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Dr. Maria Nagan
Dr. Maria Nagan
Nagan Research
The Nagan lab develops and employs computational methods to examine RNA structure and protein recognition of RNA. Historically, Nagan has been a professor at primarily undergraduate institutions and mentored over 100 undergraduate students in research. At Stony Brook University, the Nagan lab has expanded our research community to include graduate students, postdoctoral fellows, undergraduate students and collaborators. At the heart of our lab, we care about how chemistry in particular affects RNA structure. Representing these properties with computational models requires expertise across a wide area of science including understanding of computer science, biochemistry, structural biology, physics and mathematical principles.
Accurate Physics Models
Accurate Physics Models
Molecular dynamics simulations of RNA are dependent upon accurate physics models. Our lab is interested in developing better computational tools for simulating RNA . The Nagan lab strength is in understanding RNA structural biology and applying that expertise to refine the force field and solvent models. We use python, machine learning and structural analysis to understand how to improve these physics models.
Related Work:
Lauren E. Raguette, Sarah S. Gunasekera, Rebeca I. Diaz Ventura, Ethan Aminov, Jason T. Linzer, Diksha Parwana, Qin Wu, Carlos Simmerling, and Maria C. Nagan* Adjusting the Energy Profle for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simualtions. J. Chem. Phys. B. , 2024, 128 (33), 7921-7933.
Jason T. Linzer, Ethan Aminov, Aalim S. Abdullah, Colleen E. Kirkup, Rebeca I. Diaz Ventura, Vinay R. Bijoor, Jiyun Jung, Sophie Huang, Chi Gee Tse, Emily Álvarez Toucet, Hugo P. Onghai, Arghya P. Ghosh, Alex C. Grodzki, Emilee R. Haines, Aditya S. Iyer, Mark K. Khalil, Alexander P. Leong, Michael A. Neuhaus, Joseph Park, Asir Shahid, Matthew Xie, Jan M. Ziembicki, Carlos Simmerling, and Maria C. Nagan* Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. J. Chem. Inf. Model, 2024, 64, 6092-6104.
The Role of Modified Bases in RNA Structure and Function
The Role of Modified Bases in RNA Structure and Function
In addition to the standard A, G, C and U bases, there are naturally occurring modified bases found in RNA. We employ a variety of computational techniques to understand how the chemical structure of the modified bases change RNA tertiary structure and recognition.
Related Work:
Rachel N. Witts, Emily C. Hopson, Drew E. Koballa, Thomas A. Van Boening; Nicholas H. Hopkins; Eric V. Patterson and Maria C. Nagan* Backbone-Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure. J. Phys. Chem. B, 2013, 117, 7489-7497.
Oscar E. McCrate, Mychel E. Varner; Kenneth I. Kim and Maria C. Nagan* Molecular Dynamics Simulations of Human tRNALys,3UUU: The Role of Modified Bases in mRNA Recognition. Nucleic Acids Res., 2006, 34, 5361-5368.
The Role of Water in RNA Structure and Recognition
The Role of Water in RNA Structure and Recognition
Water directly mediates protein-RNA recognition. It can also screen charge when two highly charged molecules such as RNA and proteins come in contact. We simulate RNA alone and RNA in complex with proteins to understand the role of water in forming these complexes.
Related Work:
Lauren A. Michael, Jessica A. Chenault, Bill R. Miller III, Ann M. Knolhoff and Maria C. Nagan Water, Shape-Recognition, Salt Bridges and Pi-Cation Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element. J. Mol. Biol., 2009, 392, 774-786.
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