Denis Titov

We develop experimental and computational approaches to understand cell and organismal metabolism. Our lab asks how metabolism is controlled, why it is organized the way it is, and how it breaks down in aging and disease.

Control of Human Cell Metabolism

Cells run thousands of chemical reactions simultaneously, and these reactions must be precisely controlled. Failure of metabolic control causes diseases such as diabetes, cardiovascular disease, and fatty liver disease. Decades of biochemistry have measured how individual enzymes are regulated, but the function of most regulators at the pathway level remains unknown. Several roles have been proposed, but since the discovery of allosteric regulation in the 1950s, no one has systematically disabled individual regulators in metabolic enzymes and measured the consequences. Such experiments became feasible only recently, with advances in genome editing, metabolomics, and structural biology.

We build large-scale biophysical models that integrate enzyme kinetics data to predict what each regulator does for the pathway as a whole, and we test those predictions experimentally. We recently showed that glycolysis rate is set by ATP demand through mass action, not by the allosteric regulators long thought to control it (Choe et al. 2025). Instead, allosteric regulation of hexokinase and phosphofructokinase maintains high ATP levels and prevents runaway accumulation of glycolytic intermediates. This paper was selected as the 2025 Biophysical Journal Paper of the Year. In a separate study, we found that fructose-2,6-bisphosphate serves a separate role, controlling the balance between glycolytic and respiratory ATP production so that cells can adjust glycolytic flux in response to hormones and biosynthetic needs (Kober et al. 2026).

Selected publications related to this research direction:
1) Choe M, Einav T, Phillips R, Titov DV. Glycolysis model shows that allostery maintains high ATP and limits accumulation of intermediates. Biophysical Journal. 2025 May 20;124(10):1562-1586.
2) Kober MM, Yang X, Webb BA, Titov DV. F26BP enables control of glycolysis rate independent of energy state. bioRxiv 2026.01.31.703051.

Design Principles of Cell Metabolism

Cells have access to multiple routes for producing energy and building blocks, but they consistently favor specific pathways under specific conditions. Two long-standing puzzles illustrate this gap in understanding. First, rapidly growing cells, including cancer cells, rely heavily on glycolysis even when oxygen is available, a phenomenon known as the Warburg effect, even though glycolysis produces only one-tenth as much ATP per glucose molecule as respiration. Second, the same metabolic enzymes are allosterically regulated by the same metabolites in organisms as distant as bacteria and humans, but the selective pressures behind these conserved regulatory choices remain unclear.

We use computational modeling and quantitative experiments to uncover the design logic of metabolic organization. Our work has shown that the Warburg effect arises because glycolysis produces ATP faster per gram of pathway protein than respiration does (Kukurugya et al. 2024), and that this speed advantage allows glycolytic cells to grow faster than respiratory cells (Kukurugya et al. 2025). By asking why cells choose one pathway or regulatory mechanism over another, we aim to identify the fundamental constraints that shape metabolic networks.

Selected publications related to this research direction:
1) Kukurugya MA, Rosset S, Titov DV. The Warburg Effect is the result of faster ATP production by glycolysis than respiration. Proc Natl Acad Sci U S A 2024 Nov 8;121(46):e2409509121.
2) Kukurugya MA, Zhang S, Ha BT, Ekvik AE, Titov DV. Glycolytic ATP production enables rapid mammalian cell growth. bioRxiv 2025.08.12.670003.

Molecular Basis of Aging

Dietary restriction, reduced insulin signaling, and drugs like rapamycin extend lifespan across species, but the downstream biochemical processes responsible remain poorly understood. Identifying the conserved molecular mechanisms that mediate these effects is essential for developing targeted interventions to extend human healthspan.

We use the nematode C. elegans to search for these mechanisms. We found that aging worms accumulate lipoproteins called vitellogenins, homologs of human apolipoprotein B. Apolipoprotein B is the causal driver of cardiovascular disease in humans. Caloric restriction prevents this buildup, and reducing vitellogenin levels alone extends lifespan by over 60%, with no additional benefit from caloric restriction (Yang et al. 2025). These results suggest that diet- and age-dependent lipoprotein accumulation is a conserved mechanism of aging shared by worms and humans.

Selected publications related to this research direction:
1) Yang B*, Manifold B*, Han W*, DeSousa C, Zhu W, Streets A*, Titov DV*. SRS microscopy identifies inhibition of vitellogenesis as a mediator of lifespan extension by caloric restriction in C. elegans. bioRxiv 2025.01.31.636008.

Tools for Manipulation of Metabolism

Diet and exercise reshape cellular metabolism by shifting the balance of key energy currencies like ATP, NADH, and NADPH. Many studies have correlated these changes with altered cell behavior, but correlation alone cannot establish which metabolic shift drives which phenotype. Answering that question requires tools that directly manipulate individual metabolic parameters in living cells.

We have developed a suite of genetically encoded tools, named ATPGobble, LbNOX, TPNOX, and UCP1, that directly alter the ATP/ADP ratio, NAD+/NADH ratio, NADP+/NADPH ratio, and mitochondrial membrane potential in living cells. Using these tools, we showed that mitochondrial membrane potential is the specific signal that triggers a cellular stress response during ATP synthase dysfunction (Choe et al. 2025). We are expanding the toolkit to additional parameters, allowing us to systematically dissect how individual metabolic changes affect cell behavior and to refine our computational models of metabolism.

Selected publications related to this research direction:
1) Ekvik AE, Kober MM, Titov DV. Genetically encoded tool for manipulation of ATP/ADP ratio in human cells. Cell Chemical Biology. 2026 May 21;33(5):683-698.
2) Choe M, Ekvik AE, Stalnaker G, Shin HR, Titov DV. Genetically encoded tool for manipulation of ΔΨm identifies its role as the driver of ISR induced by ATP synthase dysfunction. Cell Chemical Biology. 2025 Apr 17;32(4):620-630.
3) Choe M, Titov DV. Genetically encoded tools for measuring and manipulating metabolism. Nature Chemical Biology. 2022 May;18(5):451–460.
4) 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.
5) 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.

Current Projects

How Does Metabolic Homeostosis 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.