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Conference Program
 
Biopolymers
Mechanisms of Biomolecular Interactions: From Physical Principles to Biological Insights
June 1-6, 2014
Salve Regina University
Newport, RI
Chair:
Ivet Bahar

Vice Chair:
Harald Schwalbe

It is widely established that it is essential to understand the dynamics and mechanisms of biomolecular interactions in order to develop methods for efficiently monitoring biological activities, designing new functionalities or altering existing properties. Fundamental principles of physical sciences, polymer science and engineering have played a crucial role in molecular and structural biology in establishing the physical basis and origin of complex interactions. Significant advances have been made in recent years, both computationally and experimentally. However, the cooperative dynamics and evolutionary properties of biological systems, as well as the effect of the physiological (crowded) environment present additional layers of complexity, which are limiting our ability to elucidate the mechanisms of function and allostery that underlie many observed phenomena. These complications are best reflected in the characterization of membrane proteins and biomolecular machines often composed of multiple subunits that act concertedly in restricting environments. The development of effective strategies for identifying the molecular origin and mechanisms of observed phenomena and for developing intervention methods for regulating or modifying biological function requires a deeper level of quantitative investigation and multidisciplinary collaboration. The proposed GRC is uniquely poised to bring together scientists from different disciplines and foster new collaborations toward this aim.


Contributors

SUNDAY
2:00 pm - 9:00 pmArrival and Check-in (Office Closed 6:00 pm - 7:00 pm)
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pmKeynote Presentations: Biomolecular Machinery, Signaling and Regulation
7:40 pm - 7:50 pmDiscussion Leader: Harald Schwalbe
"Introduction"
7:50 pm - 8:30 pmJohn Kuriyan (UC Berkeley)
"Molecular Mechanisms in Protein Kinase Regulation"
8:30 pm - 8:40 pmDiscussion
8:40 pm - 9:20 pmAndrej Sali (UCSF)
"Structure-Guided Modulation of Protein Assembly Function"
9:20 pm - 9:30 pmDiscussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmBiomolecular Complex Formation, Oligomerization and Assembly
9:00 am - 9:15 amDiscussion Leader: Shoshana J. Wodak (Toronto University)
"Introduction"
9:15 am - 9:45 amGideon Schreiber (Weizmann Institute)
"Assessing the Effects of Crowding on Binding and Enzyme Reaction Rates In Vitro and In Vivo"
9:45 am - 9:50 amDiscussion
9:50 am - 10:20 amCoffee Break
10:20 am - 10:50 amHolger Stark (Max Planck Institute)
"High Resolution Structure and Dynamics of Macromolecular Complexes by Cryo-EM"
10:50 am - 10:55 amDiscussion
10:55 am - 11:25 amSarah A. Woodson (John Hopkins University)
"RNA Folding and Dynamics of Ribosome Assembly"
11:25 am - 11:30 amDiscussion
11:30 am - 12:00 pmMichael Nash (University of Munich)
"Ultrastable Mechanically Shielded Protein Receptor-Ligand Complex"
12:00 pm - 12:05 pmDiscussion
12:05 pm - 12:25 pmMark Bowen (SUNY Stony Brook)
"Kinetics of Multi-Protein Complex Formation by Synaptic Scaffold Protein PSD95"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 9:30 pmStructural Dynamics of Membrane Proteins: From Single Molecules to Cell Interactions
7:30 pm - 7:35 pmDiscussion Leader: Gary Rudnick (Yale University)
"Introduction"
7:35 pm - 8:05 pmTamir Gonen (Janelia Farm, HHMI)
"The Dynamic Modulation of Water Permeability in the Lens Aquaporin-0"
8:05 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmPoul Nissen (Aarhus University, Denmark)
"Switching Sides - Why Do Transporters Do That?"
8:40 pm - 8:45 pmDiscussion
8:45 pm - 9:05 pmOded Lewinson (Technion, Israel)
"A Membrane-Bound ATPase that Benefits from Constant Activity"
9:05 pm - 9:10 pmDiscussion
9:10 pm - 9:25 pmAdam Smith (University of Akron)
"Resolving Membrane Protein Dimerization in Cell Signaling with Pulsed Interleaved Excitation Fluorescence Cross-Correlation Spectroscopy (PIE-FCCS)"
9:25 pm - 9:30 pmDiscussion
TUESDAY
7:30 am - 8:30 amBreakfast
8:30 amGroup Photo
9:00 am - 12:30 pmMembrane Proteins: Mechanisms of Interactions, Function and Dysfunction
9:00 am - 9:15 amDiscussion Leader: Benoit Roux (University of Chicago)
"Introduction"
9:15 am - 9:45 amLucy R. Forrest (NIH, NINDS)
"Ion Coupling in LeuT-Fold Transmembrane Transporters"
9:45 am - 9:55 amDiscussion
9:55 am - 10:25 amCoffee Break
10:25 am - 10:55 amOlga Boudker (Cornell University, Weill Medical School)
"Ionic Coupling and Dynamics in a Glutamate Transporter Homologue"
10:55 am - 11:00 amDiscussion
11:00 am - 11:30 amGary Rudnick (Yale University)
"How Na+ Affects Conformational Change in LeuT"
11:30 am - 11:40 amDiscussion
11:40 am - 12:00 pmMatteo Dal Peraro (Ecole Polytechnique Fédérale de Lausanne, Switzerland)
"Perturbation of the Straight Transmembrane α-Helical Structure of the Amyloid Precursor Protein Affect Is Processing by γ-Secretase"
12:00 pm - 12:05 pmDiscussion
12:05 pm - 12:25 pmOlga Gursky (Boston University)
"Novel Molecular Mechanism of Apolipoprotein Misfolding in Amyloidosis: When Good Protein Goes Bad"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:30 pm - 9:30 pmAllosteric Modulation of Function by Biomolecular Interactions
7:30 pm - 7:45 pmDiscussion Leader: Canan Atilgan (Sabanci University)
"Introduction"
7:45 pm - 8:15 pmStephen C. Blacklow (Harvard University)
"Unraveling the Mechanism of Notch Signal Transduction"
8:15 pm - 8:20 pmDiscussion
8:20 pm - 8:35 pmMarcia Levitus (Arizona State University)
"Single Molecule Studies of DNA Replication Processivity Clamps"
8:35 pm - 8:40 pmDiscussion
8:40 pm - 9:00 pmKathleen Hall (Washington University)
"RNA:Protein Binding, Linkage, and Allostery"
9:00 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pmTali Haran (Technion, Israel)
"DNA as an Allosteric Effector of p53 Transactivation"
9:25 pm - 9:30 pmDiscussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmProtein-Drug Interactions and Modulation of Function
9:00 am - 9:15 amDiscussion Leader: J. Andrew McCammon (UC San Diego)
"Introduction"
9:15 am - 9:45 amBrian K. Shoichet (Toronto University)
"Backward & Forward with Structure-Based & Classical Pharmacology"
9:45 am - 9:55 amDiscussion
9:55 am - 10:20 amCoffee Break
10:20 am - 10:50 amWolfgang Jahnke (Novartis Institutes for Biomedical Research, Switzerland)
"NMR-Guided Discovery of Allosteric Inhibitors of Cancer Targets"
10:50 am - 11:00 amDiscussion
11:00 am - 11:20 amGiorgio Colombo (National Research Council, Italy)
"Studying Protein Dynamics with an Eye to Molecular Design"
11:20 am - 11:25 amDiscussion
11:25 am - 11:55 amNikolay V. Dokholyan (UNC Chapel Hill)
"Controlling Allosteric Networks in Proteins"
11:55 am - 12:05 pmDiscussion
12:05 pm - 12:25 pmPayel Das (IBM, Thomas J Watson Research Center)
"Protective and Causative Variants of Aβ1-42 for Alzheimer's Disease Move Focus from Upstream to Downstream Effects"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
Nominations for the Next Vice Chair; Fill in Conference Evaluation Forms; Discuss Future Site and Scheduling Preferences; Election of the Next Vice Chair
7:30 pm - 9:30 pmDetection of Conformational Changes and Mechanisms of Function
7:30 pm - 7:45 pmDiscussion Leader: Robert L. Jernigan (Iowa State University)
"Introduction"
7:45 pm - 8:15 pmRobert T. Sauer (MIT)
"Dissecting the Mechanism of a Complex Proteolytic Machine"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pmYann R. Chemla (University of Illinois at Urbana-Champaign)
"Simultaneous Measurement of Protein Structure and Function with a Combined Optical Trap/Fluorescence Microscope"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pmFlorian Buhr (Goethe University Frankfurt)
"Effects of Synonymous Codon Mutations on the Structure of Gamma-B Crystalline"
9:25 pm - 9:30 pmDiscussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmDesign and Evolution
9:00 am - 9:05 amDiscussion Leader: Ivet Bahar (University of Pittsburgh)
"Introduction"
9:05 am - 9:35 amSarah A. Teichmann (MRC Cambridge, UK)
"Evolution and Assembly of Protein Complexes"
9:35 am - 9:40 amDiscussion
9:40 am - 9:55 amFrancesca Massi (U Mass Medical School)
"Disorder of the Tandem Zinc Finger Domain Controls the Activity of the TTP Family of Proteins"
9:55 am - 10:00 amDiscussion
10:00 am - 10:30 amCoffee Break
10:30 am - 11:00 amTanja Kortemme (UCSF)
"Computational Design of Reprogrammed and New Protein Functions"
11:00 am - 11:10 amDiscussion
11:10 am - 11:40 amSarel Fleishman (Weizmann Institute)
"Why Reinvent the Wheel? Computational Design of Novel Antibodies from Natural Fragments"
11:40 am - 11:50 amDiscussion
11:50 am - 12:20 pmNir Ben-Tal (Tel Aviv University)
"A Global View of the Protein Universe"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmMisfolding and Aggregation
7:30 pm - 7:45 pmDiscussion Leader: Teresa Head-Gordon (UC Berkeley)
"Introduction"
7:45 pm - 8:15 pmJohn E. Straub (Boston University)
"Role of Sequence and Membrane in Amyloid Precursor Protein Structure and Function"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pmPatricia L. Clark (Notre Dame)
"Encoding Aggregation Avoidance Using Synonymous Codon Substitutions"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pmJames Shorter (University of Pennsylvania)
"Potentiated Protein Disaggregases to Counter Neurodegeneration"
9:25 pm - 9:30 pmDiscussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

 
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