July 2019

  1. Cholko, T., Kaushik, S., Chang, C-E. A. Dynamics and Surface Interactions of ssDNA in Nucleic Acid Biosensors with Varied Surface Properties. PCCP, 2019,21,16367 - 16380. [link] (PubMed)
  2. O’Rourke, K. F. O., Debashish Sahu, D., Bosken, Y. K., Amico, R. N. D., Chang, C-E. A. and Boehr, D.D. Coordinated network changes across the catalytic cycle of α-tryptophan synthase Structure, 2019, 27, 1-11. [link] (PubMed)
  3. Allec. S.I., Sun, Y., Sun, J., Chang, C-E. A.* and Wong* B.M., Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems. J. of Chemical Theory and Computation, 2019, 15, 2807-2815. [link] (PubMed)
  4. You, W., Tang, Z. and Chang, C-E. A., Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed? J. of Chemical Theory and Computation, 2019, 15, 2433-2443. [link] (PubMed)
  5. Chen, W., Ren, X., and Chang C-E. A., Discovery of CDK8/CycC Ligands with a new Virtual Screening Tool. ChemMedChem, 2019, 1, 1-13 Invited Cover Feature. [link] (PubMed)
  6. Li, Z., Shao, S., Ren, X., Sun, J., Guo, Z., Wang, S., Chang, C-E. A., and Xue, M, Construction of a Sequenceable Bicyclic Peptide Library with a Real 3-D Diversifiable Chemical Space. J. Am. Chem. Soc. , 2018, 140, 14552-14556. [link] (PubMed)
  7. Chang, C-E. A., Tuning Free Energy by Backbone Conformational Entropy: A Strategy from Disordered Proteins. Biophysical J., 2018, 144, 2757-2758. [link] (PubMed)
  8. Cholko, T., Chen, W., Tang, Z., and Chang, C-E. A., A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery J. of Comput. Aided. Mol. Des. , 2018, 32, 671-685 . [link] (PubMed)
  9. You, W., and Chang, C-E. A., Role of Molecular Interactions and Protein Rearrangementin the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. J. of Chem. Inf. Model., 2018, 58, 968-981. [link] (PubMed)
  10. Miao, Y., Huang, Y-M. M., Walker, R. C., McCammon, J. A., Chang, C-E. A, Ligand Binding Pathways and Conformational Transitions of the HIV Protease Biochemistry, 2018, 6, 1533-1541. [link] (PubMed)
  11. Chen, W., Sun, L., Tang, Z., Ali, Z. A., Wong, B. M., Chang, C-E. A., An MM and QM Study of Biomimetic Catalysis of Diels-Alder Reactions Using Cyclodextrins Catalysts, 2018, 8,51. [link] (PubMed)
  12. Tang, Z. and Chang, C-E. A., Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition J. of Chemical Theory and Computation, 2018, 12, e1005057 . [link] (PubMed)
  13. Bakas, N. A., Schultz, C. R., Yco, L. T., Roberts, C. C., Chang, C-E. A, Bachmann, A. S., and Pirrung, M. C, Immunoproteasome inhibition and bioactivity of thiasyrbactins. Bioorganic & Medicinal Chemistry, 2018, 26, 401-412. [link] (PubMed)
  14. Tang, Z. and Chang, C-E. A., Systematic dissociation pathways searches guided by principal component modes. J. of Chemical Theory and Computation, 2017, 13, 2230-2244 . [link] (PubMed)
  15. Ahrendt, S. R., Medina, E. M., Chang, C-E. A. and Stajichi, J. E., Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PEERJ, 2017, 5, e5206. [link] (PubMed)
  16. Miyata, N., Tang, Z., Conti1, M. A., Johnson, M. E., Douglas, C. J., Hasson, S. A., Damoiseaux, R., Chang, C-E. A. and Koehler, C. M., Adaptation of a genetic screen reveals an inhibitor for mitochondrial protein import component Tim44. J. Biol. Chem.,, 2017,5429-5442. [link] (PubMed)
  17. Huang, Y.-M. M., Raymundo, M. A. V., Chen, W., and Chang, C.-E. A*. Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV‑1 Protease. Biochemistry, 2017, 1311-1323. [link] (PubMed)
  18. Tang, Z., Roberts, C. C., Chang, C-E. A.*, Understanding ligand-receptor non-covalent binding kinetics using molecular modeling. Frontiers in Bioscience,, 2017,Landmark, 22, 960-981. [link] (PubMed)
  19. You, W., Huang Y-M. M, Kizhake, S., Natarajan, A., Chang, C-E. A., Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. PLOS Computational Biology, 2016, 12, e1005057 . [link] (PubMed)
  20. Roberts, C. and Chang C-E. A., Analysis of Ligand−Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations, J. Phys. Chem. B., 2016, in press. [link] (PubMed)
  21. Gao, Y., Roberts, C. C., Zhu, J., Toop, A., Chang, C-E. A. and Wheeldon, I Mechanisms of Enhanced Catalysis in Enzyme–DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis, ChemBioChem, 2016, 17, 1430-1436. Back cover art, Very Important Paper [link] (PubMed)
  22. Chang, C-E. A., Huang, Y-M. M., Mueller, L. J. and You, W, Catalyst Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. Catalyst, 2016, 6, 82-103. [link] (PubMed)
  23. Achmann, A.S., Opoku-Ansah, J., Ibarra-Rivera, T. R., Yco, L. P., Ambadi, S., Roberts, C. C., Chang, C-E. A., and Pirrung, M. C., Syrbactin Structural Analog TIR-199 Blocks Proteasome Activity and Induces Tumor Cell Death. The Journal of Biological Chemistry, 2016, 291, 8350-8362. Cover Art [link] (PubMed)
  24. Hilario, E., Caulkins, B. G. , Huang, Y. M. M., You, W., Chang, C-E. A., Mueller, L. J., Dunn, M. F., Fan, L. Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water. Biochim Biophys Acta, 2016, 268-279. [link] (PubMed)
  25. Zhang, C., Brown, M. Q., … Huang, Y. M., Ghang, Y.J., ung, N., Li, R., Isley, J., Morikis, D., Song, J., Guo, W., Holley, R. J., Chang, C-E. A., Yang, Z., Zarsky, V., Muday, G. K., Hicks, G. R., Raikhel, N. V. Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis. Proc. Natl. Acad. Sci. U. S. A. , 2015, E41-E45. [link] (PubMed)
  26. . Huang, Y.M., You, W., Caulkins, B.G., Dunn, M.F., Mueller, L., Chang, C-E. A. Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase. Protein Sciences. 2015, 136, 12824-12827. [link] (PubMed) [Special issue for Ron Levy’s birthday]
  27. Gao, Y., Roberts, C. C., Zhu, J., Lin, J.-Y., Chang, C-E. A. and Wheeldon, I., Tuning Enzyme Kinetics through Designed Intermolecular Interactions Far from the Active Site. ACS Catalysis. 2015, 5, 2149-2153. [link] (PubMed)
  28. Roberts, C. C. and Chang, C-E. A., Modeling of Enhanced Catalysis in Multi-enzyme Nanostructures: Effect of Molecular Scaffolds, Spatial Organization, and Concentration. J. of Chemical Theory and Computation, 2015, [link] (PubMed)
  29. Zhang, X., Niu, D., Carbonell, A., Wang, A., Lee, A., Tun, V., Wang, Z., Carrington, J., Chang, C.-E. A. and Jin, H., Argonaute PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis. Nature Communications, 2014, 5, 5468. [link] (PubMed)
  30. Protonation states of the traptophan synthase internal aldimine active site from sold-state NMR spectroscopy: direct observation of the protonated Schiff base linkage to pyridoxal-5’-phosphate. Caulkins, B.G., Bastin, B., Yang, C., Neubauer, T.J., Young, R.P., Hilario, E., Huang, Y.M., Chang, C.-E. A., Fan, L., Dunn, M.F., Marsella, M.J., Mueller, L.J., J. Am. Chem. Soc. 2014, 136, 12824-12827. [link] (PubMed)
  31. Tang, Z., Zhang, Q., Yin, Y., Chang, C.-E. A., Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study. J. of Physical Chemistry C, 2014, 118, 21589-21598. [link]
  32. Huang, Y.-M. M. Kang, M., and Chang, C.-E. A., Switches of hydrogen-bonds During Ligand-protein Association Processes as Determinants of Binding Kinetics, Journal of Molecular Recognition, 2014.27, 537-548. [link] (PubMed).
  33. Huang, Y.-M. M. and Chang, C.-E. A., Achieveing Specificity and Promiscuity by Loop Recognition: Case of the FHA domains. PLoS ONE, 2014, 9, e98291. [link] (PubMed).
  34. Axe, J. M., Yezdimer, E. M., O’Rourke, K. F., Kerstetter, N. E., You, W. Chang, C.-E. A. and Boehr, D. D. J. Am. Chem. Soc., 2014, 136, 6818-6821. [link] .
  35. Zeng, S., Huang, Y-M. M., Chang, C-E. A.*, and Zhong, W*. Protein Binding for Detection of Small Changes on Nanoparticle Surface, Analyst, 2014, 139, 1364-1371. [link] .
  36. Chang, C-E. A., and Huang, Y-M. M. Atomistic Modeling of Phosphopeptide Recognition of Modular Domains, Ralph A. Wheeler, editors: Annual Reports in Computational Chemistry, 2013, Vol. 9, 61-84. [pdf]
  37. Roberts, C. and Chang C-E. A., Ligand binding pathway elucidation for cryptophane host-guest complexes. J. of Chemical Theory and Computation, 2013, 9:2010-2019, [link] . (PubMed).
  38. Kumar, E. A., Chen, Q., Kizhake, S., Kolar, C., Kang, M., Chang, C-E. A., Borgstahl, G. E. O., and Natarajan, A., The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides. Scientific Reports, 2013, 3:1639 [link] .
  39. Yaghmaei, S., Roberts, C., Ai, R., Mizwicki, M. T., and Chang C-E. A., Aognist and antagonist binding to the nuclear vitamin D receptor, dynamics, mutation effects and functional implications. In Silico Pharmacology, 2013, 1:2 [link] .
  40. Huang, Y.-M. M., Kang, M., and Chang C-E. A., Mechanistic insights into phosphopeptide-binding BRCT domains: preorganization, flexibility and phosphate recognition. J. of Physical Chemistry B, 2012, 116,10247-10258 [link] .
  41. Ai, R., and Chang, C-E. A., Ligand-Specific Homology Modeling of Human Cannabinoid (CB1) Receptor. Journal of Molecular Graphics and Modelling. 2012, [link] .
  42. Huang, Y.M.M, Chen, W., Potter, M. P., and Chang, C-E. A., Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes., Biophysical J., 2012, 103, 342-351 [link] .
  43. Kang, M., Roberts, C., Cheng, Y. and Chang, C-E. A., Gating and Intermolecular Interactions in Ligand-protein Association: Coarse-grained Modeling of HIV-1 Protease, J. of Chemical Theory and Computation, 2011, 10:3438-3446 [link] .
  44. Chang, C-E. A., Ai, R, Gutierres, M., Marsella, M. J., Successful biomedical applications: cannabinoid analogues for therapeutic use. Computer-Aided Drug Design, Methods in Molecular Biology, book editor: Baron, R. 2012, 819, 595-613 [link], [pdf] .
  45. Huang, Y.M.M and Chang, C-E. A., Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics, BMC Biophysics, 2011, 4, 12-25 [link] .
  46. Lai, J., Niks, D., Wang, Y., Domratcheva, T., Barends, T. R. M., Schwarz, F., Olsen, R. A., Elliott, D. W., Fatmi, M. Q., Chang, C-E. A., Schlichting, I., Dunn, M. F. and Mueller, L. J., X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase, J. Am. Chem. Soc., 2011, 133 (1), 4–7 [link] .
  47. Fatmi, M.Q., Chang, C.E. A. The role of oligomerization and cooperative regulation in protein function: The case of tryptophan synthase. PLos Computational Biology, 2010, 6, e1000994 [link] .
  48. Ai, R., Fatmi, M., and Chang, C-E. A., T-Analyst, a program for efficient analysis of protein conformational changes. J Comput Aided Mol Des, 2010. 24, 819-827 [link] .
  49. Peterson, F. C., Burgie, E. S., Park, S-Y, Jensen, D. R., Weiner, J. J., Bingman, C. A., Chang, C.-E. A, Cutler, S. R., Phillips Jr, G. N. and Volkman, B. F., Structural basis for selective activation of ABA receptors., Nature Structural & Molecular Biology, 2010, 17, 1109 – 1113 [link] .
  50. Fatmi, M., Ai, R., and Chang, C-E. A., Synergistic regulation and ligand-induced conformational changes of tryptophan synthase., Biochemistry, 2009. 48, 9921-9931 [link] .
  51. Garcia, A., Borchardt, D, Chang, C-E. A. and Marsella, M. J., Thermal Isomerization of Cannabinoid Analogues. J. Am. Chem. Soc, 2009, 131, 16640-16641 [link] .
  52. Gorfe, A. A. #, Chang, C-E. A. #*, Ivanov I and McCammon J. A., Dynamics of the Acetylcholinesterase Tetramer. Biophysical J. 2008, 94: 1144-1154. (# co-first authors) [link] .
  53. Cheng, Y, Chang C-E. A., Yu Z., Zhang Y., Leyhk T. S., Holst M. J. and McCammon J. A., Substrate Channeling in the Sulfate Activating Complex: Combined Continuum Modeling and Coarse-grained Brownian Dynamics Studies. Biophysical J. 2008, 95: 4659-4667 [link] .
  54. Chang, C-E. A.*, McLaughlin W. A., Baron R., Wang W., and J. Andrew McCammon J.A., Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc. Natl. Acad. Sci. U. S. A., 2008, 105:7456-7461 [link] .

  55. Publications before joining UCR

  56. Chang, C-E.*, Trylska J., Tozzini T. and McCammon J. A., Binding Pathways of Ligand to HIV-1 Protease: Coarse-grained and Atomistic Simulation, Chemical Biology and Drug Design., 2007, 1: 5-13 [link] .
  57. Chang, C-E., Chen, W. and Gilson, M. K., Analysis of the Change in Ligand Entropy upon Protein Binding. Proc. Natl. Acad. Sci. U. S. A., 2007, 104: 1534-1539 [link] .
  58. Trylska J., Tozzini, T., Chang C-E., and McCammon J. A. HIV-1 Protease Substrate Binding and Product Release Pathways Released Pathways Explored with Coarse-grained Molecular Dynamics, Biophysical J. 2007, 92: 4179-4187 [link] .
  59. Tozzini, T., Trylska J., Chang C-E., and McCammon J. A. Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-grained Model, J. or Structural Biology, 2007, 157: 606-605 [link] .
  60. Minh D.D, Chang C-E., Trylska J, Tozzini V, and McCammon J.A., The Influence of Macromolecular Crowding on HIV-1 Protease Molecular Dynamics. J. Am. Chem. Soc. 2006, 128, 6006-6007 [link] .
  61. Chang C-E., Shen T., Trylska J., Tozzini T. and McCammon J. A., Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Mode. Biophysical J, 2006, 90: 3880-3885 [link] .
  62. Chen, W., Chang, C-E., and Gilson, M. K., Concepts in Receptor Optimization: Targeting the Peptide RGD . J. Am. Chem. Soc, 2006, 128: 4675-4687 [link] .
  63. Chang, C-E., Chen, W., and Gilson, M. K., Evaluating the accuracy of the quasiharmonic approximation. J. of Chemical Theory and Computation, 2005, 1, 1017-1028 [link] .
  64. Minh, D.L., Bui, J.M., Chang, C-E., Jain T., and McCammon J.A., The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2. Biophysical J, 2005, 89:L25-L27 [link] .
  65. Chen, W., Chang, C-E., and Gilson, M. K., Calculation of Cyclodextrin Binding Affinities: Energy, Entropy and Implication in Drug Design. Biophysical J, 2004, 87:3035-3049 [link] .
  66. Chang, C-E., and Gilson, M. K., Free Energy, Entropy, and Induced Fit in Host-Guest Recognition. J. Am. Chem. Soc. 2004, 126, 13156–13164 [link] .
  67. Chang, C.-E., Potter, M. J. and Gilson, M. K., Direct Calculation of Conformational Free Energies in All Degrees of Freedom, J. Phys. Chem. B., 2003. 107, 1048-1055 [link] .
  68. DeJong, E. S.#, Chang, C.-E#., Gilson, M. K., Marino, J. P., Proflavine Acts as a Rev Inhibitor by Targeting the High-Affinity Rev Binding Site of the Rev-Responsive Element of HIV-1, Biochemistry, 2003. 42, 8035-8046. (# co-first authors) [link] .
  69. Chang, C.-E and Gilson, M. K., Tork: A Conformational Analysis Method for Molecules and Complexes, J. of Comput Chem, 2003, 24, 1987-1998 [link] .
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