/College of Arts and Sciences
Department of Chemistry

 

Maria Nagan

 

Maria C. Nagan

 Associate Professor

B.A. 1997, Grinnell College (Grinnell, IA)
Ph.D. 2001, University of Minnesota – Twin Cities

433 Chemistry
Phone: (631)-632-5793
Email: maria.nagan@stonybrook.edu  

Linkedin

LinkedIn

VISIT THE NAGAN GROUP WEBSITE

 

 

 

The Nagan lab employs computational methods to understand how chemical functional groups affect RNA  structure and recognition. 

RESEARCH LEADERSHIP

Amber Molecular Dynamics Software 

1. Ghosh, A.P., DuVal, J.N., Cavoto, A.M. and Nagan*, M.C. Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition. Current Research in Structural Biology 2026,11, 100184, doi.org/10.1016/j.crstbi.2026.100184.

2. D.A. Case, D.S. Cerutti, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, M. Ghazimirsaeed, G.M. Giambasu, T.J. Giese, A.W. Götz, J.A. Harris, K. Kasavajhala, T. Lee, Z. Li, C. Lin, J. Liu, Y. Miao, R. Salomon-Ferrrer, J. Shen, R. Snyder, J. Swails, R.C. Walker, J. Wang, X. Wu, J. Zeng, T.E. Cheatham, III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan*, K.M. Merz*, Jr. Recent Developments in Amber Biomolecular Simulations. J. Chem. Inf. Model. 2025, 65, 7835-7843, doi.org/10.1021/acs.jcim.5c01063.

3. Raguette, L.E., Gunasekera, S.S., Ventura Diaz, R.I., Aminov, E., Linzer, J.T., Parwana, D., Wu, Q., Simmerling, C. and  Nagan*, M.C. “Adjusting the energy profile for CH–O interactions leads to improved stability of RNA stem-loop structures in MD simulations” J. Phys. Chem. B, 2024, 128, 7921-7933, doi.org/10.1021/acs.jpcb.4c01910.

4. Linzer, J.T., Aminov, E.,Abdullah, A.S., Kirkup, C., Bijoor, V. R.Chong, J., Ventura Diaz, R.I., Grodzki, A.C., Haines, E.R.,Huang, S.Iyer, A.S., Khalil, M.K., Leong, A. P.Neuhaus, M. A., Onghai, H.P., Park, J., Tse, C.G., Álvarez Toucet, E.,Xie, M., Ziembicki, J. M., Simmerling, C. and Nagan*, M.C. “Accurately Folding RNA Stem-Loops in Implicit Solvent” J. Chem. Inf. Model, 2024, 64, 6092-6104, doi.org/10.1021/acs.jcim.4c00756.

5. D. A. Case; H. M. Aktulga; K. Belfon; D. S. Cerutti; G. A. Cisneros; V. W. D. Cruzeiro; N. Forouzesh; T. J. Giese; A. W. Götz; H. Gohlke; S. Izadi; K. Kasavajhala; M. C. Kaymak; E. King; T. Kurtzman; T.-S. Lee; P. Li; J. Liu; T. Luchko; R. Luo; M. Manathunga; M. R. Machado; H. M. Nguyen; K. A. O’Hearn; A. V. Onufriev; F. Pan; S. Pantano; R. Qi; A. Rahnamoun; A. Risheh; S. Schott-Verdugo; A. Shajan; J. Swails; J. Wang; H. Wei; X. Wu; Y. Wu; S. Zhang; S. Zhao; Q. Zhu; T. E. Cheatham, III; D. R. Roe; A. Roitberg; C. Simmerling; D. M. York; Nagan*, M.C. and Merz, K.M. Jr.*, AmberTools23, J. Chem. Inf. Model, 2023, 63, 6183-6191, doi.org/10.1021/acs.jcim.3c01153.

6. Anderson, K., Arradondo, S., Ball, K.A., Bruce, C., Gomez, M.A., He, K., Hendrickson, H., Madison, L., Ringer McDonald, A., Nagan, M.C., Scott, C.E., Soto, P., Tomlinson, A., Varner, M. and Parish*, C. “The Impacts of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational Chemistry” J. Chem. Inf. Model, 2022,62, 6316-6322,  doi.org/10.1021/acs.jcim.2c00566.

7. Maddula, V.,  Holtzman, N. S., Nagan*, M.C. and Rotenberg*, S. A. “Computational Studies of the α/ß-Tubulin Heterodimeric Interface in Microtubules: The Impact of Phosphorylation of Ser165 in α-Tubulin” Biochemistry, 2022, 61, 1508-1516. Cover. doi.org/10.1021/acs.biochem.2c00154.

8. Nagan*, M.C. “Using a Lab Wiki for Longevity and Knowledge Transfer in Undergraduate Research” International Journal of Quantum Chemistry, 2020,120, e26262. doi.org/10.1002/qua.26262.

9. Palermo, G.; Armacost, K.A. and Nagan, M.C. “Women Make COMP: Mentoring the Next Generation of Women in Computational Chemistry” J. Chem. Inf. Model, 2019, 59, 4061-4062, doi.org/10.1021/acs.jcim.9b00643.

10. Witts, R.N.;Hopson, E.C.; Koballa, D.E.; Van Boening, T.A.; Hopkins, N.H.; Patterson, E.V. and Nagan, M.C. “Backbone-Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure” J. Phys. Chem. B, 2013, 117, 7489-7497, doi.org/10.1021/jp400084p.

11. Michael, L.A.; Chenault, J.A.; Miller III, B.R.; Knolhoff, A.M. and Nagan, M.C. “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,  doi.org/10.1016/j.jmb.2009.07.047.

12. McCrate, N.E.; Varner, M.E.; Kim, K.I. and Nagan, M.C. “Molecular Dynamics Simulations of Human tRNALys,3UUU: The Role of Modified Bases in mRNA Recognition” Nucleic Acids Res. 2006, 34, 5361-5368,  doi.org/10.1093/nar/gkl580.

  • Fellow of the American Chemical Society
  • Godfrey Excellence in Teaching Award
  • McNair Mentor Hall of Fame
  • Walker and Doris Allen Fellowship for Faculty Excellence

Amber MD Software Development (2020-present), Chemistry Education Committee Chair (2019-present),  College of Arts and Sciences Associate Dean for Curriculum (2022-2024; Interim 2021), ACS COMP Co-chair Programming (2021-2023), Mercury Executive Committee (2020-2023), ACS COMP Division Chair (Leadership rotation 2016-2018), Adelphi University Chemistry Department Chair (2013-2016), Truman State University Director Office of Student Research (2011-2013)