IUSSTF Joint Center Award Announcement 2013
The Indo-US Science and Technology Forum are pleased to announce that based on a joint Indian and United States review process, the following workshop proposals have been selected for financial support from IUSSTF.
Protein Interactor Discovery and Structure
Debnath Pal, Associate Professor, Supercomputer Education and Research Centre Indian Institute of Science (IISc) Bangalore & David S. Eisenberg, Director, Institute of Genomics and Proteomics University of California Los Angeles (UCLA) Los Angeles
Protein molecules interact and associate with each other inside the cell to perform various functions in concerted pathways. The interaction is specific and is influenced by the physicochemical properties of the interacting molecular surface. The knowledge of protein-complex (quaternary) structure using X-ray crystallographic methods offer an atomistic glimpse into the basis of this interaction. Therefore, structural genomics of protein complexes has been one of the frontier areas in structural biology. However, structure solution of protein complexes must precede identification of natural/cognate binding partners in cell to allow attempt to protein co-crystallization and structure determination. In this proposal we want to enhance our methodology of identification of natural/cognate binding partners of proteins in a genomics scale. An already established ProLinks database of genomic-context derived functional linkage information will be used to get an initial set of physically interacting candidates at 95% expected coverage. These candidates will thereafter be screened and ranked using our interaction forcefield and expectation maximization method. The sequences will be modeled to assess and interpret the basis of the interaction as rigid bodies, and subsequently subjected to molecular dynamics simulations to confirm the viability of the protein-interaction. The candidates will be experimentally tested for protein-protein interaction screening and if successful, followed up with crystallization and structure determination. The work is expected to give a significant boost to the structural genomics of protein complexes.
The proposal to network will synergize the effort of the US collaborators on structural genomics, and Indian collaborators on protein-protein interaction algorithms, bringing together pioneers and experts in a targeted problem solving setup. The proposal is expect to bring forth new ideas and lay groundwork for long term future collaborations.
Crystallization at Interfaces
Prof. Milan K. Sanyal, Director, Saha Institute of Nuclear Physics, Kolkata & Michael J. Bedzyk, Dept. of Materials Science and Engineering, Northwestern University Cook Hall Campus Drive, Evanston, Illinois
In this collaborative program the investigators are planning to set up an Indo-US Knowledge R & D Networked Joint Center for carrying out fundamental research to understand self-organized mechanism in formation of Crystals at solid and liquid Interfaces. Under this broad theme our specific interests will be to understand the a) growth of crystals of atoms/molecules with symmetries that are generally absent in bulk, and b) growth of crystals of mono-dispersed nano-particles. We shall primarily use synchrotron scattering, high resolution microscopy and spectroscopy techniques in this collaborative project. A general interest in the above studies lays in development of materials for highly efficient energy conversion/storage and for ultra-low-power dissipation nano-devices.
Indo-US center for Biological Timing
Vinod Kumar, Professor,Department of Zoology, University of Delhi, Delhi & Satchidananda Panda, Associate Professor, Regulatory Biology Laboratory Salk Institute for Biological Studies, La Jolla, CA
Biological clocks have evolved to interact with daily changes in our environment and time appropriate physiology, metabolism, and behavior to right time of the day or to the right season. Optimum timing events underlie increased biomass production by plant species, optimum growth, cell division, reproductive success, healthy lifespan and improved prognosis in animals and in humans. In contrast, disruption of the biological timing system as in genetic mutations affecting the internal clock or changes in environmental factors impairs fitness and predisposes to chronic diseases and early aging. Biological timing is a rapidly emerging field and it has profound implications in multiple fronts common to the national interests of both the USA and India. These areas include food security, energy security, public health, and ecosystem restoration. While biological timing researchers in the USA have been at the forefront of understanding the molecular basis of biological clocks in model organisms, Indian researchers have pioneered the understanding of physiology and behavior in complex organisms that are under daily and seasonal regulation. Research teams from both countries are poised to complement their expertise and make rapid progress in the field of biological timing.
The Indo-US center for biological timing will be the hub for research, training and education by involving two important Universities of India (University of Delhi and the University of Lucknow) and two important centers of research and education of the USA (University of California and Salk Institute for Biological Studies). The basic science collaborations will center around ongoing funded research with direct relevance to public health and ecosystem restoration. Research collaborations will form the platform for cross-training of researchers and students during short-term visits. These visits and online tools will be leveraged to generate and disseminate education materials on biological timing. Success of the research program will solidify collaboration between two countries while training and education efforts will expand bilateral collaboration.
Nanostructure Genomics: Designing Functionality of 2-Dimensional Nanostructures and Nano-Bio Interfaces
Saroj K. Nayak, School of Basic Sciences Indian Institute of Technology, Bhubaneswar & George Makhatadze, Constellation Professor of Biocomputation and Bioinformatics, Department of Biology Professor, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy
The Joint Center will provide a unique platform for basic scientists, engineers and physicians to interact actively addressing fundamental questions keeping in mind possible applications through design of new atomic scale materials and biomolecules. Specifically, our group will collaborate on the fundamental study of new and emerging nanostructured materials with potential applications in low power high speed transistors, chemical and biological sensors, energy devices such as super capacitors, growth and application of robust and novel substrates (using coherent inclusion of plasmonic materials in silicon substrates) for surfaces enhanced Raman Spectroscopy (SERS) that enable to detect single molecule detection, metal clusters controlled intein proteins that could be used as an anti-tuberculosis drug, designing of new protein-nanostructure interfaces that could control or provide superior biosensors. We will harness world class super computer facilities both at Rensselaer, US, and at the Institute of Physics, India, as well as, state of the art experimental infrastructures across the institutes. Specifically, we propose to use predictive simulations not only to explain experimental findings, but also to suggest new experiments. Our team plans to address some of the above issues by focusing on two broad thrusts: Thrust I: Design of 2-dimensional Functional Nanostructures and Thrust II: Design of Optimal Nano-Bio Interfaces. Our team will leverage various existing and future funding for the success of the proposed activities.