Projects
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 the physics models.
The Role of Water in RNA Structure and Recognition
Molecular dynamics simulations are conducted to understand the role of water in RNA structure and recognition. In HIV and a form of leukemia (HLTV-I), water is important in protein recognition of key RNA molecules. 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:
Michael, L.A.; Chenault, J.A.; Miller III, B.R.; Knolhoff, A.M. and Nagan, M.C. (2009), Water, Shape-Recognition, Salt Bridges and Pi-Cation Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element. J. Mol. Biol., 392, 774-786.
The Role of Modified Bases in RNA Structure and Function
We employ a variety of computational and experimental techniques to understand how naturally occurring modified bases change RNA structure and recognition.
Related Work:
Witts, R.N.; Hopson, E.C.; Koballa, D.E.; Van Boening, T.A.; Hopkins, N.H.; Patterson, E.V. and Nagan, M.C. (2013), Backbone-Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure. J. Phys. Chem. B, 117, 7489-7497.
McCrate, N.E.; Varner, M.E.; Kim, K.I. and Nagan, M.C. (2006), Molecular Dynamics Simulations of Human tRNALys,3UUU: The Role of Modified Bases in mRNA Recognition. Nucleic Acids Res., 34, 5361-5368.
