TR&D Project 3. The Analysis Stage II: Tools for Analyzing the Connectivity and Morphology of Macromolecular Assemblies As the structure of an assembly is directly related to its functional role, we aim to define the architecture of isolated native macromolecular complexes of interest. For this, our molecular microscope pipeline needs information on the shape and connectivity of an assembly?s components, accurately representing their arrangement at the highest spatial and temporal resolution. Thus, we will develop and refine methodologies to determine the morphologies and spatial relationships between components within complexes at several distance scales, ranging from a description of the overall subunit shape and arrangement to defining atomic resolution contacts between pairs of macromolecules. Our strategy entails using orthologous methods, in order to provide complementary data and to cover a wide range of resolutions, to inform us about the shape, dimensions and connectivity of single proteins and macromolecular assemblies. We will focus on methods that have already proven particularly empowering, but which have significant scope for further advancement. These include electron microscopy (EM) and chemical cross-linking with mass spectrometry (XL-MS): through the former, we can produce morphological maps with sufficient detail to resolve the shapes and locations of complexes, proteins, domains and folds; in parallel, through the latter, we will obtain information on how each component of the assembly is positioned relative to all other components, and the entire structure. These data when combined with data from complementary, well-established methods, will be used to generate structural models of assemblies. To elucidate cellular functions, we propose to gather and interpret dynamic data about the changing morphologies of assemblies, and the changing interactions within these assemblies. Our molecular microscope pipeline thus seeks to build concrete high precision 3D models, and 4D models that change in time.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Biotechnology Resource Grants (P41)
Project #
2P41GM109824-06
Application #
9705154
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
Budget Start
2019-05-01
Budget End
2020-04-30
Support Year
6
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Rockefeller University
Department
Type
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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