Maria C. Nagan

Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition

Arghya Ghosh, Julia N. DuVal, Adrianna M. Cavoto, Maria C. Nagan

Water molecules play a vital role in stabilizing ribonucleic acid (RNA) structures, not only as a solvent but as active participants in molecular recognition. Yet how hydration patterns encode binding specificity across RNA conformations remains poorly understood. The human immunodeficiency virus (HIV) …

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Recent Developments in Amber Biomolecular Simulations

David Andrew Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden et autres

High Resolution Image Download MS PowerPoint Slide Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), …

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Deciphering Hydration Patterns Across RNA Conformations: Insights into Water-Mediated RNA Recognition

Arghya Pratim Ghosh, Adrianna M. Cavoto, Maria C. Nagan

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Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

Lauren E. Raguette, Sarah Gunasekera, Rebeca I. Diaz Ventura, Ethan Aminov et autres

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by …

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Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

Jason T. Linzer, Ethan Aminov, Aalim S. Abdullah, Colleen Kirkup et autres

Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here, we present a systematic analysis of 15 RNA stem-loop sequences simulated with molecular dynamics simulations in an …

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Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

Jason T. Linzer, Ethan Aminov, Aalim S. Abdullah, Colleen Kirkup et autres

Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here we present a systematic analysis of fifteen RNA stem-loop sequences simulated with molecular dynamics simulations in an …

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Adjusting the energy profile for CH–O interactions leads to improved stability of RNA stem-loop structures in MD simulations

Lauren E. Raguette, Sarah Gunasekera, Rebeca I. Diaz Ventura, Ethan Aminov et autres

The role of RNA in biology continues to grow but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule …

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AmberTools

David Andrew Case, Hasan Metin Aktulga, Kellon A. A. Belfon, David S. Cerutti et autres

High Resolution Image Download MS PowerPoint Slide AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

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The Impacts of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational Chemistry

Kelly E. Anderson, K. Aurelia Ball, Chrystal D. Bruce, Maria Alexandra Gomez et autres

The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% …

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Phosphomimetic Mutation at Ser165 of α-Tubulin Promotes the Persistence of GTP Caps in Microtubules

Vinay Maddula, Nathalia S. Glickman Holtzman, Maria C. Nagan, Susan A. Rotenberg

, 257-272). Ser165 lies near the interface between adjacent αβ-tubulin heterodimers and helix H8, which contains Glu254, the catalytic residue in α-tubulin that hydrolyzes the exchangeable GTP in β-tubulin (β:GTP) and triggers MT depolymerization. It was hypothesized that S165D, a phosphomimetic variant …

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Using a lab wiki for longevity and knowledge transfer in undergraduate research

Maria C. Nagan

Abstract Continuity in research group collective knowledge is critical for running a successful research program, but in an undergraduate research lab, this can be particularly challenging. A wiki site dedicated to the research laboratory, a lab wiki, can bridge gaps in student‐to‐student …

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Using a Labwiki for Longevity and Transfer of Knowledge in Undergraduate Research

Maria C. Nagan

Continuity in research group collective knowledge is critical for running a successful research program but in an undergraduate research lab, this can be particularly challenging. A wiki site dedicated to the research laboratory, a lab wiki, can bridge gaps in student-to-student knowledge …

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