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Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations SEPTEMBER 10–14, 2014 | ISTANBUL, TURKEY

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Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations SEPTEMBER 10–14, 2014 | ISTANBUL, TURKEY Biophysical Society Thematic Meeting | PROGRAM & ABSTRACTS Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations SEPTEMBER 10–14, 2014 | ISTANBUL, TURKEY Thank You to the Organizing Committee and the Scientific Advisory Board Organizing Committee Ivet Bahar, University of Pittsburgh School of Medicine, USA Ozlem Keskin, Koc University, Turkey Scientific Advisory Board Nikolay Dokholyan, University of North Carolina at Chapel Hill, USA Turkan Haliloglu, Bogazici University, Turkey John Overington, European Bioinformatics Institute (EMBL-EBI), United Kingdom Banu Ozkan, Arizona State University, USA Anna Panchenko, National Center for Biotechnology Information, NIH, USA Rebecca Wade, Heidelberg University, Germany Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Welcome Letter September 2014 Dear Colleagues, It is our great pleasure to welcome you to the Biophysical Society Thematic Meeting on Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations. We have an exciting program, covering a broad range of topics, with the participation of leading scientists, both experimental and computational, in the field. We strongly hope that the meeting will not only provide a venue for sharing our recent progress, findings and pending questions, but also foster new collaborations and many stimulating discussions toward gaining deeper insights into challenging problems of molecular biophysics and systems biology. We also encourage you to take part in social and cultural activities, because Istanbul has a lot to offer. Thank you all for joining our meeting, and we look forward to having a very enjoyable four day event together. Best regards, Ivet & Ozlem Ivet Bahar, Ph.D. Ozlem Keskin, Ph.D. Distinguished Professor and J. K. Vries Chair Professor Dept. of Computational & Systems Biology Chemical and Biological Engineering Dept. School of Medicine Koc University University of Pittsburgh Turkey United States Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Table of Contents Table of Contents General Information………………………………………………………………….………...1 Program Schedule……………………………………………………………………………...3 Speaker Abstracts……………………………………………………………………...…… ...11 Thursday Poster Session………………………………………………………………………53 Saturday Poster Session……………………………………………………………………....101 Local Area Walking Map………………………………………………………………….…150 Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery General Information GENERAL INFORMATION Registration Hours The registration desk is located in the lobby of Hall A at the American Hospital. Registration hours are as follows: Wednesday, September 10 2:00 PM – 7:00 PM Thursday, September 11 8:00 AM – 3:00 PM Friday, September 12 8:00 AM – 1:15 PM Saturday, September 13 8:00 AM – 6:20 PM Sunday, September 14 8:00 AM – 11:30 AM Instructions for Presentations (1) Presentation Facilities: A data projector will be made available in Hall A. Speakers are required to bring their laptops. Speakers are advised to preview their final presentations before the start of each session. (2) Poster Session: 1) All poster sessions will held in Hall B. 2) A display board measuring 85cm (2.7 feet) wide by 170 cm (5.5 feet) high will be provided for each poster. Poster boards are numbered according to the same numbering scheme as in the abstract book. 3) Posters being presented on Thursday, September 11, should be set up on the morning of September 11 and removed by 6:00 PM on September 11. Posters being presented on Saturday, September 13, should be set up on the morning of September 13 and removed by 6:00 PM on September 13. 4) During the poster session, presenters are requested to remain in front of their poster boards to meet with attendees. 5) All posters left uncollected at the end of the meeting will be disposed of. Coffee Breaks Coffee breaks will be held in the lobby of Hall A where tea, coffee, and snacks will be provided. Internet Wifi is available in the lobby and meeting rooms of the American Hospital. Smoking Please be advised that smoking is not permitted inside the American Hospital. 1 Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery General Information Meals Lunches (September 11-13) are included in the registration fee and the Gala Reception/Dinner for those that confirmed attendance in advance. The Welcome Reception/Gala Dinner will be held at the Divan Hotel. Buffet lunch will be provided in the cafeteria on the 7th floor of the American Hospital on September 11-13. Sightseeing Tours There will be two optional tours organized for attendees and/or accompanying guests. 1. Visit to the Old City on Friday, September 12, at 2:00 PM. (Tentative fee is $50 per person, including transportation, entry tickets to Haghia Sophia, Topkapi, Blue Mosque, dinner and an English-speaking guide) 2. Bosphorus Boat Tour on Saturday, September 13, at 6:30 PM. (Fee is $55 per person, including dinner) Pre-registration is required for the tours. If you have signed up for the tours, please pay the fees at the on-site registration desk. Name Badges Name badges are required to enter all scientific sessions and poster sessions. Please wear your badge throughout the conference. Contact If you have any further requirements during the meeting, please contact the meeting staff at the registration desk from September 10-14 during registration hours. In case of emergency, you may contact the following organizers/staff: Dorothy Chaconas: [email protected] Ozlem Keskin: [email protected] Ivet Bahar: [email protected] Or call the Divan Hotel at 90 (212) 315 55 00 and ask to leave a message in their room. 2 Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Program Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations Istanbul, Turkey September 10-14, 2014 PROGRAM All functions will be held in Hall A of the American Hospital unless otherwise noted. Wednesday, September 10, 2014 Welcome & Session I: Allosteric Transition in Proteins and How They Relate to Function Co-Chairs: Amnon Horovitz, Weizmann Institute of Science, Israel Rebecca Wade, Heidelberg University, Germany 4:00 - 4:20 PM Welcome/Opening Remarks: Ivet Bahar, University of Pittsburgh School of Medicine, USA Ozlem Keskin, Koc University, Turkey 4:20 - 4:50 PM Amnon Horovitz, Weizmann Institute of Science, Israel Distinguishing between Allosteric Mechanisms Using Structural Mass-Spectrometry Is Demonstrated for the Chaperonin GroEL 4:50 - 5:20 PM Ruth Nussinov, Tel-Aviv University, Israel, and NIH, USA Ras: A Structural Biologist View and Questions 5:20 - 5:50 PM Rebecca Wade, Heidelberg University, Germany Organism-adapted Specificity of Allosteric Regulation of Central Metabolic Enzymes in Lactic Acid Bacteria 5:50 - 6:10 PM Tom McLeish, Durham University, United Kingdom* Predicting Global Low Frequency Protein Motions in Allostery without Conformational Change: Application to CRP/FNR Family Transcription Factors 6:10 - 6:30 PM Vanessa Ortiz, Columbia University, USA* Quantifying Signal Propagation and Conformational Changes in Allosteric Proteins *Short talks selected from among submitted abstracts 3 Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Program 6:30 - 7:00 PM Banu Ozkan, University of Arizona, USA Mechanism of Protein Evolution: Conformationaly Dynamics and Allostery 7:15 - 9:30 PM Welcome Reception/Gala Dinner Divan Hotel Thursday, September 11, 2014 Session II: Protein Interactions and Complex Systems Modeling I: Evolution and Function Co-Chairs: Janet Thornton, European Bioinformatics Institute (EMBL-EBI), United Kingdom Burkhard Rost, Technical University of Munich, Germany 8:45 - 9:15 AM Janet Thornton, European Bioinformatics Institute (EMBL-EBI), United Kingdom The Evolution of Enzyme Mechanisms and Functional Diversity 9:15 - 9:45 AM Anne-Claude Gavin, EMBL Heidelberg, Germany Lipid-Protein Networks 9:45 - 10:00 AM Sebnem Essiz Gokhan, Kadir Has University, Turkey* Soman Induced Conformational Changes of Human Acetylcholine Esterase 10:00 - 10:30 AM Burkhard Rost, Technical University of Munich, Germany Evolution Teaches Predicting Protein Interactions from Sequence 10:30 - 10:45 AM Andrew Pohorille, NASA Ames Research Center, USA* Proteins with Novel Function, Structure and Dynamics 10:45 - 11:00 AM Srinath Krishnamurthy, National University of Singapore, Singapore* How Enzymes Access Caged Substrates? Phosphodiesterase- Protein Kinase A Interactions Mediate Hydrolysis of PKA Receptor Bound Cyclic AMP 11:00 - 11:30 AM Coffee Break Hall A Lobby Session III: Protein Interactions and Complex Systems Modeling II: Cell Regulatory and Signaling Mechanisms Co-Chairs: Leslie Loew, University of Connecticut Health Center, USA Anna Panchenko, National Center for Biotechnology Information, NIH, USA *Short talks selected from among submitted abstracts 4 Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Program 11:30 AM - 12:00 PM Leslie Loew, University of Connecticut Health Center, USA Clusters and Comets: Regulation of Actin Assembly 12:00 - 12:30 PM Anna Panchenko, National Center for Biotechnology Information, NIH, USA Regulation of Protein-Protein Binding and Pathway Crosstalk 12:30 - 1:00 PM Zaida Luthey-Schulten, University of Illinois at Urbana- Champaign, USA Stochastic Simulations of Cellular Processes: from Single Cells to Colonies 1:00 - 1:15 PM Yaman Arkun, Koc University, Turkey*
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