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High-resolution Molecular Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2).
Chemistry
November 2024
Sorbonne Université - Campus Pierre et Marie Curie, Laboratoire de Chimie Théorique, 4 place Jussieu, 75005, Paris, FRANCE.
Glucose metabolism plays a pivotal role in physiological processes and cancer growth. The final stage of glycolysis, converting phosphoenolpyruvate (PEP) into pyruvate, is catalyzed by the pyruvate kinase (PK) enzyme. Whereas PKM1 is mainly expressed in cells with high energy requirements, PKM2 is preferentially expressed in proliferating cells, including tumor cells.
View Article and Find Full Text PDFImpact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain.
Chemphyschem
October 2024
Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
Article Synopsis
- Molecular dynamics (MD) simulations help researchers analyze the atomic behavior of molecules over time, but optimal use of resources is necessary to maximize outcomes.
- The study examines the variability in MD measurements based on different simulation lengths and the number of replicas using independent trajectories compared to a benchmark trajectory.
- Findings indicate that a standardized approach to MD simulations is not practical; sometimes, longer trajectory lengths are more beneficial than multiple replicas, depending on the research goals.
Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain.
Elife
September 2024
Tetrad Graduate Program, University of California, San Francisco, San Francisco, United States.
MET is a receptor tyrosine kinase (RTK) responsible for initiating signaling pathways involved in development and wound repair. MET activation relies on ligand binding to the extracellular receptor, which prompts dimerization, intracellular phosphorylation, and recruitment of associated signaling proteins. Mutations, which are predominantly observed clinically in the intracellular juxtamembrane and kinase domains, can disrupt typical MET regulatory mechanisms.
View Article and Find Full Text PDFModulation of the conformational landscape of the PDZ3 domain by perturbation on a distal non-canonical α3 helix: decoding the microscopic mechanism of allostery in the PDZ3 domain.
Phys Chem Chem Phys
August 2024
School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
While allosteric signal transduction is crucial for protein signaling and regulation, the dynamic process of allosteric communication remains poorly understood. The third PDZ domain (PDZ stands for the common structural domain shared by the postsynaptic density protein (PSD95), Drosophila disc large tumor suppressor (DlgA), and zonula occludens-1 protein (ZO-1)) serves as a classic example of a single-domain allosteric protein, demonstrating a long-range coupling between the C-terminal α helix (known as the α3 helix) and ligand binding. A molecular level understanding of how the α3 helix modulates the ligand binding affinity of the PDZ3 domain is still lacking.
View Article and Find Full Text PDFMultiple Functional Protein-Protein Interaction Interfaces Allosterically Regulate ATP-Binding in Cyclin-Dependent Kinase-1.
Proteins
November 2024
Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
The ATP-dependent phosphorylation activity of cyclin-dependent kinase 1 (CDK1), an essential enzyme for cell cycle progression, is regulated by interactions with Cyclin-B, substrate, and Cks proteins. We have recently shown that active site acetylation in CDK1 abrogated binding to Cyclin-B which posits an intriguing long-range communication between the catalytic site and the protein-protein interaction (PPI) interface. Now, we demonstrate a general allosteric link between the CDK1 active site and all three of its PPI interfaces through atomistic molecular dynamics (MD) simulations.
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