Publications of R. I. Cukier

Publications of R. I. Cukier 2005-1015 1. Wang, B., Opron, K., Burton, Z. F., Cukier, R. I., and Feig, M. (2015) Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details, Nucleic Acids Research 43, 1133-1146. 2. Cukier, R. I. (2015) Dihedral Angle Entropy Measures for Intrinsically Disordered Proteins, Journal of Physical Chemistry B 119, 3621-3634. 3. Banerjee, R., Yan, H., and Cukier, R. I. (2015) Conformational transition in signal transduction: metastable States and transition pathways in the activation of a signaling protein, The journal of physical chemistry. B 119, 6591-6602. 4. Banerjee, R., Yan, H., and Cukier, R. I. (2014 ) Conformational Transition of Response Regulator RR468 in a Two-Component System Signal Transduction Process, Journal of Physical Chemistry B 118, 4727-4742. 5. Liu, J., Cukier, R. I., Bu, Y., and Shang, Y. (2014) Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation, Journal of Chemical Theory and Computation 10, 4189-4197. 6. Cukier, R. I. (2014) Simulations of Potentials of Mean Force for Separating a Leucine Zipper Dimer and the Basic Region of a Basic Region Leucine Zipper Dimer, Journal of Physical Chemistry B 118, 10341-10354. 7. Banerjee, R., and Cukier, R. I. (2014) Transition Paths of Met-Enkephalin from Markov State Modeling of a Molecular Dynamics Trajectory, Journal of Physical Chemistry B 118, 2883-2895. 8. Wang, B. B., Feig, M., Cukier, R. I., and Burton, Z. F. (2013) Computational Simulation Strategies for Analysis of Multisubunit RNA Polymerases, Chemical Reviews 113, 8546-8566. 9. Nedialkov, Y. A., Opron, K., Assaf, F., Artsimovitch, I., Kireeva, M. L., Kashlev, M., Cukier, R. I., Nudler, E., and Burton, Z. F. (2013) The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation, Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms 1829, 187-198.

10. Liu, J. X., Wang, Z. P., Zhang, M., Cukier, R. I., and Bu, Y. X. (2013) Excess Dielectron in an Ionic Liquid as a Dynamic Bipolaron, Physical Review Letters 110. 11. Liu, J. X., Cukier, R. I., and Bu, Y. X. (2013) Bending Vibration-Governed Solvation Dynamics of an Excess Electron in Liquid Acetonitrile Revealed by Ab Initio Molecular Dynamics Simulation, Journal of Chemical Theory and Computation 9, 4727-4734. 12. Cukier, R. I. (2013) Variance of a Potential of Mean Force Obtained Using the Weighted Histogram Analysis Method, Journal of Physical Chemistry B 117, 14785-14796. 13. Wang, Z. P., Liu, J. X., Zhang, M., Cukier, R. I., and Bu, Y. X. (2012) Solvation and Evolution Dynamics of an Excess Electron in Supercritical CO2, Physical Review Letters 108. 14. Kireeva, M. L., Opron, K., Seibold, S. A., Domecq, C., Cukier, R. I., Coulombe, B., Kashlev, M., and Burton, Z. F. (2012) Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase, Bmc Biophys 5. 15. Cukier, R. L. (2012) Simulations of Temperature and Salt Concentration Effects on bzip, a Basic Region Leucine Zipper, Journal of Physical Chemistry B 116, 6071-6086. 16. Cukier, R. I. (2011) Ferreting out correlations from trajectory data, J Chem Phys 135. 17. Cukier, R. I. (2011) A Hamiltonian Replica Exchange Method for Building Protein-Protein Interfaces Applied to a Leucine Zipper, J. Chem. Phys. 134, 045104. 18. Zhang, L. B., Chen, X. H., Liu, H. Y., Han, L., Cukier, R. I., and Bu, Y. X. (2010) Exploration of the Biological Micro-Surrounding Effect on the Excited States of the Size-Expanded Fluorescent Base x-cytosine in DNA, Journal of Physical Chemistry B 114, 3726-3734. 19. Wang, Z. P., Zhang, L., Cukier, R. I., and Bu, Y. X. (2010) States and migration of an excess electron in a pyridinium-based, room-temperature ionic liquid: an ab initio molecular dynamics simulation exploration, Physical Chemistry Chemical Physics 12, 1854-1861. 20. Seibold, S. A., Singh, B. N., Zhang, C. F., Kireeva, M., Domecq, C., Bouchard, A., Nazione, A. M., Feig, M., Cukier, R. I., Coulombe, B., Kashlev, M., Hampsey, M., and Burton, Z. F. (2010) Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase, Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms 1799, 575-587.

21. Cukier, R. I. (2010) How many atoms are required to characterize accurately trajectory fluctuations of a protein?, The Journal of Chemical Physics 132, 245101. 22. Chen, X. H., Zhang, L. B., Zhang, L., Sun, W. M., Zhang, Z. W., Liu, H. Y., Bu, Y. X., and Cukier, R. I. (2010) alpha-helix C-Terminus Acting as a Relay to Mediate Long-Range Hole Migration in Proteins, Journal of Physical Chemistry Letters 1, 1637-1641. 23. Zhang, L. B., Li, H. F., Chen, X. H., Cukier, R. I., and Bu, Y. X. (2009) Absorption and Fluorescence Emission Spectroscopic Characters of Size-Expanded ydna Bases and Effect of Deoxyribose and Base Pairing, Journal of Physical Chemistry B 113, 1173-1181. 24. Wang, Z. P., Zhang, L., Chen, X. H., Cukier, R. I., and Bu, Y. X. (2009) Excess Electron Solvation in an Imidazolium-Based Room-Temperature Ionic Liquid Revealed by Ab Initio Molecular Dynamics Simulations, Journal of Physical Chemistry B 113, 8222-8226. 25. Wang, Z., Zhang, L., Chen, X., Cukier, R. I., and Bu, Y. (2009) Excess Electron Solvation in an Imidazolium-Based Room-Temperature Ionic Liquid Revealed by Ab Initio Molecular Dynamics Simulations, The Journal of Physical Chemistry B 113, 8222-8226. 26. Su, L., and Cukier, R. I. (2009) Hamiltonian Replica Exchange Method Studies of a Leucine Zipper Dimer, The Journal of Physical Chemistry B 113, 9595-9605. 27. Su, L., and Cukier, R. I. (2009) Hamiltonian Replica Exchange Method Study of E. coli and Y. pestis HPPK, The Journal of Physical Chemistry B 113, 16197 16208. 28. Su, L., and Cukier, R. I. (2009) An Enhanced Molecular Dynamics Study of HPPK ATP Conformation Space Exploration and ATP Binding to HPPK, The Journal of Physical Chemistry A 113, 2025-2035. 29. Li, H. F., Zhang, L. B., Han, L., Cukier, R. I., and Bu, Y. X. (2009) Theoretical prediction of size-expansion effect on the C8-site activity in the modified guanine-cytosine analogs, Journal of Physical Organic Chemistry 22, 1114-1119. 30. Han, L., Li, H. F., Cukier, R. I., and Bu, Y. X. (2009) Hetero-Ring-Expansion Design for Adenine-Based DNA Motifs: Evidence from DFT Calculations and Molecular Dynamics Simulations, Journal of Physical Chemistry B 113, 4407-4412.

31. Cukier, R. I., and Bu, Y. (2009) Computational Studies: Proton/Water Coupling to Metals in Biological Reaction Mechanisms, In Computational Inorganic and Bioinorganic Chemistry (Solomon, E. I., Scott, R. A., and King, R. B., Eds.), pp 363-372, John Wiley & Sons, Chichester. 32. Cukier, R. I. (2009) Apo Adenylate Kinase Encodes Its Holo Form: A Principal Component and Varimax Analysis, The Journal of Physical Chemistry B 113, 1662-1672. 33. Chen, X. H., Xing, D. X., Zhang, L., Cukier, R. I., and Bu, Y. X. (2009) Effect of Metal Ions on Radical Type and Proton-Coupled Electron Transfer Channel: sigma-radical vs pi-radical and sigma-channel vs pi-channel in the Imide Units, Journal of Computational Chemistry 30, 2694-2705. 34. Zhang, L., Yan, S., Cukier, R. I., and Bu, Y. X. (2008) Solvation of excess electrons in LiF ionic pair matrix: Evidence for a solvated dielectron from ab initio molecular dynamics simulations and calculations, Journal of Physical Chemistry B 112, 3767-3772. 35. Li, H., Cukier, R. I., and Bu, Y. (2008) Remarkable Metal Counterion Effect on the Internucleotide J-Couplings and Chemical Shifts of the N-H--N Hydrogen Bonds in the W-C Base Pairs, J. Phys. Chem. B 112, 9174-9181. 36. Zhang, J. M., Cukier, R. I., and Bu, Y. X. (2007) Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks, Journal of Physical Chemistry B 111, 8335-8341. 37. Yao, L. S., Yan, H. G., and Cukier, R. I. (2007) A molecular dynamics study of the ligand release path inyeast cytosine deaminase, Biophysical Journal 92, 2301-2310. 38. Yao, L. S., Cukier, R. I., and Yan, H. G. (2007) Catalytic mechanism of guanine deaminase: An ONIOM and molecular dynamics study, Journal of Physical Chemistry B 111, 4200-4210. 39. Yan, S. H., Zhang, L., Cukier, R. I., and Bu, Y. X. (2007) Exploration on regulating factors for proton transfer along hydrogen-bonded water chains, Chemphyschem 8, 944-954. 40. Xing, D. X., Sun, L. X., Cukier, R. I., and Bu, Y. X. (2007) Theoretical prediction of the p53 gene mutagenic mechanism induced by trans-4-hydroxy-2-nonenal, Journal of Physical Chemistry B 111, 5362-5371.

41. Xiang, F., Cukier, R. I., and Bu, Y. (2007) Ca2+ selectivity of the sarcoplasmic reticulum Ca2+-ATPase at the enzyme-water interface and in the Ca2+ entrance channel, Journal of Physical Chemistry B 111, 12282-12293. 42. Sun, L. X., Cukier, R. I., and Bu, Y. X. (2007) Factors determining the deriving force of DNA formation: Geometrical differences of base pairs, dehydration of bases, and the arginine assisting, Journal of Physical Chemistry B 111, 1802-1808. 43. Su, L., and Cukier, R. I. (2007) Hamiltonian and distance replica exchange method studies of Met-enkephalin, Journal of Physical Chemistry B 111, 12310-12321. 44. Seibold, S. A., and Cukier, R. I. (2007) A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: Differences in flap and aspartate 25 cavity dimensions, Proteins-Structure Function and Bioinformatics 69, 551-565. 45. Liu, J. Y., Seibold, S. A., Rieke, C. J., Song, I., Cukier, R. I., and Smith, W. L. (2007) Prostaglandin endoperoxide H synthases - Peroxidase hydroperoxide specificity and cyclooxygenase activation, Journal of Biological Chemistry 282, 18233-18244. 46. Liu, H. C., Zhang, L., Li, P., Cukier, R. I., and Bu, Y. X. (2007) Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist, Chemphyschem 8, 304-314. 47. Yao, L. S., Yan, H. G., and Cukier, R. I. (2006) A combined ONIOM quantum chemicalmolecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase, J. Phys. Chem. B 110, 26320-26326. 48. Yao, L. S., Yan, H. G., and Cukier, R. I. (2006) Mechanism of dihydroneopterin aldolase: A molecular dynamics study of the apo enzyme and its product complex, J. Phys. Chem. B 110, 1443-1456. 49. Yan, S. H., Bu, Y. X., and Cukier, R. I. (2006) Electron bridging dihydrogen bond in the imidazole-contained anion derivatives, J. Chem. Phys. 124, -. 50. Xiang, F., Li, P., Yan, S. H., Sun, L. X., Cukier, R. I., and Bu, Y. X. (2006) Hydration effect on interaction mode between glutamic acid and Ca2+ and its biochemical implication: a theoretical exploration, New Journal of Chemistry 30, 890-900.

51. Lou, H. F., and Cukier, R. I. (2006) Molecular dynamics simulation of apo Escherichia coli adenylate kinase:a distance replica exchange method for the free energy of conformational fluctuations, J. Phys. Chem. B 110, 24121-24137. 52. Lou, H. F., and Cukier, R. I. (2006) Molecular dynamics of apo-adenylate kinase: A principal component analysis, J. Phys. Chem. B 110, 12796-12808. 53. Li, H. F., Bu, Y. X., Yan, S. H., Li, P., and Cukier, R. I. (2006) Proton character of the peptide unit in the Ca2+-binding sites of calcium pump, J. Phys. Chem. B 110, 11005-11013. 54. Yao, L., Sklenak, S., Yan, H., and Cukier, R. I. (2005) A molecular dynamics exploration of the catalytic mechanism of yeast Cytosine Deaminase, J. Phys. Chem. B 109, 7500-7510. 55. Seibold, S. A., Mills, D. A., Ferguson-Miller, S., and Cukier, R. I. (2005) Water chain formation and possible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: A molecular dynamics comparison of the wild type and R481K mutant, Biochemistry 44, 10475-10485. 56. Krishnamurthy, H., Lou, H. F., Kimple, A., Vieille, C., and Cukier, R. I. (2005) Associative mechanism for phosphoryl transfer: A molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates, Proteins-Structure Function and Bioinformatics 58, 88-100. 57. Cukier, R. I., and Morillo, M. (2005) A targeted reweighting method for accelerating the exploration of high-dimensional configuration space, J Chem Phys 123, 234908. 58. Cukier, R. I. (2005) A Molecular Dynamics Study of Water-Chain Formation in the Proton- Conducting K Channel of Cytochrome c Oxidase, Biochim. et Biophys. Acta 1706, 134-146. 59. Bu, Y., and Cukier, R. I. (2005) Structural character and energetics of tyrosyl radical formation by electron/proton transfers of a covalently linked histidine-tyrosine: A model for Cytochrome c Oxidase, J. Phys. Chem. B 109, 22013-22026.