Robert Joseph Tomko

Research topics

Matched from this investigator's NIH project titles and abstracts.

• Alzheimer's and Dementia

Active NIH awards

• Investigation of the proteasome assembly landscape

  5R01GM144550-04

  NIGMS · FY 2025 · $430K

  Project Summary Abstract The 26S proteasome conducts most regulated protein degradation and eliminates toxic proteins in vivo. The proteasome is an unusually large and complex ATP-dependent protease comprising nearly 70 individual polypeptide subunits. Although the conventional thinking has been that the proteasome is assembled from these subunits in a single, rigid stepwise sequence, recent evidence from our group and others unexpectedly suggests a broader “landscape” of assembly routes may exist in vivo. Although this possibility has not yet been tested, such an assembly landscape would ensure that this essential biological process can continue effectively in the face of assembly roadblocks, and would provide a powerful means to adjust the speed or volume of proteasome biogenesis in response to the cellular environment. There is an increasing interest in harnessing proteasome biogenesis to help treat conditions as diverse as cancer and neurodegenerative disorders. Understanding whether such an assembly landscape exists, and if so, how it is harnessed to ensure rapid and faithful proteasome biogenesis, will be critical to guide development of such assembly-targeted therapies. The goal of this multi-PI application is to test the hypothesis that a proteasome assembly landscape exists in vivo, and that the relative flux through possible routes within this landscape is governed largely by kinetic factors that change in response to the intracellular environment. By combining the PIs’ respective expertise in proteasome biology and in enzyme kinetics and single molecular biophysics, we hope to validate this new paradigm for proteasome biogenesis. The proposed studies, described below, will add a critical new dimension— time—to our understanding of proteasome assembly in vivo. Our experimental approach contains two complementary but independent Aims. In Aim 1, we will utilize a newly established collection of cutting-edge single-molecule and ensemble fluorescence assays to characterize the kinetics of specific proteasome assembly steps. Experiments under this aim are designed to test the hypothesis that the relative flux through two possible assembly routes is primarily under kinetic control, but can be tuned by exogenous factors such as ligands or proteasome-interacting accessory proteins. Aim 2 will employ a suite of newly developed chemical-genetic approaches to assess the relative flux through two possible assembly routes in vivo, and to understand how the flux changes in response to environmental stimuli. Experiments under this Aim will also test in living cells the predictions derived from our in vitro kinetic model of assembly established in Aim 1. The outcomes of these studies will lead to a deeper understanding of proteasome biology and of macromolecular assembly in general, and also promise to illuminate new therapeutic avenues for cancer, neurodegeneration, and other diseases.

• Engagement and Communication Between Proteasomal Subcomplexes

  5R01GM118600-08

  NIGMS · FY 2025 · $301K

  Project Summary Abstract The 26S proteasome conducts most regulated protein degradation and eliminates toxic proteins from cells. The proteasome is a validated anti-cancer target, and holds substantial promise as a target for treatment of neurodegenerative disorders and some infectious diseases. Our long-term goal is to understand how the three major complexes of the proteasome—the lid, base, and core particle—engage and communicate within and between one another. We have thus far made significant progress toward this goal and have developed a number of novel tools and reagents that have furthered our understanding of intra- and inter-complex communication. Conceptual advances have included: i) discovery of additional conformational states of the yeast proteasome relevant to substrate catalysis; ii) demonstration that six highly similar ATP-hydrolyzing subunits differentially influence the activation state of the proteasome; iii) discovery of a link between the conformational state of the proteasome and release of a dedicated proteasome assembly chaperone; and iv) and the finding that proteasomal subcomplexes disengage one another prior to their destruction by autophagy. A paradigm emerging from this initial budget period is that rather small binding events or molecular movements are transmitted, often over long distances, to enact largescale conformational changes. Understanding how such local events are amplified and transmitted to distant areas of the proteasome to coordinate assembly and catalysis is thus a critical knowledge gap. In this first renewal, we propose three Aims that explore examples of this paradigm newly discovered by us during the initial budget period. Together, they will push our knowledge of proteasome dynamics and inter-complex communication into new arenas. In the first, we will use newly developed FRET-based kinetic assays to decipher how local changes to the lid-base interface regulate the timely binding and release of dedicated assembly chaperones from nascent proteasomes. In the second, we will explore a surprising allosteric conduit originating from the substrate unfolding center of the proteasome that regulates the stability between two key subcomplexes. In the third Aim, we will investigate an unusual eukaryotic proteasome from a poorly studied human parasite from the phylum of Microsporidia. Microsporidia lack several proteasome subunits that normally span a key inter-complex interface. The missing subunits contain several small sequence elements with essential roles in assembly and catalysis in other eukaryotes, so exploring these unusual proteasomes will thus reveal both conserved and unique elements of inter-complex communication. These studies are anticipated to produce important insights into the engagement and communication between the proteasomal subcomplexes, significantly advancing several aspects of proteasome biology and drug discovery. Further, microsporidia are NIH priority pathogens of interest for which no broadly effective treatments exist. Insights into microsporidial proteasomes thus may reveal new targets to combat certain parasitic infections.

• Investigation of the proteasome assembly landscape

  5R01GM144550-03

  NIGMS · FY 2024 · $430K

  Project Summary Abstract The 26S proteasome conducts most regulated protein degradation and eliminates toxic proteins in vivo. The proteasome is an unusually large and complex ATP-dependent protease comprising nearly 70 individual polypeptide subunits. Although the conventional thinking has been that the proteasome is assembled from these subunits in a single, rigid stepwise sequence, recent evidence from our group and others unexpectedly suggests a broader “landscape” of assembly routes may exist in vivo. Although this possibility has not yet been tested, such an assembly landscape would ensure that this essential biological process can continue effectively in the face of assembly roadblocks, and would provide a powerful means to adjust the speed or volume of proteasome biogenesis in response to the cellular environment. There is an increasing interest in harnessing proteasome biogenesis to help treat conditions as diverse as cancer and neurodegenerative disorders. Understanding whether such an assembly landscape exists, and if so, how it is harnessed to ensure rapid and faithful proteasome biogenesis, will be critical to guide development of such assembly-targeted therapies. The goal of this multi-PI application is to test the hypothesis that a proteasome assembly landscape exists in vivo, and that the relative flux through possible routes within this landscape is governed largely by kinetic factors that change in response to the intracellular environment. By combining the PIs’ respective expertise in proteasome biology and in enzyme kinetics and single molecular biophysics, we hope to validate this new paradigm for proteasome biogenesis. The proposed studies, described below, will add a critical new dimension— time—to our understanding of proteasome assembly in vivo. Our experimental approach contains two complementary but independent Aims. In Aim 1, we will utilize a newly established collection of cutting-edge single-molecule and ensemble fluorescence assays to characterize the kinetics of specific proteasome assembly steps. Experiments under this aim are designed to test the hypothesis that the relative flux through two possible assembly routes is primarily under kinetic control, but can be tuned by exogenous factors such as ligands or proteasome-interacting accessory proteins. Aim 2 will employ a suite of newly developed chemical-genetic approaches to assess the relative flux through two possible assembly routes in vivo, and to understand how the flux changes in response to environmental stimuli. Experiments under this Aim will also test in living cells the predictions derived from our in vitro kinetic model of assembly established in Aim 1. The outcomes of these studies will lead to a deeper understanding of proteasome biology and of macromolecular assembly in general, and also promise to illuminate new therapeutic avenues for cancer, neurodegeneration, and other diseases.

• Engagement and Communication Between Proteasomal Subcomplexes

  5R01GM118600-07

  NIGMS · FY 2024 · $301K

  Project Summary Abstract The 26S proteasome conducts most regulated protein degradation and eliminates toxic proteins from cells. The proteasome is a validated anti-cancer target, and holds substantial promise as a target for treatment of neurodegenerative disorders and some infectious diseases. Our long-term goal is to understand how the three major complexes of the proteasome—the lid, base, and core particle—engage and communicate within and between one another. We have thus far made significant progress toward this goal and have developed a number of novel tools and reagents that have furthered our understanding of intra- and inter-complex communication. Conceptual advances have included: i) discovery of additional conformational states of the yeast proteasome relevant to substrate catalysis; ii) demonstration that six highly similar ATP-hydrolyzing subunits differentially influence the activation state of the proteasome; iii) discovery of a link between the conformational state of the proteasome and release of a dedicated proteasome assembly chaperone; and iv) and the finding that proteasomal subcomplexes disengage one another prior to their destruction by autophagy. A paradigm emerging from this initial budget period is that rather small binding events or molecular movements are transmitted, often over long distances, to enact largescale conformational changes. Understanding how such local events are amplified and transmitted to distant areas of the proteasome to coordinate assembly and catalysis is thus a critical knowledge gap. In this first renewal, we propose three Aims that explore examples of this paradigm newly discovered by us during the initial budget period. Together, they will push our knowledge of proteasome dynamics and inter-complex communication into new arenas. In the first, we will use newly developed FRET-based kinetic assays to decipher how local changes to the lid-base interface regulate the timely binding and release of dedicated assembly chaperones from nascent proteasomes. In the second, we will explore a surprising allosteric conduit originating from the substrate unfolding center of the proteasome that regulates the stability between two key subcomplexes. In the third Aim, we will investigate an unusual eukaryotic proteasome from a poorly studied human parasite from the phylum of Microsporidia. Microsporidia lack several proteasome subunits that normally span a key inter-complex interface. The missing subunits contain several small sequence elements with essential roles in assembly and catalysis in other eukaryotes, so exploring these unusual proteasomes will thus reveal both conserved and unique elements of inter-complex communication. These studies are anticipated to produce important insights into the engagement and communication between the proteasomal subcomplexes, significantly advancing several aspects of proteasome biology and drug discovery. Further, microsporidia are NIH priority pathogens of interest for which no broadly effective treatments exist. Insights into microsporidial proteasomes thus may reveal new targets to combat certain parasitic infections.

• Investigation of the proteasome assembly landscape

  5R01GM144550-02

  NIGMS · FY 2023 · $430K

  Project Summary Abstract The 26S proteasome conducts most regulated protein degradation and eliminates toxic proteins in vivo. The proteasome is an unusually large and complex ATP-dependent protease comprising nearly 70 individual polypeptide subunits. Although the conventional thinking has been that the proteasome is assembled from these subunits in a single, rigid stepwise sequence, recent evidence from our group and others unexpectedly suggests a broader “landscape” of assembly routes may exist in vivo. Although this possibility has not yet been tested, such an assembly landscape would ensure that this essential biological process can continue effectively in the face of assembly roadblocks, and would provide a powerful means to adjust the speed or volume of proteasome biogenesis in response to the cellular environment. There is an increasing interest in harnessing proteasome biogenesis to help treat conditions as diverse as cancer and neurodegenerative disorders. Understanding whether such an assembly landscape exists, and if so, how it is harnessed to ensure rapid and faithful proteasome biogenesis, will be critical to guide development of such assembly-targeted therapies. The goal of this multi-PI application is to test the hypothesis that a proteasome assembly landscape exists in vivo, and that the relative flux through possible routes within this landscape is governed largely by kinetic factors that change in response to the intracellular environment. By combining the PIs’ respective expertise in proteasome biology and in enzyme kinetics and single molecular biophysics, we hope to validate this new paradigm for proteasome biogenesis. The proposed studies, described below, will add a critical new dimension— time—to our understanding of proteasome assembly in vivo. Our experimental approach contains two complementary but independent Aims. In Aim 1, we will utilize a newly established collection of cutting-edge single-molecule and ensemble fluorescence assays to characterize the kinetics of specific proteasome assembly steps. Experiments under this aim are designed to test the hypothesis that the relative flux through two possible assembly routes is primarily under kinetic control, but can be tuned by exogenous factors such as ligands or proteasome-interacting accessory proteins. Aim 2 will employ a suite of newly developed chemical-genetic approaches to assess the relative flux through two possible assembly routes in vivo, and to understand how the flux changes in response to environmental stimuli. Experiments under this Aim will also test in living cells the predictions derived from our in vitro kinetic model of assembly established in Aim 1. The outcomes of these studies will lead to a deeper understanding of proteasome biology and of macromolecular assembly in general, and also promise to illuminate new therapeutic avenues for cancer, neurodegeneration, and other diseases.

• Engagement and Communication Between Proteasomal Subcomplexes

  2R01GM118600-06A1

  NIGMS · FY 2023 · $302K

  Project Summary Abstract The 26S proteasome conducts most regulated protein degradation and eliminates toxic proteins from cells. The proteasome is a validated anti-cancer target, and holds substantial promise as a target for treatment of neurodegenerative disorders and some infectious diseases. Our long-term goal is to understand how the three major complexes of the proteasome—the lid, base, and core particle—engage and communicate within and between one another. We have thus far made significant progress toward this goal and have developed a number of novel tools and reagents that have furthered our understanding of intra- and inter-complex communication. Conceptual advances have included: i) discovery of additional conformational states of the yeast proteasome relevant to substrate catalysis; ii) demonstration that six highly similar ATP-hydrolyzing subunits differentially influence the activation state of the proteasome; iii) discovery of a link between the conformational state of the proteasome and release of a dedicated proteasome assembly chaperone; and iv) and the finding that proteasomal subcomplexes disengage one another prior to their destruction by autophagy. A paradigm emerging from this initial budget period is that rather small binding events or molecular movements are transmitted, often over long distances, to enact largescale conformational changes. Understanding how such local events are amplified and transmitted to distant areas of the proteasome to coordinate assembly and catalysis is thus a critical knowledge gap. In this first renewal, we propose three Aims that explore examples of this paradigm newly discovered by us during the initial budget period. Together, they will push our knowledge of proteasome dynamics and inter-complex communication into new arenas. In the first, we will use newly developed FRET-based kinetic assays to decipher how local changes to the lid-base interface regulate the timely binding and release of dedicated assembly chaperones from nascent proteasomes. In the second, we will explore a surprising allosteric conduit originating from the substrate unfolding center of the proteasome that regulates the stability between two key subcomplexes. In the third Aim, we will investigate an unusual eukaryotic proteasome from a poorly studied human parasite from the phylum of Microsporidia. Microsporidia lack several proteasome subunits that normally span a key inter-complex interface. The missing subunits contain several small sequence elements with essential roles in assembly and catalysis in other eukaryotes, so exploring these unusual proteasomes will thus reveal both conserved and unique elements of inter-complex communication. These studies are anticipated to produce important insights into the engagement and communication between the proteasomal subcomplexes, significantly advancing several aspects of proteasome biology and drug discovery. Further, microsporidia are NIH priority pathogens of interest for which no broadly effective treatments exist. Insights into microsporidial proteasomes thus may reveal new targets to combat certain parasitic infections.