We use computational and experimental approaches to work on the following long-term research directions:

Quantitative Understanding of Human Metabolic Pathway Regulation

The goal of this research direction is to achieve a predictive understanding of human metabolism regulation. Decades of biochemical studies of purified enzymes have yielded extensive knowledge of metabolic enzyme regulation by small molecules and posttranslational modifications. We are using this wealth of information to quantitatively understand how the control of individual enzymes by known and unknown regulators allows human cells to maintain homeostasis and how it breaks down in disease. Our ultimate goal is to accurately predict human metabolism in any cell type, under any condition, and in response to any perturbation.

Deciphering the Molecular Basis of Aging

The goal of this research direction is to understand the molecular mechanisms of aging using model organisms. Decades of aging research identified several environmental conditions (e.g., caloric restriction, temperature), genetic mutants (e.g., daf-2, UPR-MT), and small molecules (e.g., rapamycin) that robustly extend the lifespan of evolutionarily diverse model organisms. We are using a powerful model organism nematode C. elegans to identify the evolutionarily conserved biochemical processes that control lifespan downstream of these classical interventions, which will allow us to rationally design interventions to extend human lifespan.

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Current Projects

HOW DOES METABOLIC HOMEOSTASIS EMERGE FROM THE ACTIVITIES OF INDIVIDUAL ENZYMES?

The function of metabolic homeostasis is to ensure an adequate supply of energy and precursors for macromolecules under variable conditions. We know most of the reactions and enzymes that make up human metabolic pathways. However, we know surprisingly little about the specific control mechanisms that achieve metabolic homeostasis. Our lab uses mathematical modeling in combination with experiments in live cells and in vitro reconstituted metabolic pathways to investigate the following broad questions: What are the specific functions of allosteric regulation of metabolic pathways? How do cells maintain ATP homeostasis and coordinate conflicting demands of energy production and biosynthesis? What are the trade-offs that drove the evolution of specific metabolic pathways and their control mechanisms? A better understanding of metabolic homeostasis is urgently needed as dysregulation of metabolism, collectively referred to as metabolic syndrome, contributes to several common disorders, including diabetes, cardiovascular disease, and nonalcoholic fatty liver disease (NAFLD). Our long-term goal is to develop the ability to accurately predict human metabolism under any conditions.

Selected publications related to this project:
1) Choe M, Einav T, Phillips R, Titov DV. Data-driven model of glycolysis identifies the role of allostery in maintaining ATP homeostasis. bioRxiv 2022.12.28.522046.
2) Kukurugya MA, Titov DV. The Warburg Effect is the result of faster ATP production by glycolysis than respiration. bioRxiv 2022.12.28.522160.

WHAT IS THE MECHANISM OF LIFESPAN EXTENSION BY CALORIC RESTRICTION?

Caloric restriction (CR) extends the lifespan of evolutionarily diverse animals by up to two-fold including, yeast, worms, flies, spiders, mice, rats, and monkeys. In humans, increased body mass index, a correlate of calorie intake, is associated with increased mortality from cancer, heart disease, stroke, diabetes, and infectious disease. Estimates show that one in five deaths in the US are due to high body mass index. Our lab is interested in elucidating the mechanism of CR-mediated lifespan extension and in developing approaches to identify the diet that will maximize the lifespan of an animal. We are using a powerful model organism C. elegans to uncover the specific molecular mechanism that lead to lifespan extension in response to CR. To facilitate these studies, we have setup an automated lifespan imaging machine that allows us to automatically measure the lifespan and motility of > 5,000 worms simultaneously. Our long-term goal is to apply the insights from model organisms towards developing science-based nutrition recommendations that will delay the onset of age-associated diseases in humans.

GENETICALLY-ENCODED TOOLS FOR THE MANIPULATION OF METABOLISM

At a cellular level, the key response to dietary manipulations and exercise involves changes in intracellular bioenergetic parameters such as ATP/ADP, NADH/NAD+, NADPH/NADP+, GSH/GSSG ratios, and mitochondrial membrane potential (ΔΨm). The causal relationship between changes in these crucial parameters and downstream effects of diet and exercise is currently unknown. A key bottleneck in understanding the role of intracellular bioenergetic parameters in regulation of metabolism has been the lack of methods for direct manipulation of these parameters in vivo. To fill this methodological gap, we have introduced three genetically encoded tools – LbNOX, TPNOX, and UCP1 – for manipulation of NADH/NAD+, NADPH/NADP+ ratios and ΔΨm in living cells. We are working on expanding this toolkit to other metabolic parameters, which will allow us to mimic metabolic changes induced by exercise and dietary changes in cell culture and model organisms.

Selected publications related to this project:
1) Choe M, Titov DV. Genetically encoded tool for manipulation of ΔΨm identifies the latter as the driver of integrative stress response induced by ATP synthase dysfunction. bioRxiv 2023.12.27.573435.
2) Choe M, Titov DV. Genetically encoded tools for measuring and manipulating metabolism. Nature Chemical Biology. 2022 May;18(5):451–460.
3) Cracan V*, Titov DV*, Shen H, Grabarek Z, Mootha VK. Genetically encoded tool for manipulation of NADP+/NADPH ratio. Nature Chemical Biology. 2017 Oct;13(10):1088-1095.
4) Titov DV*, Cracan V*, Goodman RP, Peng J, Grabarek Z, Mootha VK. Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio.  Science. 2016 Apr 8;352(6282):231-5.