Publications by authors named "Lauren Raguette"

Article Synopsis
  • Phosphorylated amino acids play a critical role in cell regulation and are extensively studied through various simulations to understand biomolecular behaviors like binding and folding.
  • The Amber program's ability to accurately model proteins with phosphorylated amino acids has lagged behind that of standard amino acids, particularly in popular models like ff14SB and ff19SB, which lack these specific parameters.
  • This study develops and validates dihedral parameters for common phosphorylated amino acids using quantum mechanics calculations, and provides compatible libraries and parameter files for both ff14SB and ff19SB models.
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Article Synopsis
  • RNA research is expanding, but understanding its structural dynamics and interactions with small molecules remains limited, especially when compared to protein studies.
  • This study focuses on addressing the weak CH···O interactions in RNA, which are significant yet often overlooked in force field development, particularly in widely used Amber RNA force fields.
  • By adjusting the CH···O repulsion in these force fields, the study found that RNA simulations became more stable, resulting in improved accuracy in modeling RNA structures during molecular dynamics simulations.
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The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 pandemic. The spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell and is the primary target of neutralizing antibodies. The receptor binding domain (RBD) of the spike samples multiple conformations in a compromise between evading immune recognition and searching for the host-cell surface receptor.

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The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine development efforts are underway, there are many outstanding questions on the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and host cell entry. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular spike glycoprotein and at the receptor-binding domain (RBD)-receptor interface, suggesting a role in infection.

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Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago.

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