Publications-Lalith Perera

  1. G.L. Butterfoss, E.F. DeRose, S.A. Gabel, L. Perera, J. M. Krahn, G.A. Mueller, X.H. Zheng, R.E. London (2010) Conformational dependence of C-13 shielding and coupling constants for methionine methyl groups JOURNAL OF BIOMOLECULAR NMR, 48:31-47
  2. D.M. Elking, L. Perera L, R. Duke, T. Darden, L.G. Pedersen, (2010) Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models. Journal of Computational Chemistry, 31:2702-2713.
  3. S. Mutoh, M. Osabe, K. Inoue, R. Moore, L. Pedersen, L. Perera, Y. Rebolloso, T. Sueyoshi, M. Negishi, (2009) Dephosphorylation of Threonine 38 Is Required for Nuclear Translocation and Activation of Human Xenobiotic Receptor CAR (NR1I3) JOURNAL OF BIOLOGICAL CHEMISTRY, 284:34785-34792
  4. M. Garcia-Diaz, K. Bebenek, A.A. Larrea, J.M. Havener, L. Perera, J.M. Krahn, L.C. Pedersen, D.A. Ramsden, T.A. Kunkel, (2009) Template strand scrunching during DNA gap repair synthesis by human polymerase lambda NATURE STRUCTURAL & MOLECULAR BIOLOGY, 16:967-U91
  5. C.A. Hobbs, L.J. Deterding, L. Perera, B.G. Bobay, R.J. Thompson, T.A. Darden, J. Cavanagh, K.B. Tomer, (2009) Structural Characterization of the Conformational Change in Calbindin-D-28k upon Calcium Binding Using Differential Surface Modification Analyzed by Mass Spectrometry BIOCHEMISTRY, 48:8603-8614
  6. G.A. Cisneros, L. Perera, R.M. Schaaper, L.C. Pedersen, R.E. London, L.G. Pedersen, T.A. Darden, (2009) Reaction Mechanism of the epsilon Subunit of E-coli DNA Polymerase III: Insights into Active Site Metal Coordination and Catalytically Significant Residues JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:1550-1556
  7. A.K. Zaas, G.C. Liao, J.W. Chien, C. Weinberg, D. Shore, S.S. Giles, K.A. Marr, J. Usuka, L.H. Burch, L. Perera, J.R. Perfect, G. Peltz, D.A. Schwartz, (2009) Plasminogen Alleles Influence Susceptibility to Invasive Aspergillosis PLOS GENETICS, 4:e1000101
  8. G. A. Cisneros, L. Perera, M. Garcia-Diaz, K. Bebenek, T.A. Kunkel, L.G. Pedersen, (2008) Catalytic Mechanism of Human DNA Polymerase Lambda with Mg2+ and Mn2+ from ab initio QM/MM studies. DNA Repair, 7:1824-1834
  9. V. Chandrasekaran, C.J. Lee, R.E. Duke, L. Perera, L.G. Pedersen, (2008) Computational study of the putative active form of protein Z (PZa): Sequence design and structural modeling. Prot. Sci. 17: 1354-1361.
  10. J-K. Tie, M-Y. Zheng, K-L. Hsiao, L. Perera, D. Stafford, D. Straight, (2008) Transmembrane Domain Interactions and Residue Proline378 Are Essential for Proper Structure, Especially Disulfide Bond Formation, in the Human Vitamin K-Dependent Gamma-Glutamyl Carboxylase. Biochemistry 47: 6301-6310.
  11. G.A. Cisneros, S. Na-Im Tholander, O. Parisel, T.A. Darden, D. Elking, L. Perera, J-P. Piquemal (2008) Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hydrid Quantum Mechanical/Molecular Mechanical Embedding. International J. Quantum Chemistry 108: 1905-1912.
  12. D. L. Croteau, M.J. DellaVecchia, L. Perera, B. Van Houten, (2008) Cooperative damage recognition by UvrA and UvrB: Identification of UvrA residues that mediate DNA binding. DNA Repair 7:392-404.
  13. M.M. Alhamadsheh, S. Gupta, R.A. Hudson, L. Perera, L.M.V.Tillekeratne (2008) Total synthesis and selective activity of a new class of conformationally restirained epothilones. Chemistry-A European J. 14: 570-581.
  14. C.J. Lee, P. Lin, V. Chandrasekaran, R.E. Duke, S.J. Everse, L. Perera, L. G. Pedersen, (2008) Proposed structural models of human factor Va and prothrombinase. J. Thromb. Haemost. 6:83-89.
  15. S-B. Liu, L. Perera, L.G. Pedersen, (2007) Binuclear manganese(II) complexes in biological systems. Mol. Phys. 105:19-22.
  16. S. J. Lee, L. Perera, S. J. Coulter, H. W. Mohrenweiser, A. Jetten, and J. A. Goldstein, (2007) The discovery of new coding alleles of human CYP26A1 that are potentially defective in the metabolism of all-trans retinoic acid and their assessment in a recombinant cDNA expression system. Pharmacogenet Genomics. 17:169-80.
  17. C. J. Lee, V. Chandrasekaran, R. E. Duke, L. Perera, and L. G. Pedersen, (2007) A proposed structural model of human protein Z (PZ). J. Thromb. Haemost. 5: 1558-1561.
  18. C. Roux, N. Gresh, L. Perera, J-P. Piquemal, and L. Salmon, (2007) Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J. Comp. Chem. 28:938-57.
  19. C. M. Colina, D. Venkateswarlu, R. E. Duke, L. Perera, and L. G. Pedersen, (2006) What causes the enhancement of activity of factor VIIa by tissue factor? J Thromb Haemost. 4:2726-9.
  20. J-P. Piquemal, L. Perera, G. A. Cisneros, P. Ren, L. G. Pedersen, and T. A. Darden, (2006) Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys. 125:054511.
  21. L. Perera and L. G. Pedersen, (2005) A reconsideration of the evidence for structural reorganization in FVII zymogen. J Thromb Haemost. 3:1543-5.
  22. D. H. Herce, L. Perera, T. A. Darden, and C. Sagui, (2005) Surface solvation for an ion in a water cluster.
    J Chem Phys. 122:024513.
  23. D. Venkateswarlu, R. E. Duke, L. Perera, T. A. Darden, and L. G. Pedersen, (2003) An all-atom solution-equilibrated model for human extrinsic blood coagulation complex (sTF-VIIa-Xa): a protein-protein docking and molecular dynamics refinement study. J. Thromb. Haemost. 1:2577-2588 (abstract)
  24. A. Gorokhov, M. Negishi, E.F. Johnson, L. C. Pedersen, L. Perera, T.A. Darden and L.G. Pedersen, (2003) Explicit Water Near the catalytic I-helix Thr in the Predicted Solution Structure of CYP2A4. Biophys. J.84: 57-68 (pdf)
  25. L. Perera, T. Darden, and L. G. Pedersen. (2003) Predicted Solution Structure of Zymogen Human Coagulation Factor VII. J. Comp. Chem. 23: 35-47. (pdf)
  26. D. Venkateswarlu, L. Perera, T. Darden, and L. G. Pedersen. (2002) Structure and Dynamics of Zymogen Human Blood Coagulation Factor X. Biophys. J. 82, 1190-206.
  27. C.D. Bruce, M. L. Berkowitz, L. Perera, M. D. E. Forbes, (2002) A Molecular Dynamics Simulation of Sodium Dodecyl Sulphate: The Behavior of Water. J. Phys. Chem 106; 10902-10907 (pdf).
  28. C.D. Bruce, M. L. Berkowitz, L. Perera, M. D. E. Forbes, (2002) A Molecular Dynamics Simulation of Sodium Dodecyl Sulphate Micelle in Water: Micellar Structural Characteristics and Counterion Distribution. J. Phys. Chem. 106, 3788-3793. (pdf)
  29. J. Jin, L. Perera, D. Stafford, and L. G. Pedersen. (2001) Four Loops of the Catalytic Domain of Factor VIIa Mediate the Effect of the First EGF-like Domain Substitution on Factor VIIa Catalytic Activity. J. Mol. Biol. 307, 1503-1517. (pdf)
  30. L. Perera, T. Darden, and L. G. Pedersen. (2001) Modeling Human Zymogen Factor IX. Thromb. Hemost. 85, 596-603.
  31. L. Perera, C. Foley, T. Darden, D. Stafford, T. Mather, C. Esmon, and L. G. Pedersen. (2000) Modeling Zymogen Protein C. Biophys J. 79, 2925-43. (pdf)
  32. Gorokhov A, Perera L, Darden TA, Negishi M, Pedersen LC, Pedersen LG. (2000) Heparan sulfate biosynthesis: a theoretical study of the initial sulfation step by N-deacetylase/N-sulfotransferase. Biophys J. 79, 2909-17. (pdf)
  33. T. Darden, L. Perera, L. Li, and L. G. Pedersen. (1999) New Tricks for Modelers from the Crystallography Toolkit: The Particle Mesh Ewald Algorithm and Its Use in Nucleic Acid Simulations. Structure 7, 55. (pdf)
  34. L. Perera, T. Darden, and L. G. Pedersen. (1999) Probing the Structural Changes in the Light Chain of Human Coagulation Factor VII due to Tissue Factor Association. Biophys. J. 77, 99.
  35. L. Perera, T. Darden, and L. G. Pedersen. (1998) Trans-Cis Isomerization of Pro22 in Bovine Prothrombin Fragment 1: A Surprising Result of Structure Characterizations. Biochemistry 31, 10920. (pdf)
  36. A. Lim, M. J. Sederholm, A. M. Makhov, M. Kroll, Y. Yan, L. Perera, and B. W. Erickson, (1998) Engineering of betabellin 15D: A 64-Residue Beta-sheet Protein That Forms Long Narrow Multimeric Fibrils. Prot. Sci. 7, 1545. (pdf)
  37. L. Perera, L. Li, T. Darden, D. M. Monroe and L. G. Pedersen. (1997) Prediction of Solution Structure of Ca2+-Bound g-Carboxyglutamic Acid Domains of Protein S and Homolog Growth Arrest Specific Protein 6: Use of the Particle Mesh Ewald Method. Biophys. J. 73, 1847.
  38. I. Yeh, L. Perera, and M. L. Berkowitz. (1997) Photodetachment Spectra of Cl-(H2O)n Clusters: Predictions and Comparisions. Chem. Phys. Lett 264, 31. (pdf)
  39. L. Perera, U. Essmann and M. L. Berkowitz. (1997) The role of Water in the Hydration force: Molecular Dynamics Simulations. Progr. Colloid. Polym. Sci. 103, 107.
  40. L. Perera, U. Essmann and M. L. Berkowitz. (1996) Role  of Water in the Hydration Force Acting Between Lipid Bilayers. Langmuir 12 , 2625. (pdf)
  41. L. Sremaniak, L. Perera and M. L. Berkowitz, (1996) Cube to Cage Transitions in (H2O)n n=12,16 and 20. J. Chem. Phys. 105, 3715. (pdf)
  42. G. Markovich, L. Perera, M. L. Berkowitz and O. Cheshnovsky, (1996) The Solvation of Cl-, Br- and I- in Acetonitrile Clusters: Photoelectron Spectroscopy and Molecular Dynamics Simulations. J. Chem. Phys. 105, 2675. (pdf)
  43. L. S. Sremaniak, L. Perera and M. L. Berkowitz. (1996) Thermally Induced Structural Changes in F-(H2O)11 and Cl-(H2O)11 Clusters: Molecular Dynamics Computer Simulations, J. Phys. Chem. 100, 1350. (pdf)
  44. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen, (1995) A Smooth Particle Mesh Ewald Method, J. Chem. Phys . 103, 8577. (pdf)
  45. U. Essmann, L. Perera and M. L. Berkowitz, (1995) The Origin of the Hydration Interaction of Lipid Bilayers from MD Simulation of Dipalmitoylphosphatidylcholine membranes  in Gel and Liquid Crystalline Phases, Langmuir. 11, 4519. (pdf)
  46. M. Berkowitz and L. Perera, (1995) Molecular Dynamics Computer Simulations of Aqueous Solution/Platinum Interface, in "Theoretical and Computational Approaches to Interface Phenomena," ed., H. Sellers and J. Golab, (Plenum Press, N.Y.).
  47. X. Xia, L. Perera, U. Essmann and M. L. Berkowitz. (1995) The Structure of Water at Platinum/Water Interface. Molecular Dynamics Computer Simulations, Surf. Science, 335, 401.
  48. L. Perera, U. Essmann and M. L. Berkowitz. (1995) Effect of the Treatment of Long Range Forces on the Dynamics of Ions in Aqueous Solutions, J. Chem. Phys. 102, 450. (pdf)
  49. L. S. Sremaniak, L. Perera and M. L. Berkowitz. (1994) Enthalpies of Formation and Stabilization Energies of Br-(H2O)n (n=1,2..15) Clusters: Comparisons between Molecular Dynamics Computer Simulations and Experiment, Chem. Phys. Lett. 218, 377.
  50. L. Perera and M. L. Berkowitz. (1994) Structures of Cl-(H2O)n and F-(H2O)n (n=2,3..15) Clusters: Molecular Dynamics Computer Simulations, J. Chem. Phys. 100, 3085. (pdf)
  51. L. Perera and M. L. Berkowitz, (1993) Free Energy Profiles for Li+ and I- Ions  Approaching the Pt/water(100) surface: A Molecular Dynamics Study, J. Phys. Chem. 97, 13803. (pdf)
  52. L. Perera and M. L. Berkowitz. (1993) Stabilization Energies of Chloride, Bromide and Iodide Ions in Water Clusters, J. Chem. Phys. 99 4222. (pdf)
  53. L. Perera and M. L. Berkowitz, (1993) Ion Solvation in Water Clusters, Z. Phys. D. 26 166.
  54. I. I. Vaisman, L. Perera and M. L. Berkowitz, (1993) Mobility of Stretched Water, J. Chem. Phys. 98, 9859. (pdf)
  55. L. Perera and M. L. Berkowitz, (1993) Solvation Dynamics in a Stockmayer Fluid, in "Condensed Matter Theories", ed., L. Blum. (Plenum Press, N.Y.).
  56. F. G. Amar, D. Levandier, L. Perera and G. Scoles, (1994) IR Spectroscopy of Solvated Molecules, in "Clusters of Atoms and Molecules", ed., H Haberland. (Springer-Verlag, N.Y.).
  57. L. Perera and M. L. Berkowitz, (1992) Ultrafast Solvation Dynamics in a Stockmayer Fluid, J. Chem. Phys. 97 5253. (pdf)
  58. L. Perera and M. L. Berkowitz, (1992) Structure and Dynamics of Cl-(H2O)20 Clusters: The Effect of the Polarizability and the Charge of the Ion, J. Chem. Phys. 96 8288. (pdf)
  59. L. Perera and M. L. Berkowitz, (1992) Dynamics of Ion Solvation in a Stockmayer Fluid, J. Chem. Phys. 96 3092. (pdf)
  60. L. Perera and M. L. Berkowitz, (1991) Many Body Effects in Molecular Dynamics Simulations of Na+(H2O)n and Cl-(H2O)n Clusters, J. Chem. Phys. 95 1954. (pdf)
  61. F. G. Amar and L. Perera, (1991) Energetics and Structure in I2-(CO2)n Clusters, Z. Phys. D. 18 173.
  62. L. Perera and F. G. Amar, (1990) Spectral Shifts and Structural Classes in Microsolutions of Rare Gas Clusters Containing a Molecular Chromophore, J. Chem. Phys. 93 4884. (pdf)
  63. L. Perera, (1990) Simulation Studies of the Spectra, Structures and Dynamics of Heterogeneous and Ionic Clusters, Dissertation, Department of Chemistry, University of Maine, Orono, Maine.
  64. L. Perera and F. G. Amar, (1989) Charge Localization in Negative Ion Dynamics: Effect on Caging of Br2- in Arn and (CO2)n Clusters, J. Chem. Phys. 90 7354. (pdf)
  65. L. Perera and R. A. Thuraisingham, (1985) A Compact Configurational Interaction Wave Function For He And H-, Physics Letters A, 107A 310.







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