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Workshop on Structural and Computational Proteomics of Biological Complexes

Workshop on Structural and Computational Proteomics of Biological Complexes. Wah Chiu Baylor College of Medicine. http://ncmi.bcm.tmc.edu/ncmi/ccbc. About C 2 BC. Focused on the development of computational tools for studying structures and functions of biological complexes

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Workshop on Structural and Computational Proteomics of Biological Complexes

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  1. Workshop on Structural and Computational Proteomics of Biological Complexes

  2. Wah Chiu Baylor College of Medicine

  3. http://ncmi.bcm.tmc.edu/ncmi/ccbc

  4. About C2BC • Focused on the development of computational tools for studying structures and functions of biological complexes • A virtual center of cross-disciplinary and cross-institutional research • Bring together investigators from diverse disciplines including crystallography, electron cryomicroscopy, mass spectroscopy, bioinformatics, cell biology, biochemistry, genetics, virology, system biology, clinical medicine, computational science, computer science and software engineering

  5. What is a biological complex (machine)? "We have always underestimated cells. … The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. … Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.“ (Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92: 291, 1998)

  6. Why Study Large Complexes? • Proteins typically function in association with other proteins. • Protein complexes are important for virtually every biological process and most diseases. • Genome sequences identify tens of thousands of genes: linking these to 200-300 core biological processes will make their study manageable. • Recently developed and/or improved technologies and methodologies make studies of large complexes more feasible and informative.

  7. Ribosome

  8. Chaperonin: GroEL

  9. Nuclear Pore

  10. Pipeline for Studying Complexes Sample selection Sample purification Structure determination Structure analysis Visualization Archiving

  11. Experimental Challenges • Identification of complexes • Purification of complexes • Sample quantity/concentration • Sample solubility • Heterogeneous samples • Multiple functional states • Structural solutions of conformationally heterogeneous samples • Validation of complexes in the living cell

  12. Computational Challenges • No defined ontology • Distributed, heterogeneous data • Large data sets • Multiple conformational states • Data processing techniques • Archival of complexes • Complex visualization • Specialized software

  13. C2BC Theme and Policy • Computational methodology innovations • Establishing standards • Methodology validation • Cellular validation • Adopting open source policy • Community participation • Enabling tools for biological end-users

  14. C2BC Vision: Organization Leadership Team Structure Determination Visualization Structure Analysis Biological Complexes Archiving Software design and integration Dissemination and training

  15. Workshop Goals • Discuss recent developments in the study of large biological complexes • Engage the participants in discussing the future directions of structural studies of large complexes • Identify and address present and future problems in such studies • Search for a common framework for inter-disciplinary data exchange

  16. Day 1 8:30 am Wah Chiu Welcome remarks and agenda 9:00 am Ray Jacobson Purification of S. Cerevisiae TFIID for Structural Studies 9:30 am Xiangwei He Molecular architecture of kinetochore in fission yeast 10:00 am Trisha Davis The Lattice Structure of the Yeast Spindle Pole Body Probed by FRET 10:30 am Coffee break 11:00 am Debananda Pati Insights Into Chromosomal Cohesion and Segregation: A Handcuff Model For the Cohesin Complex 11:30 am Frazer Rixon Structural Investigations of HSV Infection 12:00 pm Lunch@ Rice University Faculty Club

  17. Day 1 1:30 pm Ted Wensel Structural Dynamics of Signal-Transducing Membrane Complexes 2:00 pm Mary Porter Structural organization of the I1 inner arm dynein in Chlamydomonas and its implication for the regulation of flagellar motility 2:30 pm Tim Palzkill Systematic Cloning of Bacterial Open Reading Frames for Functional Genomics Studies 3:00 pm Coffee break 3:30 pm Eddy Arnold HIV-1 reverse transcriptase structures: chemistry, biology, and drug design 4:00 pm Wei Wang Computational study of the binding specificities of SH2 and SH3 domains 4:30 pm Orna Resnekov Center for Genomic Experimentation and Computation 5:00 pm Jose Lopez Platelets

  18. Day 2 8:30 am Andrej Sali Modeling the structures of proteins and macromolecular assemblies 9:00 am Alex Milosavljevic Emerging opportunities at the interface between comparative genomics, genomic resequencing and structural biology 9:30 am John Markley Sesame: a Data Management System for Structural Proteomics 10:00 am Steve Ludtke EMEN2 - A Distributed Object-oriented Electronic Notebook for Data Archival, Sharing and Mining 10:30 am Coffee break 11:00 am Zheng Li Modeling Platform for Collaboration 11:30 am Helen Berman Data Management in the Protein Data Bank 12:00 pm Tom Ferrin Enhancing Data Sharing in Collaborative Research Projects with DASH

  19. Day 2 1:30 pm Amy Swain 1:45 pm Wah Chiu Discussion and recommendation 2:30 pm Meeting adjourns

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