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Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.
J Chem Theory Comput
January 2025
IBiTech - BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Entrance 98, 9000 Gent, Belgium.
Molecular oxygen (O) is essential for life, and continuous effort has been made to understand its pathways in cellular respiration with all-atom (AA) molecular dynamics (MD) simulations of, e.g., membrane permeation or binding to proteins.
View Article and Find Full Text PDFKinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling.
J Chem Inf Model
December 2024
Department of Chemistry, University of California, Irvine, 1120 Natural Sciences II, Irvine, California 92697, United States.
As a model system, the binding pocket of the L99A mutant of T4 lysozyme has been the subject of numerous computational free energy studies. However, previous studies have failed to fully sample and account for the observed changes in the binding pocket of T4 L99A upon binding of a congeneric ligand series, limiting the accuracy of results. In this work, we resolve the closed, intermediate, and open states for T4 L99A previously reported in experiment in MD and establish definitions for these states based on the dynamics of the system.
View Article and Find Full Text PDFAccounting for Fast vs Slow Exchange in Single Molecule FRET Experiments Reveals Hidden Conformational States.
J Chem Theory Comput
December 2024
Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.
Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Förster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a protein's structural ensemble.
View Article and Find Full Text PDFA pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins.
Protein Sci
December 2024
Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary and tertiary structure and for monitoring conformational changes in proteins of any degree of complexity, including membrane proteins, with high sensitivity. SDSL-EPR also provides information on protein dynamics in the timescale of ps-μs using continuous wave lineshape analysis and spin lattice relaxation time methods. However, the functionally important time domain of μs-ms, corresponding to large-scale protein motions, is inaccessible to those methods.
View Article and Find Full Text PDFIdentification and antibacterial activity of a novel phage-type lysozyme from the freshwater mussel Hyriopsis cumingii.
Dev Comp Immunol
January 2025
Science & Technology Normal University of Jiangxi, Nanchang, 330013, China. Electronic address:
A cDNA encoding a phage-type lysozyme, designated as HcPLYZ, was successfully cloned from Hyriopsis cumingii. The full-length cDNA sequence of HcPLYZ was determined to be 896 base pairs in length. Analysis revealed the absence of a signal peptide at its N-terminus, and identified two highly conserved phage-type lysozyme activity sites, Glu and Asp, within the deduced amino acid sequence of HcPLYZ.
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