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Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation.
ACS Phys Chem Au
September 2023
Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.
Article Synopsis
- Bioinformatic analysis of the Delta SARS-CoV-2 genome identified a mutation (G15U) in the stem-loop II motif (s2m) that affected its structure and dynamics compared to the ancestral strain.
- The Delta s2m adopted a linear structure instead of the characteristic L-shaped kink found in SARS-CoV-2, which limited its bending dynamics and altered its helical parameters, impacting its behavior in electrophoresis experiments.
- The increased fluctuation and entropic penalty in the Delta s2m's terminal loop explain its reduced ability to homodimerize compared to SARS-CoV-2, resulting in fewer dimer formations.
Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.
J Chem Theory Comput
July 2023
Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs 105, Salt Lake City, Utah 84112, United States.
Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields.
View Article and Find Full Text PDFIonic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations.
J Phys Chem A
August 2022
Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India.
We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method.
View Article and Find Full Text PDFCorrigendum: Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments.
Front Microbiol
May 2022
Plant Molecular Genetics Laboratory, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
[This corrects the article DOI: 10.3389/fmicb.2021.
View Article and Find Full Text PDFRNA-Specific Force Field Optimization with CMAP and Reweighting.
J Chem Inf Model
January 2022
State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 20024 Shanghai, China.
RNA plays a key role in a variety of cell activities. However, it is difficult to capture its structure dynamics by the traditional experimental methods because of the inherent limitations. Molecular dynamics simulation has become a valuable complement to the experimental methods.
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