Cmc

Scialog

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Chemical Machinery of the Cell

2018-2021

Cells obtain and use energy, reproduce, and respond to their surroundings using their chemical machinery. The macromolecules that make up this machinery are assembled, disassembled, and reorganized throughout the cell’s life cycle, enabling the cell to adapt rapidly in response to environmental cues. Intricate and highly organized machinery synthesize, assemble, and transport components around, in, and out of the cell through highly regulated mechanisms.

These cellular processes have been studied over many decades, often by purifying molecular components and studying reaction mechanisms under carefully controlled experimental conditions. But these experimental systems fall short in letting us see what actually occurs in the extremely dense and complex cellular environment to optimize the efficiency and specificity of the myriad reactions that are happening simultaneously in close proximity. To understand these processes more fully at the molecular and atomic level, new tools and approaches from chemistry and biology will be required. This Scialog is based on the conviction that the time is right to bring together chemists and biologists to spark collaborations and develop interdisciplinary projects that will catapult us to a deeper understanding of chemical machinery and reactions in the intact cell. Examples of questions that might be considered are:

  • How can advances in chemical theory and modeling, computation and data analytics, simulations and artificial cellular systems reveal new ideas about the chemical machinery of the cell?
  • How does the cell organize reactions in functionally distinct compartments that are not bound by membranes?
  • How do molecules move through the dense cytoplasm of the cell so that reactions are not limited by passive diffusion rates?
  • Do small molecules, some not yet discovered, contribute to increasing reaction rates and specificity through covalent and non-covalent attachment to proteins, nucleic acids, carbohydrates, and lipids?
  • Do macromolecules take advantage of electron delocalization to achieve more than binary (on/off) states in information flow and metabolic reactions?
  • What combination of new chemical tools including chemical probes, optical techniques, and quantum methods can bring about molecular resolution of the chemical machinery in intact, living cells?

Fellows & Facilitators

Fellows
Facilitators

Team Awards

Goal: to catalyze breakthroughs in fundamental understanding of chemical processes which underlie the workings of intact living cells that will lead to a new era of advancement in cell biology.

2021 Team Awards

Intercepting the Cell’s Hidden Signals via Peptide-Activated RNA Switches

  • Julien Berro
    Molecular Biophysics & Biochemistry, and Cell Biology
    Yale University

    Alexander Green
    Biomedical Engineering
    Boston University

Structure-Function of Enzyme Filaments: Regulators of Cell Metabolism in Space and Time

  • Caitlin Davis
    Chemistry
    Yale University

    Lars Plate
    Chemistry and Biological Sciences
    Vanderbilt University

Toward an Atlas of All Biomolecular Condensates

  • W. Seth Childers
    Chemistry
    University of Pittsburgh

    Stephen Fried
    Chemistry
    Johns Hopkins University

    Ross Wang
    Chemistry
    Temple University

Putting Bacteria to Sleep: Establishing an Artificial Circadian Clock

  • W. Seth Childers
    Chemistry
    University of Pittsburgh

    Elizabeth Read
    Chemical and Biomolecular Engineering
    University of California, Irvine

    Haoran Zhang
    Chemical and Biochemical Engineering
    Rutgers University

The Butterfly Effect in Cellular Phase Separation: from Molecular Interactions to Emergent Behavior

  • Maria Kamenetska
    Chemistry and Physics
    Boston University

    Jan-Hendrik Spille
    Physics
    University of Illinois at Chicago

    Lu Wang
    Chemistry and Chemical Biology
    Rutgers University

Visualizing Inheritance through the Lens of Phase Separation

  • Jan-Hendrik Spille
    Physics
    University of Illinois at Chicago

    Stephen Yi
    Biomedical Engineering & Oncology
    University of Texas at Austin

Elucidating the Polygenic Origins of Schizophrenia: Linking Protein Trafficking to Synapse Function

  • Stephanie Gupton
    Cell Biology and Physiology
    University of North Carolina at Chapel Hill

    Alexis Komor
    Chemistry and Biochemistry
    University of California, San Diego

    Yan Yu
    Chemistry
    Indiana University

Stretching Reality to Discover the (un)Knowns

  • Ronit Freeman
    Applied Physical Sciences
    University of North Carolina at Chapel Hill

    Lydia Kisley
    Physics and Chemistry
    Case Western Reserve University

    Laura Sanchez
    Chemistry and Biochemistry
    University of California, Santa Cruz

Decoding Host-Pathogen Molecular Cross-talk via Unbiased Multiplex Profiling

  • Stephen Fried
    Chemistry
    Johns Hopkins University

    Tania Lupoli
    Chemistry
    New York University

    Wenjing Wang
    Chemistry and Life Sciences Institute
    University of Michigan
  • All funded by RCSA and the Gordon and Betty Moore Foundation
2019 Team Awards

Metabolite Pools: Where are they, who’s using them, and can we?

  • Caitlin Davis
    Chemistry
    Yale University

    Elizabeth Read
    Chemical and Biomolecular Engineering
    University of California, Irvine

    Kamil Godula
    Chemistry
    University of California, San Diego

    Funded by the Gordon and Betty Moore Foundation

ProFIDs: Probes to Fold the Intrinsically Disordered

  • Alice Soragni
    Orthopaedic Surgery
    University of California, Los Angeles

    Matthias Heyden
    Molecular Sciences
    Arizona State University

    Funded by the Gordon and Betty Moore Foundation

Reconstructing Time-resolved Single-cell Genome Organization?

  • Bin Zhang
    Chemistry
    Massachusetts Institute of Technology

    Brian Liau
    Chemistry
    Harvard University

    G.W. Gant Luxton
    Genetics, Cell Biology, and Development
    University of Minnesota

    Funded by the Gordon and Betty Moore Foundation

Seeing the Forces of Life

  • Rongsheng (Ross) Wang
    Chemistry
    Temple University

    Abhishek Singharoy
    Molecular Sciences
    Arizona State University

    Alison Ondrus
    Chemistry and Chemical Engineering
    California Institute of Technology

    Funded by the Gordon and Betty Moore Foundation

Small-Molecule Cathodophores for Multicolor Electron Microscopy

  • Maxim Prigozhin
    Molecular and Cellular Biology / Applied Physics
    Harvard University

    Xin Zhang, Chemistry / Biochemistry and Molecular Biology
    Pennsylvania State University

    Jefferson Chan
    Chemistry
    University of Illinois at Urbana-Champaign

    Funded by the Gordon and Betty Moore Foundation

Understanding the Dark Side of the Genome

  • Ronit Freeman
    Applied Physical Sciences
    University of North Carolina at Chapel Hill

    Alexis Komor
    Chemistry and Biochemistry
    University of California, San Diego

    Davide Donadio
    Chemistry
    University of California, Davis

    Funded by the Gordon and Betty Moore Foundation
2018 Team Awards

Finding Mitochondrial Memory

  • Abhishek Chatterjee
    Chemistry
    Boston College

    Gulcin Pekkurnaz
    Neurobiology
    University of California, San Diego

    Juan Perilla
    Chemistry and Biochemistry
    University of Delaware

    Funded by the Gordon and Betty Moore Foundation

What Does “Self” Look Like?

  • Kamil Godula
    Chemistry and Biochemistry
    University of California, San Diego

    Jennifer Heemstra
    Chemistry
    Emory University

    Abhishek Singharoy
    Molecular Sciences
    Arizona State University

    Funded by the Gordon and Betty Moore Foundation

A Plant Cell-Based Platform to Target Human Proteostasis Diseases

  • Kathryn Haas
    Chemistry
    Saint Mary’s College

    Alice Soragni
    Orthopaedic Surgery
    University of California, Los Angeles

    Jing-Ke Weng
    Biology
    Massachusetts Institute of Technology

    Funded by the Gordon and Betty Moore Foundation

Breaking the Central Dogma: Reverse Translation of the Proteome

  • Christian Kaiser
    Biology
    Johns Hopkins University

    David Limmer
    Chemistry
    University of California, Berkeley

    Rebecca Voorhees
    Biology and Biomedical Engineering
    California Institute of Technology
  • Funded by the Gordon and Betty Moore Foundation

Optical Mind Reading

  • Markita del Carpio Landry
    Chemical and Biomolecular Engineering
    University of California, Berkeley

    Gulcin Pekkurnaz
    Neurobiology
    University of California, San Diego

    Jennifer Prescher
    Chemistry
    University of California, Irvine

    Funded by the Gordon and Betty Moore Foundation

Synthetic Organelle Biology: Engineering Photosynthetic Animal Cells

  • Markita del Carpio Landry
    Chemical and Biomolecular Engineering
    University of California, Berkeley

    Jing-Ke Weng
    Biology
    Massachusetts Institute of Technology

    Joshua Widhalm
    Horticulture and Landscape Architecture
    Purdue University

    Funded by Research Corporation

Identifying and Detecting Diseases Prior to Physical Presentation of Symptoms

  • Laura Sanchez
    Pharmaceutical Sciences
    University of Illinois, Chicago

    Judith Su
    Optical Sciences and Biomedical Engineering
    University of Arizona

    Funded by the Flinn Foundation and Research Corporation

Understanding Biological Systems Using Resonator-Mediated Single-Molecule Raman Detection and Spectroscopy

  • Judith Su
    Optical Sciences and Biomedical Engineering
    University of Arizona

    Lu Wei
    Chemistry
    California Institute of Technology

    Funded by the Gordon and Betty Moore Foundation

Conference Booklets

2021 Scialog CMC Conference Booklet

2019 Scialog CMC Conference Booklet

2018 Scialog CMC Conference Booklet

SPONSORS

Gordon and Betty Moore Foundation

Research Corporation for Science Advancement

Additional Support

Paul G. Allen Frontiers Group

Flinn Foundation

National Institutes of Health Common Fund