List of publications

Krzysztof Kuczera

Initialized : Mar-1998 ; Updated Dec-2018

  1. A.L. Sobolewski, R. Czerminski, and K. Kuczera, Mol. Phys. 50 (1983) 971-979. ``On the nature of the background absorption in vibrational overtone spectroscopy''

  2. K. Kuczera and R. Czerminski, J. Mol. Struct. 105 (1983) 269-280. ``Properties of quadratic force fields in redundant coordinates''

  3. K. Kuczera, J. Mol. Struct. 117 (1984) 11-18. ``Linear force constants in harmonic force fields''

  4. R. Czerminski, K. Kuczera, H. Rostkowska, M.J. Nowak and K. Szczepaniak, J. Mol. Struct. 140 (1986) 235-251. ``Autoassociation and tautomerism of 2-oxo-5-halogeno-pyrimidines: theoretical and experimental study''

  5. K. Kuczera, Acta. Phys. Polon. A70 (1986) 797-806. ``CNDO/2 FORCE calculation of the vibrational spectrum of methanol''

  6. K. Kuczera, J. Mol. Struct. 160 (1987) 159-177. ``Uniquely defined harmonic force constants in redundant coordinates''

  7. K. Kuczera, M. Szczesniak and K. Szczepaniak, J. Mol. Struct. 172 (1988) 73-88. ``Calculation of the vibrational spectra of cytosine derivatives by the CNDO/2 FORCE method. Part I. Planar vibrations of 1-methylcytosine''

  8. K. Kuczera, M. Szczesniak and K. Szczepaniak, J. Mol. Struct. 172 (1988) 89-99. ``Calculation of the vibrational spectra of cytosine derivatives by the CNDO/2 FORCE method. Part II. Planar vibrations of 5-fluorocytosine''

  9. K. Kuczera, M. Szczesniak and K. Szczepaniak, J. Mol. Struct. 172 (1988) 101-112. ``Calculation of the vibrational spectra of cytosine derivatives by the CNDO/2 FORCE method. Part III. Planar vibrations of cytosine''

  10. J. Smith, K. Kuczera, B. Tidor, W. Doster, S. Cusack and M. Karplus, Physica B 156 - 157 (1989) 437-443. ``Internal dynamics of globular proteins: comparison of neutron scattering measurements and theoretical models''

  11. J. Gao, K. Kuczera, B. Tidor and M. Karplus, Science 244 (1989) 1069-1072. ``Hidden thermodynamics of mutant proteins: a molecular dynamics analysis''

  12. J. Smith, K. Kuczera and M. Karplus, Proc. Natl. Acad. Sci. USA 87 (1990) 1601-1605. ``Molecular dynamics of myoglobin: comparison of simulation results with neutron scattering spectra''

  13. K. Kuczera, J. Kuriyan and M. Karplus, J. Mol. Biol. 213 (1990) 351-373. ``Molecular dynamics of CO-myoglobin at 325 and 80 K''

  14. K. Kuczera, J. Gao, B. Tidor and M. Karplus, Proc. Natl. Acad. Sci. USA 87 (1990) 8481-8485. ``Free energy of sickling: A simulation analysis''

  15. J.W. Petrich, J.-C. Lambry, K.Kuczera, M.Karplus, C.Poyart and J.-L. Martin, Biochemistry 30 (1991) 3975-3987. ``Ligand binding and protein relaxation in heme proteins: A room temperature analysis of NO geminate recombination''

  16. K. Kuczera, J.-C. Lambry, J.-L. Martin and M. Karplus Proc. Natl. Acad. Sci. USA, 90 (1993) 5805-5807, ``Nonexponential Relaxation after Ligand Dissociation from Myoglobin: A Molecular Dynamics Simulation''

  17. E. Barth, K. Kuczera, B. Leimkuhler and R.D. Skeel J. Comp. Chem., 16 (1995) 1192-1209, ``Algorithms for constrained molecular dynamics''

  18. Y. Wang and K. Kuczera, Proceedings of the First Electronic Computational Chemistry Conference, [CD-ROM], (1995). Paper 47, ``Molecular dynamics study of peptide flexibility''.

  19. G. S. Jas, K. Kuczera, C. Wan, and C. K. Johnson Proceedings of the Seventh International Conference on Time-Resolved Vibrational Spectroscopy, (1995), pp. 315-316, ``Picosecond Time-Resolved Fourier Transform Raman Spectroscopy of the Excited Singlet State of Anthracene''

  20. G. S. Jas and K. Kuczera, Proceedings of the Seventh International Conference on Time-Resolved Vibrational Spectroscopy, (1995), pp. 317-318, ``Normal Mode Analysis of S1 excited States of Benzene, Naphthalene and Anthracene from ab initio Quantum Chemical Calculations''

  21. K. Kuczera, Proceedings of the Conference on Free Boundary Problems, Zakopane, Poland, 1995, ``Free energy simulations in chemistry and biology''

  22. G. Papoyan, K. Gu, J. Wiórkiewicz-Kuczera, K. Kuczera and K. Bowman-James, J. Am. Chem. Soc., (1996), 118, 1354-1364. ``Molecular dynamics simulations of nitrate complexes with polyammonium macrocycles: Insight on Phosphoryl Transfer Catalysis''

  23. Y. Wang and K. Kuczera, J. Phys. Chem. (1996), 100, 2555-2563, ``Molecular dynamics simulations of cyclic and linear DPDPE: Influence of the disulfide bond on peptide flexibility''

  24. Y. Yao, D. Yin, G. Jas, K. Kuczera, T.D. WIlliams, C. Schöneich and T.C. Squier, Biochemistry (1996), 35, 2767-2787, ``Oxidative modification of a carboxyl-terminal vicinal methionine in calmodulin by peroxide inhibits calmodulin-dependent activation of the plasma-membrane Ca-ATPase''

  25. G. Jas and C. Wan and K. Kuczera and C. K. Johnson , J. Phys. Chem. (1996), 100, 11857-11862, ``Picosecond time-resolved Fourier-transform Raman spectroscopy and normal mode analysis of the ground state and singlet excited state of anthracene''

  26. K. Kuczera, Biopolymers (1996), 39, 221-242, ``Free energy simulations of axial contacts in sickle-cell hemoglobin''

  27. K. Kuczera, J. Comp. Chem. (1996), 17, 1726-1742. ``One- and multidimensional conformational free energy simulations''

  28. K. Kuczera, ``Dynamics and Thermodynamics of the Globins'', invited chapter for book ``Recent Developments in Theoretical Studies of Proteins'', edited by Ron Elber. World Scientific, Singapore, 1996, pp. 1-63. Series: ``Advances in Physical Chemistry'', vol. 7.

  29. G. Jas and K. Kuczera, Chem. Phys. (1997), 214, 229-241. ``Ab initio calculations of S1 excited state vibrational spectra of benzene, naphthalene and anthracene''

  30. Y. Wang and K. Kuczera, J. Phys. Chem. B, (1997), 101, 5205-5213, ``Exploration of conformational free energy surfaces of helical Ala and Aib peptides.''

  31. G. S. Jas, Y. Wang, S. W. Pauls, C. K. Johnson and K. Kuczera, J. Chem. Phys., (1997), 107, 8800-8812, ``Influence of Temperature and Viscosity on Anthracene Rotational Diffusion in Organic Solvents: Molecular Dynamics Simulations and Fluorescence Anisotropy Study.''

  32. A. Hermone and K. Kuczera, Biochemistry, (1998), 37, 2843-2853, ``Free energy of retinal cis -> trans isomerization in bacteriorhodopsin''.

  33. B. L. Miller and K. Kuczera and C. Schoneich, Am. Chem. Soc. , (1998), 120 , 3345-3356, ``One-electron photooxidation of N-methionyl peptides. Mechanism of sulfoxide and azasulfonium diastereomer formation through reaction of sulfide radical cation complexes with oxygen or superoxide''.

  34. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin and M. Karplus, J. Phys. Chem. B, (1998), 102, 3586-3616, ``All-atom empirical potential for molecular modeling and dynamics studies of proteins''

  35. S. Mason, T. Clifford, L. Seib, K. Kuczera and K. Bowman-James, J. Am. Chem. Soc., (1998), 120, 8899-8900, ``Unusual Encapsulation of Two Nitrates in a Single Bicyclic Cage''

  36. K. Kuczera, ``Exploration of peptide free energy surfaces'', in ``Computational Molecular Dynamics: Challenges, Methods, Ideas'', P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich and R. D. Skeel, Eds., vol. 4 in the series ``Lecture Notes in Computational Science and Engineering on Algorithms for Molecular Modeling'', Springer, Berlin, 1999, pp. 163-175.

  37. Y. Wang, S.-Y. Goh and K. Kuczera, J. Peptide Res., (1999), 53 , 188-200, ``Molecular dynamics study of disulfide bond influence on properties of an RGD peptide''

  38. Y. Wang and K. Kuczera, Theor. Chem. Acc. , (1999), 101 , 274-281, ``Conformational free energy surface of the linear DPDPE peptide: cost of pre-organization for disulfide bond formation''

  39. E. V. Rybak-Akimova, K. Kuczera, G. S. Jas, Y. Deng and D. H. Busch, Inorg. Chem., (1999), 38 , 3423-3434. ``Molecular Shape and Solvation of the Lacunar, Saddle-Shaped, and Planar Metal Cyclidene Complexes: Molecular Dynamics Studies''.

  40. J. Wiórkiewicz-Kuczera, K. Kuczera, C. Bazzicalupi, A. Bencini, B. Valtancoli, A. Bianchi and K. Bowman-James, New J. Chem., (1999), 23 , 1007-1013. ``Solid State to Solution: Crystal Structure and Molecular Dynamics Simulations of a Polyammonium Nitrate Host''.

  41. D. Yin, K. Kuczera and T. C. Squier, Chem. Res. Toxicol., (2000), 13 , 103-110. ``Sensitivity of Carboxyl-Terminus Methionines in Calmodulin Isoforms to Oxidation by H2O2 Modulates the Ability to Activate the Plasma Membrane Ca-ATPase''.

  42. E. V. Rybak-Akimova and K. Kuczera, Inorg. Chem., (2000), 39, 2462-2472. ``Ligand Binding Inside the Cavities of Lacunar and Saddle-Shaped Cyclidene Complexes: Molecular Mechanics and Molecular Dynamics Studies''.

  43. D. Yin, X. Yang, Y. Hu, K. Kuczera, R. L. Schowen, R. T. Borchardt and T. C. Squier, Biochemistry (2000), 39, 9811-9818. ``Substrate binding stabilizes S-adenosylhomocysteine hydrolase in a closed conformation.''

  44. C. E. MacBeth, A. P. Golombek, V. G. Young Jr., C. Yang, K. Kuczera, M. P. Hendrich and A. S. Borovik, Science , (2000), 289, 938-941. ``O2 activation by non-heme iron complexes: A monomeric Fe(III)-oxo complex derived from O2.''

  45. K. Kuczera, ``Molecular Modeling in Peptide and Protein Analysis'', review article in the Encyclopedia of Analytical Chemistry, R. A. Meyers, (Ed.), pp. 5894-5930, John Wiley & Sons, Ltd., Chichester, (2000).

  46. G. S. Jas, E. Larson, C. K. Johnson, and K. Kuczera, J. Phys. Chem. A, (2000), 104, 9841-9852. ``Microscopic Details of Rotational Diffusion of Perylene in Organic Solvents: Molecular Dynamics Simulations and Experiment vs. Debye-Stokes-Einstein Theory.''

  47. K.-H. Lee, D. R. Benson and K. Kuczera, Biochemistry, (2000), 39, 13737-13747. ``Transitions from .alpha. to .pi. helix observed in molecular dynamics simulations of synthetic peptides.''

  48. M. A. Turner, X. Yang, D. Yin, K. Kuczera, R. T. Borchardt and P. L. Howell, Cell Biochem. Biophys., (2001), 33, 101-125. ``Structure and function of S-adenosylhomocysteine hydrolase.''

  49. J. Mahadevan, K.-H. Lee and K. Kuczera, J. Chem. Phys. B, (2001), 105, 1863-1876. ``Conformational free energy surfaces of Ala10 and Aib10 peptide helices in solution.''

  50. R. Guenther, H.-J. Hofmann and K. Kuczera, J. Phys. Chem. B, (2001), 105, 5559-5567. ``Searching for Periodic Structures in beta-Peptides''.

  51. A. Altuve, S. Silchenko, K.-H. Lee, K. Kuczera, S. Terzyan, X. Zhang, D. R. Benson, and M. Rivera, Biochemistry (2001), 40, 9469-9483. ``Probing the Differences between Rat Liver Outer Mitochondrial Membrane Cytochrome b5 and Microsomal Cytochromes b5''.

  52. C. Yang, G. S. Jas and K. Kuczera, J. Biomol. Struct. Dyn., (2001), 19 247-271. ``Structure and dynamics of calcium-activated calmodulin in solution''.

  53. Y. Hu, X. Yang, D. H. Yin, J. Mahadevan, K. Kuczera, R. L. Schowen and R. T. Borchardt, Biochemistry, (2001), 40 15143-15152. ``Computational characterization of substrate binding and catalysis in S-adenosylhomocysteine hydrolase''.

  54. J. Mahadevan, C. Xu, T. Siaahan and K. Kuczera, J. Biomol. Struct. Dyn., (2002), 19, 775-788. ``Molecular dynamics simulations of conformational behavior of linear RGD peptidomimetics and cyclic prodrugs in aqueous and octane solutions''

  55. C. Yang, and K. Kuczera, J. Biomol. Struct. Dyn., (2002), 19, 801-820. ``Molecular dynamics simulations of calcium-free calmodulin in solution''.

  56. G. S. Jas and K. Kuczera, Proteins, (2002), 48, 257-268. ``Free energy simulations of the oxidation of C-terminal methionines in calmodulin''.

  57. I. T. Makagiansar, P. D. Nguyen, A. Ikesue, K. Kuczera, W. Dentler, J. L. Urbauer, N. Galeva, M. Alterman and T. Siahaan, J. Biol. Chem., (2002), 277, 16002-16010, ``Disulfide bond formation promotes cis- and trans-dimerization of the E-cadherin derived first repeat''.

  58. Yang, C. and Kuczera, K., J. Biomol. Struct. Dyn. (2002), 20 179-197, ``Molecular dynamics simulations of a calmodulin-peptide complex in solution''.

  59. X. Yang, Y. Hu, D. Yin, M. A. Turner, M. Wang, R. T. Borchardt, P. L. Howell, K. Kuczera and R. L. Schowen, Biochemistry (2003), 42, 1900-1909. ``The Catalytic Strategy of S-Adenosyl-L-homocysteine Hydrolase: Transition State Stabilization and the Avoidance of Abortive Reactions''.

  60. K.-H. Lee and K. Kuczera. ``Molecular dynamics simulation studies of cytochromes b5 from outer Biopolymers, (2003), 69, 260-269. mitochondrial and microsomal membrane''.

  61. K. Zheng, I. T. Makagiansar, M. Wang, J. L. Urbauer, K. Kuczera and T. J. Siahaan. ``Expression, purification and structural study of the EC4 domain of E-cadherin.'' Protein Expression and Purification (2004) 33, 72-79.

  62. C. Yang, G. S. Jas and K. Kuczera. ``Structure, dynamics and interactions with kinase targets: Computer simulations of calmodulin.'' Biochim. Biophys. Acta, 1697, 289-300 (2004).

  63. G. S. Jas and K. Kuczera. ``Equilibrium structure and folding of a helix-forming peptide: circular dichroism measurements and replica-exchange molecular dynamics simulations.'' Biophysical J., 87, 3786-3798 (2004).

  64. Y. Houndonougbo, G. S. Jas and K. Kuczera. ``Structure and dynamics of phospholamban in solution and membrane bilayer: Computer simulations.'' Biochemistry, 44, 1780-1792 (2005).

  65. M. Wang, J. Zhang, D. Andrei, K. Kuczera, R. T. Borchardt and S. F. Wnuk. ``Are L-adenosine and its derivatives substrates for S-Adenosyl-L-homocysteine hydrolase?'' Med. Chem. Commun., 48, 3649-3653, (2005).

  66. M. Wang, R. L. Schowen, R. T. Borchardt and K. Kuczera. ``Domain motions and the open-to-closed conformational transition of an enzyme: A normal mode analysis of S-adenosyl-L-homocysteine hydrolase.'' Biochemistry, 44 7228-7239 (2005).

  67. M. R. Richter, H. S. Samra, F. He, A. J. Giessel and K. Kuczera. J. Bioenerg. Biomembr., 37 467-473 (2005). ``Coupling proton movement to ATP synthesis in the chloroplast ATP synthase.''

  68. Y. Houndonougbo, H. Jiu, B. Rajagopalan, K. Wong, K. Kuczera, B. Subramaniam and B. Laird. J. Phys. Chem. B, 110:13195-13202 (2006). ``Phase equilibria in carbon-dioxide expanded solvents: Experiments and molecular simulations.''

  69. M. Wang, J.R. Unruh, C. K. Johnson, R.L. Schowen, R.T. Borchardt and K. Kuczera. Biochemistry 45:7778-7786 (2006). ``Effects of ligand binding and oxidation on hinge-bending motions in S-adenosyl-L-homocysteine hydrolase.''

  70. Q. Cheng, D. R. Benson, M. Rivera-Laos and K. Kuczera, Biopolymers 83:297-312 (2006). ``Influence of point mutations on the flexibility of cytochrome b5: Molecular dynamics simulations of holoproteins.''

  71. Y. Houndonougbo, B. Laird and K. Kuczera, J. Chem. Phys. 126:074507 (2007). ``Transport properties of CO2-expanded acetonitrile from molecular dynamics simulations.''

  72. Q.-S. Li, S. Cai, R. T. Borchardt, J. Fang, K. Kuczera, C. R. Middaugh and R. L. Schowen. Biochemistry 46:5798-5809 (2007). ``Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolase.''

  73. Y. Houndonougbo, K. Kuczera, B. Subramaniam, and B. B. Laird. Molecular Simulation 33:861-869 (2007). ``Prediction of phase equilibria and transport properties in carbon dioxide-expanded solvents by molecular simulation.''

  74. S. Cai, Q.-S. Li, R. T. Borchardt, K. Kuczera and R. L. Schowen. Bioorganic and Medicinal Chemistry, 15:7281-7287 (2007). ``The antiviral drug ribavirin is a selective inhibitor of S-adenosyl-L-homocysteine hydrolase from Trypanosoma cruzi.''

  75. C. Hu, J. Fang, R. T. Borchardt, R. L. Schowen and K. Kuczera. Proteins, 71:131-143 (2008). ``Molecular dynamics simulations of domain motions of substrate-free S-adenosyl-L-homocysteine hydrolase.''

  76. Y. Houndonougbo, K. Kuczera and G. S. Jas. Phospholamban Dynamics in Complex Environments: Effects of CMAP Correction and Electrostatic Cutoffs. J. Biomol. Struct. Dyn., 26: 17-34 (2008).

  77. Q.-S. Li, S. Cai, J. Fang, R. T. Borchardt, K. Kuczera, C. R. Middaugh and R. L. Schowen. Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolase. 2. The role of helix 18 stability. Biochemistry, 47: 4983-4991 (2008).

  78. B. B. Laird, Y. Houndonougbo and K. Kuczera. Phase equilibrium, structure and transport properties of carbon dioxide expanded liquids: A molecular simulation study. In ACS Symposium Series vol 1006: Gas-Expanded Liquids and Near-Critical Media, K.W. Hutchenson, A.M. Scurto and B. Subramaniam, Editors, pp. 41-65, American Chemical Society (2009).

  79. K. Kuczera, G.S. Jas and R. Elber. Molecular dynamics simulations with milestoning. J. Phys. Chem. A 113: 7461-7473 (2009).

  80. B.R.Brooks, C.L. Brooks III, A.D. MacKerell, Jr., L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Calflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J.Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis,, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, M.R. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York and M. Karplus. CHARMM: The Biomolecular Simulation Program. J.Comput.Chem. 30:1545-1614 (2009).

  81. M. Myllykoski, K. Kuczera and P. Kursula. Complex formation between calmodulin and a peptide from the intracellular loop of the gap junction protein connexin43: molecular conformation and energetics of binding. Biophysical Chem 144:130-135 (2009).

  82. K. Zheng, J. Laurence, K. Kuczera, C. R. Middaugh and T. J. Siahaan. Characterization of multiple stable conformers of the EC5 domain of E-cadherin and the interaction of EC5 with E-cadherin peptides. Chemical Biology and Drug Design, 73:584-598 (2009).

  83. Q.-S. Li, S. Cai, J. Fang, R.T. Borchard, K. Kuczera, C.R. Middaugh, R.L. Schowen. Evaluation of NAD(H) Analogues as Selective Inhibitors for Trypanosoma cruzi S-Adenosylhomocysteine Hydrolase. Nucleosides, Nucleotides and Nucleic Acids, 28:485-503 (2009).

  84. Unruh, K. Kuczera and C.K. Johnson. Conformational Heterogeneity of a Leucine Enkephalin Analog in Aqueous Solution and SDS Micelles: Comparison of Time-Resolved FRET and Molecular Dynamics Simulations. J.Phys.Chem. B, 113:14381-14392 (2009).

  85. R. Elber, K. Kuczera and G. S. Jas. Tubes, funnels and milestones. In Energy, Heat and Signal Flow, E. Leitner and J. Straub, Editors. pp. 295-314,Taylor and Francis/CRC Press (2009).

  86. K. Kuczera, J. Unruh, C.K. Johnson and G.S. Jas. Reorientations of Aromatic Acids and Their Side Chains Models: Anisotropy Measurements and Molecular Dynamics Simulations. J.Phys.Chem. A, 114:133-142 (2010).

  87. Q.-S. Li, S. Cai, J. Fang, Q.-S. Li, R.T. Borchard, K. Kuczera, C.R. Middaugh and R.L. Schowen. Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-Adenosylhomocysteine Hydrolases. 3. The role of lysyl and tyrosyl residues of the C-terminal extension. Biochemistry, 49:8434-8441 (2010).

  88. W. Hegefeld, S.-E. Chen, K. DeLeon, K. Kuczera and G.S. Jas. Helix formation in a pentapeptide: Experiment and force-field dependent dynamics. J. Phys. Chem. B, 114:12391-12402 (2010).

  89. K.-H. Lee, K. Kuczera and M.M. Banaszak Holl. The severity of osteogenesis imperfecta: A comparison of relative free energy differences of collagen model peptides. Biopolymers, 95:182-193 (2011).

  90. K.-H. Lee, K. Kuczera and M.M. Banaszak Holl. Efect of osteogenesis imperfecta on free energy of collagen model peptides: A molecular dynamics simulation. Biophys. Chem., 156:145-152 (2011).

  91. W. Hegefeld, K. Kuczera and G.S. Jas. Structural dynamics of neuropeptide hPYY. Biopolymers, 95:487-502 (2011).

  92. K.C. Song, P.W. Livanec, J. B. Klauda, K. Kuczera, R. C. Dunn and W. Im. Orientation of fluorescent lipid analog BODIPY-PC to probe lipid membrane properties: Insights from molecular dynamics simulations. J.Phys.Chem.B, 115:6157-6165 (2011).

  93. S. Parthasarathy, A. Altuve, S. Terzyan, X. Zhang, K. Kuczera, M. Rivera and D.R. Benson. Accomodating a non-conservative internal mutation by water-mediated hydrogen bonding between beta-sheet strands: A comparison of human and rat type B (mitochondrial) cytochrome b5. Biochemistry, 50:5544-5554 (2011).

  94. A. Cardenas, G.S. Jas, K. Kuczera and R. Elber. Unassisted transport of N-acetyl-L-Tryptophanamide through DOPC membrane: Experiment and simulation. J. Phys. Chem. B., 116:2739-2750 (2012).

  95. K.Y. DeLeon, A. P. Patel, K.Kuczera, C.K. Johnson and G.S. Jas. Structure and Reorientational Dynamics of Angiotensin I and II: A Microscopic Physical Insight. J. Biomol. Struct. Dyn., 29:671-690 (2012).

  96. K. Kuczera and P. Kursula. Interaction of calmodulin with death-associated protein kinase peptides: experimental and modeling studies. J. Biomol. Struct. Dyn., 30:45-61 (2012).

  97. G.S. Jas and K. Kuczera. Computer simulations of helix folding in homo- and hetero-peptides. Molecular Simulation, 38:682-694 (2012). Invited article for special issue New Developments in Molecular Simulation.

  98. G.S. Jas, W. Hegefeld, P. Majek, K. Kuczera and R. Elber. Experiments and comprehensive simulations of the formation of a helical turn. J. Phys. Chem. B 116:6598-6610 (2012).

  99. G.S. Jas, C. R. Middaugh and K. Kuczera. Non-exponential kinetics and a complete folding pathway of an Alpha-Helical Heteropeptide: Direct Observation and Comprehensive Molecular Dynamics, J. Phys. Chem B 118:639-647 (2014).

  100. N. Ploscariu, K. Kuczera, K.E. Malek, M. Wawrzyniuk, A. Dey and R. Szoszkiewicz. Single molecule studies of force-induced S2 site exposure in the mammalian Notch Negative Regulatory Domain. J. Phys. Chem. B 118:4761-4770 (2014).

  101. G.S. Jas, W.A. Hegefeld, C.R Middaugh, C.K. Johnson and K. Kuczera. Detailed Microscopic Unfolding Pathways of an alpha-helix and a beta-hairpin: Fluorescence Energy Transfer and Molecular Dynamics, J. Phys. Chem B 118:7233-7246 (2014).

  102. G.S. Jas, E. Rentchler, A. Slowicka, J. Hermansen, C.K. Johnson, C.R. Middaugh and K. Kuczera. Reorientational motion and Preferential Solvation of a Peptide in Denaturants and Osmolyte. J. Phys. Chem B, ,120:3089-3099 (2016).

  103. B.L. Lee, K. Kuczera, C.R. Middaugh and G.S. Jas. Permeation of the three aromatic dipeptides through lipid bilayers: experimental and computational study. J. Chem. Phys. 144:245103 (2016).

  104. G.S. Jas, C.R. Middaugh and K. Kuczera. Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution. J. Phys. Chem. B, 120:6939-6950 (2016).

  105. A. Alaofi, E. Farokhi, V.D. Prasathy, A. Anbanandam, K. Kuczera, J. Laurence and T.J. Siahaan. Probing the interaction between cHAVc3 peptide and EC1 domain of E-cadherin using NMR and molecular dynamics. J. Biomolec. Struct. Dyn. 35:92-104 (2017).

  106. B.L. Lee and K. Kuczera. Simulating the free energy of passive membrane permeation for small molecules. Mol. Sim. 44:1147-1157 (2018). https://doi.org/10.1080/08927022.2017.1407029

  107. G.S. Jas and K. Kuczera. Deprotonation of a single amino acid residue induces significant stability in an alpha-helical heteropeptide. J. Phys. Chem. B, in press, (2018).

  108. G.S. Jas and K. Kuczera. Helix-Coil Transition Courses Through Multiple Pathways and Intermediates: Fast Kinetic Measurements and Dimensionality Reduction. J. Phys. Chem. B, 122:10806-10816,(2018)

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