Biology subjects

Anastasiou, D.

Publications and source records attributed to Anastasiou, D..

5 recordsLinked to original sources

bioRxiv2025

TS2CG as a membrane builder

Molecular dynamics (MD) simulations excel at capturing biological processes at the molecular scale but rely on a well-defined initial structure. As MD simulations now extend to whole-cell-level modeling, new tools are needed to efficiently build initial structures. Here, we introduce TS2CG version 2, designed to construct coarse-grained membrane structures with any desired shape and lateral organization. This version enables precise placement of lipids and proteins based on curvature preference, facilitating the creation of large, near-equilibrium membranes. Additional features include controlled pore generation and the placement of specific lipids at membrane edges for stabilization. Moreover, a Python interface allows users to extend functionality while maintaining the high performance of the C++ core. To demonstrate its capabilities, we showcase challenging simulations, including a Mobius strip membrane, a vesicle with lipid domain as continental plates (Martini globe), and entire mitochondrial membranes exhibiting lipid heterogeneity due to curvature, along with a comprehensive set of tutorials.

biophysics↗

bioRxiv2023

GOT1 primes the cellular response to hypoxia by supporting glycolysis and HIF1α stabilisation

Adaptation to chronic hypoxia occurs through changes in protein expression, which are controlled by hypoxia inducible factor 1a (HIF1) and are necessary for cancer cell survival. However, the mechanisms that enable cancer cells to adapt in early hypoxia, prior to full activation of HIF1, remain poorly understood. Here we show that aspartate transaminase 1 (GOT1), which supports NAD+ production by malate dehydrogenase 1 (MDH1), is required, in addition to reserve lactate dehydrogenase (LDH) capacity, for the HIF1-independent increase in glycolysis we observe early upon exposure of cells to hypoxia. Additionally, GOT1 maintains low -ketoglutarate levels, thereby limiting prolyl hydroxylase activity to promote HIF1 stabilisation in early hypoxia and robust HIF1 target gene expression in later hypoxia. Our findings reveal that, in normoxia, GOT1 maintains cells in a primed state and ready to support increased glycolysis and HIF1 stabilisation upon oxygen limitation, until other adaptive processes that require more time, are fully established.

cancer biology↗

bioRxiv2021

Development of novel MOG analogues with increased stability to explore MCT2 and α-ketoglutarate biology in vivo

-ketoglutarate (KG) is a central metabolic node with a broad influence on cellular physiology. The KG analogue N-oxalylglycine (NOG) and its membrane-permeable pro-drug derivative dimethyl-oxalylglycine (DMOG) have been extensively used as tools to study prolyl hydroxylases (PHDs) and other KG-dependent processes. In cell culture media, DMOG is rapidly converted to MOG, which enters cells through monocarboxylate transporter MCT2, leading to intracellular NOG concentrations that are sufficiently high to inhibit glutaminolysis enzymes and cause cytotoxicity. Therefore, the degree of (D)MOG instability together with MCT2 expression levels determine the intracellular targets NOG engages with and, ultimately, its effects on cell viability. Here we designed and characterised a series of MOG analogues with the aims of improving stability and exploring the functional requirements for interaction with MCT2, a relatively understudied member of the SLC16 family. We report MOG analogues that maintain ability to enter cells via MCT2, and identify compounds that do not inhibit glutaminolysis or cause cytotoxicity but can still inhibit PHDs. We use these analogues to show that glutaminolysis-induced activation of mTORC1 can be uncoupled from PHD activity. Therefore, these new compounds can help deconvolute cellular effects that result from the polypharmacological action of NOG.

biochemistry↗

bioRxiv2018

Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation

Allosteric regulation is central to the role of the glycolytic enzyme pyruvate kinase M2 (PKM2) in cellular metabolism. Multiple activating and inhibitory allosteric ligands regulate PKM2 activity by controlling the equilibrium between high activity tetramers and low activity dimers and monomers. However, it remains elusive how allosteric inputs upon simultaneous binding of different ligands are integrated to regulate PKM2 activity. Here, we show that, in the presence of the allosteric inhibitor L-phenylalanine (Phe), the activator fructose 1,6-bisphosphate (FBP) can induce PKM2 tetramerisation, but fails to maximally increase enzymatic activity. Guided by a new computational framework we developed to identify residues that mediate FBP-induced allostery, we generated two PKM2 mutants, A327S and C358A, in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings demonstrate a role for residues involved in FBP-induced allostery in enabling the integration of allosteric input from Phe and reveal a mechanism that underlies the co-ordinate regulation of PKM2 activity by multiple allosteric ligands.

biochemistry↗

bioRxiv2018

Glycosylation-dependent modulation of the lL-2 signaling axis determines Th17 differentiation and IL-10 production

Metabolism plays an essential role in shaping T helper (Th) cell responses including the production of pro-inflammatory cytokines, however the effects on IL-10 have not been investigated. We show that the glucose analogue 2-deoxyglucose (2DG) specifically inhibits Th1 and Th2 cell differentiation and accompanying IL-10 production. In contrast, 2DG promotes IL-17A production by Th17 cells, even in the presence of IL-2 known to limit Th17 differentiation, whilst totally abrogating the production of IL-10. Notably, rather than inhibiting glycolysis, 2DG acts through the inhibition of glycosylation, which is critical for IL-2R surface expression and downstream signaling in both mouse and man. Strikingly, IL-2 is essential for IL-10 production by Th17 cells, in contrast to its inhibitory effect on the production of IL-17A. Our study reveals a previously unappreciated, anti-inflammatory role for IL-2 in Th17 cell production of IL-10 and thus identifies a novel mechanism to limit Th17 pathogenicity.

immunology↗