High-resolution Molecular Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2)

• Published in: bioRxiv 2024-01
• Main Authors: Delobelle, Quentin, Jaffrelot-Inizan, Theo, Olivier Passi Adjoua, Lagardere, Louis, Celerse, Frederic, Marechal, Vincent, Jean-Philip Piquemal
• Format: Article
• Language: English
• Subjects: Amoeba; Antitumor agents; Biological activity; Energy requirements; Glucose metabolism; Glycolysis; Kinases; Oligomerization; Pyruvate kinase; Pyruvic acid; Tumor cells; Tumors
• DOI: 10.1101/2024.01.07.574528

Glucose metabolism plays a pivotal role in both normal physiological processes and cancer cell growth. The final stage of glycolysis, converting phosphoenolpyruvate (PEP) into pyruvate, is catalyzed by the pyruvate kinase (PK) enzyme. Whereas PKM1 (isoform 1) is mainly expressed in cells with high energy requirements, PKM2 (isoform 2) is preferentially expressed in proliferating cells, including many tumor cells. Structural analysis of both PKM1 and PKM2 is essential to the design of new molecules with anti-tumor activity. To understand the structural dynamics of PKM1 and PKM2, we performed extensive high-resolution molecular dynamics (MD) simulations using adaptive sampling techniques coupled to the polarizable AMOEBA force field. Performing more than 6μs of simulation, we consider PKM2 in its various oligomerization states and propose structural insights for PKM1. We particularly focus on the structuring of key sites including the active site and the natural substrate Fructose Bi-Phosphate (FBP) fixation pocket. Additionally, we propose the first high-resolution MD simulation of the biologically active PKM1 and uncover important similarities between the constitutive, tetrameric form of PKM1 and its PKM2 counterpart bounded to FBP. Finally, we analyze the impact of the fixation of TEPP-46, a pharmacological activator, on PKM2 structuring and highlight the structural differences with PKM2 bound to FBP.Competing Interest StatementThe authors have declared no competing interest.