Molecular Machines: Lessons from Integrating Structure, Biophysics and Chemistry

T. Carlomagno, J. Chin, J. Puglisi
EMBL Heidelberg, Germany
Sunday 18 May - Wednesday 21 May 2014

Why attend

Topics

• Dynamical machines in cell division
• The spliceosome
• Molecular complexes in gene expression regulation
• The transcription machinery
• Membrane transporters
• Signaling network
• Nuclear trafficking and localisation
• Role of omics in understanding molecular mechanisms

Summary

The conference programme is designed for biochemists, molecular and structural biologists who are interested in molecular machines. It should provide an overview of how structural biology, and more generally biophysical techniques can be applied to different biological problems. The techniques covered in the programme include classical high resolution structural biology techniques such as electron microscopy, crystallography and nuclear magnetic resonance spectroscopy, as well as fluorescence, mass spectrometry, small angle scattering and chemical biology.Â

Aims

The aim of the conference is to show the interdisciplinary nature of the diverse experimental approaches and promote a modern way of thinking, where barriers between specific expertises are crossed. The sessions are organised according to the biological questions, ranging from gene expression to cell division. Experts in the different techniques will present their work back to back, showing the multiplicity of routes that can be followed to understand molecular machines in the cell.

ICM Workshop: Protein Structure and Drug Design

Conducted By

• Ruben Abagyan Ph.D. (Professor UCSD and MolSoft Founder)
• Maxim Totrov Ph.D. (Principal Scientist, MolSoft LLC)
• Andrew Orry Ph.D. (Senior Scientist, MolSoft LLC)

Workshop Content Summary

The workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery, molecular modeling, and bioinformatics. No prior knowledge in this field is required to participate in this workshop. The workshop will consist of lectures, demonstrations, and "hands-on" experiments covering the following topics:

• Molecular Graphics and Displaying Interactive Molecules in PowerPoint and the Web using ActiveICM.
• Sequence and Protein Structure Analysis.
• Protein Modeling and Simulations.
• Structure Validation and Optimization.
• Ligand Binding Site Prediction.
• Protein-Protein Docking.
• Small Molecule Docking and Virtual Ligand Screening.
• ICM 3D Interactive Ligand Editor.
• Structure-based development of target-specific compound libraries.
• Cheminformatics: chemical clustering, searching, superposition etc...
• QSAR

Synchrotron radiation has become an indispensable tool for many macromolecular crystallography groups. Some synchrotron-specific skills are difficult to learn without ones having an intensive hands-on training program. But not all research groups have the luxury of providing long training sessions for students and postdocs. To provide such an educational experience, we have designed a course in Rapid Data Collection and Structure Solving.

Related Information

• RapiData Header Image: View | Download | About (pdf)
• Previous Course Pictures:Â 2013Â |Â 2012Â |Â 2011Â |Â 2010Â |Â 2009Â |Â 2008Â |Â 2002-2007
• Brookhaven National Laboratory: View Videos (YouTube)

Sponsors

This course is sponsored by a grant from the Biomedical Technology Research Centers (BTRC) of NIH's National Institute of General Medical Sciences (NIGMS) to Photon Sciences and the Biosciences Department at Brookhaven, and in part by support from the Department of Energy Office of Biological and Environmental Research.

We also thank the International Union of Crystallography and Brookhaven Science Associates for financial assistance for this course.

Macromolecular Crystallography School 2014

"From data processing to structure refinement and beyond"

April 8th - 16th, 2014 Instituto de Física de São Carlos/USP, São Paulo, Brasil
Intended for advanced PhD students, postdocs and young scientists Theoretical and in-depth tutorial training on state-of-the-art methods in macromolecular crystallography
Main Topics

• Diffraction data processing
• Phasing and structure determination
• Model refinement and validation

Organised by IOP Biological Physics Group, IOP Liquids and Complex Fluids Group, IOP Molecular Physics Group and IOP Polymer Physics GroupÂ

Co-sponsored by the British Biophysical Society, European Biophysical Societies' Association (EBSA), European Physical Society (EPS) and Society of Biology
This conference will bring together the broad and diverse community interested in the physics of soft and biological matter, which includes liquids, liquid crystals, polymers, colloids, membranes, interfaces, cellular biophysics, and biological macromolecules.
The programme will span a number of key cross-cutting themes, including self-assembly and patterning, rheology, biomimetics, non-equilibrium phenomena, as well as molecular imaging, optical methods and spectroscopies, which are all relevant to the wide range of length- and time-scales present in these fascinating systems.

WORKSHOP - "The Best of Crystallography in 180 minutes!"

Instructor: Dr Teresa Santos SilvaÂ

Day 1 - Saturday, April 12, 2014

9:15 a.m. and 10:00 am Introduction to X-ray crystallography.
Basics of crystallization and resolution structures of biomolecules.
10h00-10h45 Preparation and visualization of protein crystals under the microscope ( hands-on ).

Day 2 - Sunday, April 13, 2014

9:15 a.m. to 9:45 a.m. Refinement and validation of crystallographic structures.
9:45 a.m.-10.45
Construction and validation of the model using the GUI ( coot , molprobity )

• On both days there will be protocols to follow with programs in order to facilitate the processing and analysis of data.
• 1st day of classes will be held in the Department of Chemistry and the 2nd day in a computer room, the Ed VII, limited to 16 registrants.

Â

« Evolution, biogenesis and dynamics of energy transducing membrane»

House of the Oceans - Oceanographic Institute Foundation Albert 1er, Prince of Monaco, Paris, France.
Three main themes will be developed:

• Evolution of protein translocation systems and gene expression
• Biogenesis of membranes and energy transducing proteins
• Supramolecular organization and modeling of power converters systems

EMBO Practical Course on Computational Structural Biology - from data to structure to function

Venue: European Bioinformatics Institute, CB10 1SD, United Kingdom

Overview

This course aims to teach computational aspects of protein structure determination, validation and analysis. It will cover the background of different structural biology techniques and provide hands-on experience in building a model from X-ray diffraction data. In addition, participants will learn how to critically assess the quality of data and models, and gain expertise in the integration and visualisation of data from different techniques, thus enabling the analysis of protein structure data for functional relationships. The importance of protein structure to drug discovery will also be illustrated with sessions dedicated to small-molecules, protein-ligand docking and model validation.

Audience

This course aims to teach computational aspects of protein structure determination, validation and analysis to PhD students and post-docs working on the collection and analysis of protein structure data. The course will be highly interactive and will include many practical sessions. Attendees are strongly encouraged to bring their own data and ideas of work to be addressed during these sessions.

Strategic pipeline planning: from sample preparation to 3D structure determination with bio SAXS and other biophysical techniques

The location will be at the National Hellenic Research Foundation (NHRF).
The course will provide training on creating a roadmap towards determining the 3D structure of a macromolecular target including troubleshooting and rational decision-making. Emphasis will be given on Bio SAXS as a method of choice to characterize the structure of a single protein and protein complexes in solution coupled with X-ray crystallography, NMR spectroscopy, and electron microscopy (EM). An overview of mainstream methods will also be presented and attention will be drawn to techniques developed the last years like X-ray imaging. In addition, the participants will have a chance to get informed about the options they have for career development. Overall, the course will enable the attendees to adopt a broader way of thinking and get acquainted with state-of-the-art approaches currently employed in structural biology. This will increase researchers' awareness on the facilities and services provided and capitalize on the investment that has already been made by Europe with the aim to promote innovative research.
Target Group & Selection process: The course targets mainly PhD students and post-doctoral scientists who are currently working in the structural biology field and have already some experience in working with macromolecules. Experienced researchers will also be considered but priority will be given to younger scientists. A total of 25 participants will be accepted in the course. The applicants will be expected to send a CV (max. 2 pages), a motivation letter (max. 1 page) explaining why they wish to participate and what they expect from the course and a reference letter. The Biostruct-X and local organizers will be responsible for the selection process to ensure that equivalent criteria will be applied.

G Protein-Coupled Receptors: Structural Dynamics and Functional Implications (Z1)

joint with the meeting on Frontiers of Structural Biology (Z2)

Scientific Organizers: Christopher G. Tate and Fiona H. Marshall
March 30-April 4, 2014 Snowbird Resort, Snowbird, Utah, USA

Keystone Symposia on Molecular and Cellular Biology

Meeting Summary

G protein-coupled receptors are essential for intercellular communication in multicellular organisms and they are also the targets for many drugs already in use or under development, for the treatment of, for example, cardiovascular disease, asthma, cancer, neurological dysfunction and metabolic disorders. The field of GPCR biology has undergone a radical transformation with the structure determination of over 15 different GPCRs, including the first complex of an activated GPCR bound to a heterotrimeric G protein. This wealth of structural detail is now being translated into both a deeper understanding of GPCR function and into the development of new therapeutics. Structure is, however, only capable of defining atomic details of particular conformational states of a receptor. This meeting will focus on how an integration of structural data and information from experiments that study molecular dynamics in vitro, in vivo and in silico can be integrated to form an in-depth view of GPCR function. In addition, key therapeutic areas of cancer, inflammation and disorders of the central nervous system will be highlighted in relation to the development of novel therapeutics targeting GPCRs.

Ligand Recognition & Molecular GatingÂ

Structure and Dynamics of Ion Channels, G-Protein Coupled Receptors, and Solute Transporters

March 23-28, 2014Â

Four Points Sheraton / Holiday Inn Express
Ventura, CA

• Chair: Dirk Jan SlotboomÂ
• Vice Chair: Crina Nimigean

 Scope

This conference aims at reiterating the success of the first "international school and conference on biological materials science (Bio-inspired Materials)" which took place in March 2012 in Potsdam. At the same place and at a similar time of the year from March 18-21 2014, we will cover recent advances in all areas of biological materials science and, in particular, in the field of bio-inspired materials. Scientists with diverse backgrounds will discuss new results about structure and function of natural materials and the ways in which those may influence the bio-inspired design of engineering materials and systems. The meeting will cover experimental characterization and theoretical modeling of structure-property relations, as well as concepts and strategies for the fabrication of bio-inspired materials with unusual combinations of properties or capabilities to self-assemble, self repair and/or evolve. Because material properties can be critical for the biological function of molecules, tissues and organs, the conference will also address materials science approaches which contribute to some areas of biology or medicine.
The conference will host several invited keynote lectures, oral as well as poster contributions. The Conference will be preceded on March 17-18 by satellite meetings of two related research programs of the German Science Foundation, the DFG Programs SPP1420 (Biomimetic Materials Research: Functionality by Hierarchical Structuring of Materials) and SP1569 (Generation of multifunctional inorganic materials by molecular bionics).

Structural Biology Symposium

When:Â Mar 17, 2014Â

from 10:00 AM to 05:00 PM Â

Venue: Campus Gasthuisberg, building O&N2, auditorium BMW2

Programme

10:00 Welcome
10:05 Sergei Strelkov (KU Leuven): “Facilites for biomolecular crystallography in Leuven”
10:30 Chris Ulens (KU Leuven): “Structural studies on ligand-gated ion channels”
10:55 Eveline Lescrinier (KU Leuven): “Solution NMR on modified nucleic acids”
11:20 BIOMED Distinguished Lecture by Michael G. Rossmann, Hanley Distinguished Professor of Biological Sciences, Purdue University, USA: “A personal history of structural virology: from haemoglobin to paramyxoviruses”
12:20 Lunch break (served)
13:15 Jan Steyaert (VIB-VUB) “Nanobodies as tools for the structural and functional investigation of GPCR transmembrane signaling”
13:45 Christian Ottmann (TU Eindhoven) “A structural view on small molecule modulation of protein-protein interactions”
14:15 Michelle Heirbaut (S. Strelkov lab) “Structural and functional studies of human small heat-shock proteins”
14:35 Elke De Zitter (L. Van Meervelt lab) “Rational design of fluorescent proteins using X-ray diffraction”
14:55 Coffee
15:20 Kenneth Verstraete (U Gent) "Structural basis of the pro-inflammatory signaling complex mediated by TSLP"
15:40 Abel Garcia-Pino (VIB-VUB) “The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu”
16:00 Xiaohua Zhou (P. Declerck lab) “Elucidation of the molecular mechanism of a nanobody that inhibits TAFI activation”
16:20 An Van den Bossche (R. Lavigne lab) "Shutdown of the Pseudomonas RNA degradosome by bacteriophage phiKZ"
16:40 End of main programme “Meet the Expert” session (Prof. Rossmann and selected PhD students, room HP7)
Everyone interested in the latest structural biology research at the KU Leuven and beyond, in particular PhD students, is warmly invited.

This workshop will focus on cutting edge techniques for image analysis in Cryo-EM. Intended to be more technical than the annual Gordon Conference, speakers at this event represent many of the leading software developers in this field. Attendance by post-docs and grad students is encouraged, and we hope to have active dialog, with a generous discussion section after each talk. We will also have a poster session, and will select a few of the best posters/abstracts to give short talks.

Protons & Membrane Reactions

Connecting Membrane Protein Function with StructureÂ

February 23-28, 2014

Four Points Sheraton / Holiday Inn Express
Ventura, CA

• Chair: Stephen H. WhiteÂ
• Vice Chair: Thomas E. DeCourse

Protein Transport Across Cell MembranesÂ

Mechanisms, Structure, and Physiology

March 9-14, 2014

Hotel Galvez
Galveston, TX

• Chairs: Ramanujan S. Hegde & Andreas KuhnÂ
• Vice Chairs: Steven M. Theg & Shu-Ou Shan