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Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study.
Proteins
January 2025
Institute of Transformative bio-Molecules, Nagoya University, Nagoya, Japan.
In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions.
View Article and Find Full Text PDFStructures of ATP-binding cassette transporter ABCC1 reveal the molecular basis of cyclic dinucleotide cGAMP export.
Immunity
January 2025
Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA. Electronic address:
Cyclic nucleotide GMP-AMP (cGAMP) plays a critical role in mediating the innate immune response through the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. Recent studies showed that ATP-binding cassette subfamily C member 1 (ABCC1) is a cGAMP exporter. The exported cGAMP can be imported into uninfected cells to stimulate a STING-mediated innate immune response.
View Article and Find Full Text PDFDeciphering Saquinavir-Bovine Serum Albumin Interactions: Spectroscopic and Computational Insights.
J Mol Recognit
January 2025
Biopolymer Modeling and Protein Chemistry Laboratory, Centre for Advanced Studies in Crystallography and Biophysics, University of Madras, Chennai, India.
Bovine serum albumin (BSA) plays a crucial role as a carrier protein in plasma, binding various ligands, including drugs. Understanding the interaction between BSA and saquinavir, an antiretroviral drug, is essential for predicting its pharmacokinetics and pharmacodynamics. We employed spectroscopic approaches, including circular dichroism spectrometry and fluorescence spectroscopy, to investigate the binding of saquinavir to BSA.
View Article and Find Full Text PDFRanking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations.
J Chem Inf Model
January 2025
Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey.
Genetically encoded fluorescent biosensors (GEFBs) have become indispensable tools for visualizing biological processes A typical GEFB is composed of a sensory domain (SD) that undergoes a conformational change upon ligand binding or enzymatic reaction; the SD is genetically fused with a fluorescent protein (FP). The changes in the SD allosterically modulate the chromophore environment whose spectral properties are changed. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable, and simple to use due to their single-wavelength operation.
View Article and Find Full Text PDFDynamics, mechanistic and energetic evaluation of thiazole-thiadiazole compounds in flavin dependent thymidylate synthase of Mycobacterium tuberculosis.
Int J Biol Macromol
December 2024
Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, MS (Maharashtra), India. Electronic address:
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge due to the emergence of drug-resistant strains. This study targets Flavin-dependent thymidylate synthase (ThyX), an essential enzyme in the thymidylate biosynthesis pathway crucial for bacterial DNA replication. We utilized advanced computational techniques, including molecular dynamics (MD) simulations and interaction energy analysis, to examine the binding interactions and stability of various thiazole-thiadiazole compounds with Mtb ThyX.
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