The emergent properties of life require the dynamic interactions of macromolecules, the two major classes of which are proteins and nucleic acids. These interactions form macromolecular machines and dynamic liaisons that shape the cell, transmit information and control cellular behaviors, and pathogenic alterations in molecular interaction networks (interactomes) underlie disease. Our understanding and modulation of biological systems, as well as their pathologies, thus relies on the ability to elucidate and interpret these interactions and their dynamics. For nucleic acids, recent advances have led to an explosion of genomic data. However, proteins are incredibly diverse in their abundance and their properties, making them highly versatile for their dynamic tasks, but at the same time exceptionally difficult to analyze. It is for these reasons that the interactomic revolution still ags very far behind the genomic revolution. The proposed National Center for Dynamic Interactome Research (NCDIR) couples cell biology laboratories, an established mass spectrometry resource, a systems biology resource, and a computational structural biology center. The goal of the NCDIR is to synergistically pioneer new and improved approaches, integrating these technologies into a fundamentally novel """"""""pipeline"""""""" approach to address the urgent need of the biomedical community for technologies that can rapidly, reliably and routinely identify and characterize the dynamic cellular interactome. We will begin by developing technologies for purifying and preserving, with high fidelity, various defined forms of the hierarchical arrangement of interactors surrounding any chosen macromolecule. We will then provide comprehensive, highly quantitative, detailed temporal and structural data for dynamic complexes. Such data will be used to generate structural and mechanistic models that are predictive, testable, actionable, and guide experiments to focus on those that are most informative. The models aim to provide the biomedical community with the means for rational target-based intervention and drug design strategies. These approaches will be developed, refined and beta-tested via a selected set of Driving Biological Projects and Collaborations that can enter and exit our pipeline at any point, and which present specific technological challenges. Critical to the design of the NCDIR is an effective training and dissemination program that is responsive to the urgent needs of the biomedical community.

Public Health Relevance

Most of the properties of living cells are mediated by the ever-changing interactions of their component macromolecules. Pathogenic alterations in these interactions mechanistically underlie diseases such as viral infection and cancer. Much better tools are needed to reveal these interactions. Thus, the goal of the proposed Center is to create new and useful tools to elucidate the dynamics of macromolecular interactions, and to spread these tools amongst the biomedical community. The Center will empower the community to assemble the kinds of detailed, dynamic representations of the interactions in the cell that will help elucidate the principles underlying all cellular processes. These tools will enable researchers to delve into the molecular details of biological processes with unprecedented facility. The resulting insights will impact all areas of medical research, from fundamental discovery to pharmaceutical development.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Biotechnology Resource Grants (P41)
Project #
1P41GM109824-01
Application #
8668348
Study Section
Special Emphasis Panel (ZRG1-BST-J (40))
Program Officer
Sheeley, Douglas
Project Start
2014-08-01
Project End
2019-04-30
Budget Start
2014-08-01
Budget End
2015-04-30
Support Year
1
Fiscal Year
2014
Total Cost
$2,322,803
Indirect Cost
$473,870
Name
Rockefeller University
Department
Biology
Type
Other Domestic Higher Education
DUNS #
071037113
City
New York
State
NY
Country
United States
Zip Code
10065
Delgado-Benito, VerĂ³nica; Rosen, Daniel B; Wang, Qiao et al. (2018) The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination. Mol Cell 72:636-649.e8
Kazantsev, Fedor; Akberdin, Ilya; Lashin, Sergey et al. (2018) MAMMOTh: A new database for curated mathematical models of biomolecular systems. J Bioinform Comput Biol 16:1740010
Jishage, Miki; Yu, Xiaodi; Shi, Yi et al. (2018) Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol 25:859-867
Mast, Fred D; Herricks, Thurston; Strehler, Kathleen M et al. (2018) ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum. J Cell Biol 217:2087-2102
Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona et al. (2018) Integrative structure and functional anatomy of a nuclear pore complex. Nature 555:475-482
Kleiner, Ralph E; Hang, Lisa E; Molloy, Kelly R et al. (2018) A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells. Cell Chem Biol 25:110-120.e3
Sanghai, Zahra Assur; Miller, Linamarie; Molloy, Kelly R et al. (2018) Modular assembly of the nucleolar pre-60S ribosomal subunit. Nature 556:126-129
Vallat, Brinda; Webb, Benjamin; Westbrook, John D et al. (2018) Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. Structure 26:894-904.e2
Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano et al. (2018) Integrative structure modeling with the Integrative Modeling Platform. Protein Sci 27:245-258
Singla, Jitin; McClary, Kyle M; White, Kate L et al. (2018) Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic ? Cell. Cell 173:11-19

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