: X-ray crystallography, EM and SAXS are critically dependent on the other biophysical methods like circular dichroism and NMR to define correct folding of components and complexes, and nanospray mass spectrometry to define stoichiometries of complexes and larger assemblies. Isothermal Calorimetry (ITC), which measures enthalpy in complex formation, is playing an increasingly central role in defining stoichiometries, association constants and free energies, and entropic contributions. Surface Plasmon Resonance can estimate dynamics by measuring on and off rates, from which equilibrium constants can be estimated.
2.6. MASS SPECTROMETRY: Collision induced dissociation allows the identification of the individual components of assemblies and quantifies their relative abundance; Ion mobility spectrometry leading to 2D MS; Combination of MS plus EM as a powerful tool to get good insights into the stoichiometry and shape of large assemblies.
3. CLASSES OF MACROMOLECULAR ASSEMBLIES
3.1. MEMBRANE PROTEINS: Discontinuous helices are active in ion translocation mechanisms; Addition of antibody fragments can be used to trap different conformations and could possibly lead to higher resolution; Structure of complex I gives new insights into the proton pumping mechanism; The power of electron-tomography has a unique ability to put molecular detail into cellular context, as shown with ageing of mitochondria; The ultimate goal with electron-tomography is a pseudoatomic atlas of inner space of cells; Cell surface signalling requires mechanisms of specificity, clustering and localization control; Protein engineering has a huge potential for the development of new therapies; The structure of ß2- AR receptor with an antagonist used chimeric crystals with lysozyme and antibodies.
3.2. SIGNALLING: Structural studies of cyclin-dependent kinases that regulate cell cycle have been extensively studied and have been used to design inhibitors that target the active and inactive states and protein-protein interactions; The power of X-ray structures when combined with EM data and also other methods such as MS, can allow the interpretation of the APC assembly and the functional contribution to the assembly of various subunits.
3.3. RIBOSOMES: Historic overview; New methods appeared as a result of ribosome crystallization: cryo-cooling, heavy atom cluster derivatives; Fascinating movies; Antibiotic targets – structure-based drug design; Molecular snapshots of various intermediates of the translational process in atomic detail revolutionized our understanding of the mechanism of protein synthesis; Striking advance in field: follow translation by single ribosomes using mRNA hairpins tethered to optical tweezers. Structural studies of SRP assembly and function in archeae reveal some insights into the mechanism of signal-sequence binding.
3.4. CHAPERONES: Progressive conformational changes of GroEL were mapped using Cryo-EM allowing the understanding of this molecular machine as a promoter of protein folding; FRET and EM studies with chaperonins showed that the concerted mode is the preferred mechanism to assist protein folding of single domain proteins while the sequential one is preferred for multi domain proteins; Developments with NMR and MD methodologies allow the detection of transient states with a low relative population.
3.5. VIRUSES – LARGE PARTICLES: Rational
structure based design for improved vaccines is grossly unexploited - used
in virus field and in other areas; Vaults as nano containers can be used in
the near future to deliver drugs. Structure based drug development against
HIV reverse transcriptase may anticipate virus resistance.