Office: 300 E Science Hall (SH)
Phone: 817 272 1091
B.S. Korea University, 1995
M.S. Korea University, 1998
Ph.D. University of Minnesota, 2006
Post Doctorate: Harvard University, 2006-2011
(Martin Karplus and Gregory L. Verdine)
In my lab, we develop and apply computational and theoretical methods with the aim of investigating the chemical and physical problems presented by biomolecular systems. Our current developmental efforts are focused on advancing our ability to simulate protein systems where chemistry is linked with large-scale protein conformational dynamics and corresponding free energy computation. The application part involves, but not limited to, kinases, ATP hydrolases and DNA repair enzymes. These biomolecules present unique set of challenges that present experimental techniques have difficulties to address, while theory can provide detailed understanding at the atomic level.
Kwangho Nam joined the University of Texas at Arlington in Oct 2017. He was born in Korea and received a bachelor’s and master’s degree from the Department of Agricultural Chemistry at Korea University, Seoul, Korea. After serving mandatory military service, he came to the University of Minnesota in 2001 to pursue a Ph.D. in chemistry. During his doctoral study, which was conducted under the guidance of Professors Jiali Gao and Darrin M. York, he has focused on studying chemical reactions in biophysical systems using various computational and theoretical methods and designing new theoretical methods for the modeling of chemical reactions in the condensed phase. After completing his doctorate in 2006, he joined the laboratories of Professors Martin Karplus (Nobel Prize in Chemistry 2013) and Gregory L. Verdine, both of Harvard University, where he learned and developed state-of-the-art simulation methodologies for large scale computer simulation studies. In 2011, he moved to Sweden at Umeå University to begin his independent research career as an assistant professor and research fellow. AT UT Arlington, his research interest is in the development of novel multiscale QM/MM and free energy simulation methods for accelerated simulations of enzymatic catalysis, protein conformational change and ligand recognition and their application to challenging biological systems to aid to understand their working principles.
Publications in last 5 years:
22. Bokka, A.; Mao, J. X.; Hartung, J.; Martinez, S. R.; Simanis, J. A.; Nam, K.; Jeon, J.; Shen, X. Asymmetric synthesis of remote quaternary centers by copper-catalyzed desymmetrization: An enantioselective total synthesis of(+)-mesembrine, Org. Lett. 2018, 20, 5158.
21. Nestor, S. T.; Hawkins, A. N.; Xhani, X.; Sykora, R. E.; Mao, J. X.; Nam, K.; McManus, G. J.; Mirjafari, A. Studies on solubility and S-alkylation of 2-thiouracil in ionic liquids, J. Mol. Liq. 2018, 265, 463.
20. Spulber, S.; Raciti, M.; Dulko-Smith, B.;, Lupu, D.; Rüegg, J.; Nam, K.; Ceccatelli, S. Methylmercury interferes with glucocorticoid receptor: Potential role in the mediation of developmental neurotoxicity, Toxicol. Appl. Pharmacol. 2018, 354, 94.
19. Das, S.; Nam, K.; Major, D. T. Rapid convergence of energy and free energy profiles with QM size in QM/MM simulations of proton transfer in DNA, J. Chem. Theory Comput. 2018, 14, 1695.
18. Mishra, Y.; Hall, M.; Locmelis, R.; Nam, K.; Söderberg, C. A. G.; Strom P.; Chaurasia, N.; Rai, L. C.; Jansson, S.; Schröder, W.; Sauer, U. H. Active site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC7120, Sci. Rep., 2017, 7, 17151.
17. Ojeda-May, P; Nam, K. Acceleration of semiempirical QM/MM methods through MPI, hybrid MPI/OpenMP, and SCF accelerator implementations, submitted.
16. Mishra, Y.; Hall, M.; Nam, K.; Strom P.; Chaurasia, N.; Rai, L. C.; Jansson, S.; Schröder, W.; Sauer, U. H. Active site plasticity revealed in the asymmetric dimer of AnPrx6 – a peroxidase and chaperone from the cyanobacterium Anabaena sp. PCC7120, submitted.
15. Liem-Nguyen, V.; Skyllberg, U.; Nam, K.; Björn, E. Stability constants for mercury(III) complexes with low molecular mass thiols as determined by competing ligand exchange and liquid chromatography inductively coupled plasma mass spectroscopy, submitted.
14. Li, Y.; Nam, K. Dynamic, structural, and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation, Chem. Sci. 2017, 8, 3453.
13. Yeh, J. T.-H.; Nam, K.; Yeh, J. T.-H.; Perriomn, N. eUnaG: a new ligand-inducible fluorescent reporter to detect drug transporter activity in live cells, Sci. rep. 2017, 7, 41619.
12. Ovchinnikov, V.; Nam, K.; Karplus, M. A simple and accurate method to calculate free energy profiles and reaction rates from restrained molecular simulations of diffusive processes, , J. Phys. Chem. B 2016, 120, 8457.
11. Zhang, J.; Li, Y.; Gupta, A.; Nam, K.*; Andersson, P.* Identification and molecular interaction studies of thyroid hormone receptor disruptors among household dust, Chem. Res. Toxicol. 2016, 29, 1345.
10. Ojeda-May, P.; Li, Y.; Ovchinnikov, V.; Nam, K. Role of protein dynamics in allosteric control of the catalytic phosphoryl transfer of insulin receptor kinase, J. Am. Chem. Soc. 2015, 137, 12454.
9. Nam, K. ; Pu, J. ; Karplus, M. Trapping the ATP binding state leads to a detailed understanding of F1-ATPase mechanism, Proc. Natl. Acad. Sci. USA 2014, 111, 17851.
8. Nam, K. Acceleration of ab initio QM/MM calculations under periodic boundary conditions by multiscale and multiple time step approaches, J. Chem. Theory Comput. 2014, 10, 4175.
7. Koag, M.-C.; Nam, K. ; Lee, S. The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β, Nucleic Acids Res. 2014, 42, 11233.
6. Doron, D.; Kohen, A.; Nam, K.; Major, D. T. How accurate are transition states from simulations of enzymatic reactions?, J. Chem. Theory Comput. 2014, 10, 1863.
5. Nam, K. Acceleration of semiempirical quantum mechanical calculations by extended Lagrangian molecular dynamics approach, J. Chem. Theory Comput. 2013, 9, 3393.
4. Nilson, N.; Åden, J.; Niemiec, M. S.; Nam, K.; Wittung-Stafshede, P. Small pH and salt variations radically alter thermal stability and fluctuations of metal-binding domains in the copper transporter, Wilson disease protein, J. Phys. Chem. B 2013, 117, 13038.
3. Huang, Y.; Nam, K.; Westlund, P. The water R1(ω) NMRD profiles of a hydrated protein from molecular dynamics simulation, Phys. Chem. Chem. Phys. 2013, 15, 14089.
2. Crenshaw, C.M.; Nam, K.; Oo, K.; Kutchukian, P.; Bowman, B. R.; Karplus, M.; Verdine, G. L. Enforced presentation of an extrahelical guanine to the lesion-recognition pocket of the human 8-oxoguanine glycosylase, hOGG1, J. Biol. Chem. 2012, 287, 24916.
1. Qi, Y.; Nam, K.; Spong, M. C.; Banerjee, A.; Karplus, M.; Verdine, G. L. Strandwise translocation of a DNA glycosylase along undamaged DNA during the search for lesions, Proc. Natl. Acad. Sci. USA 2012, 109, 1086.
2007-2009. Postdoctoral fellowship from the National Cancer Canter
1992-1995. Honored student scholarships from Korea University
1991. Student entrance scholarship from Korea University