Publications

At Department of Chemistry
Georgia State University

  1. Doshi U., Holliday M. J., Eisenmesser E. Z., Hamelberg D., (2016). Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation. Proceedings of the National Academy of Sciences of the United States of America, 113, 4735–4740

  2. Barman A., Hamelberg D., (2016). Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. Journal of Physical Chemistry B, 120, 8405−8415

  3. Barman A., Smitherman C., Souffrant M., Gadda G., Hamelberg D., (2016). Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. Journal of Chemical Information and Modeling, 56, 139-147

  4. Elvira Romero, Safieh Tork Ladani, Hamelberg D., Gadda G. (2016). Solvent-Slaved Motions in the Hydride Tunneling Reaction Catalyzed by Human Glycolate Oxidase. ACS Catalysis, 6, 2113-2120

  5. Ho K. C., Hamelberg D., (2016). Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation. Journal of Chemical Theory and Computation, 12, 372–382

  6. Francesca Salvi, Isela Rodriguez, Hamelberg D., Gadda G. (2016). Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase. Biochemistry, 55, 1473-1484

  7. Rodriguez-Bussey I. G., Doshi U., Hamelberg D., (2016). Enhanced molecular dynamics sampling of drug target conformations. Biopolymers, 105, 35-42

  8. Tork-Ladani S., Souffrant M. G.,Barman A., Hamelberg D., (2015). Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochimica et Biophysica ACTA-General Subjects, 1850, 1994-2004

  9. Barman A., Batiste B., Hamelberg D., (2015). Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH-pi Interactions in Proteins. Journal of Chemical Theory and Computation, 11, 1854-1863

  10. Liu F. G., Geng J. F., Gumpper R. H., Barman A., Davis I., Ozarowski A., Hamelberg D., Liu A. M. , (2015). An Iron Reservoir to the Catalytic Metal: The Rubredoxin Iron In An Extradiol Dioxygenase. Journal of Biological Chemistry, 290, 15621-15634

  11. Mishra R. C., Gundala S. R., Karna P., Lopus M., Gupta K. K., Nagaraju M., Hamelberg D., Tandon V., Panda D., Reid M. D., Aneja R., (2015). Design, synthesis and biological evaluation of di-substituted noscapine analogs as potent and microtubule-targeted anticancer agents. Bioorganic & Medicinal Chemistry Letters, 25, 2133-2140

  12. Velazquez H. A., Hamelberg D., (2015). Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations. Journal of Chemical Physics, 142, 075102

  13. Doshi U., Hamelberg D., (2015). Towards fast, rigorous and efficient conformational sampling of biomolecules: advances in Accelerated Molecular Dynamics. Biochimica et Biophysica Acta (BBA) - General Subjects, 1850, 878-888

  14. Barman A., Hamelberg D., (2015). Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis–tau peptide. Proteins: Structure, Function, and Bioinformatics, 83, 436–444

  15. Barman A., Hamelberg D., (2014). Cysteine-Mediated Dynamic Hydrogen-Bonding Network in the Active Site of Pin1. Biochemistry, 53, 3839–3850

  16. Tork-Ladani S., Hamelberg D., (2014). Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A. Molecular Simulation, 40, 765-776

  17. Doshi U., Hamelberg D., (2014). Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent. Journal of Physical Chemistry Letters, 5, 1217–1224

  18. Madan J., Gundala S. R., Baruah B., Nagaraju M., Yates C., Turner T., Rangari V., Hamelberg D., Reid M. D., Aneja R., (2014). Cyclodextrin Complexes of Reduced Bromonoscapine in Guar Gum Microspheres Enhance Colonic Drug Delivery. Molecular Pharmaceutics, 11, 4339-4349

  19. Zhang C., Mulpuri N., Hannan F. M., Nesbit M. A., Thakker R. V., Hamelberg D., Brown E. M., Yang J. J., (2014). Role of Ca2+ and L-Phe in Regulating Functional Cooperativity of Disease-Associated "Toggle" Calcium-Sensing Receptor Mutations. PLoS ONE, 11, e113622

  20. Henary M., Narayanaa L., Ahad S., Gundala S. R., Mukkavilli R., Sharma V., Owens E. A., Yadav Y., Nagaraju M., Hamelberg D.,Tandon V., Panda D., Aneja R., (2014). Novel third-generation water-soluble noscapine analogs as superior microtubule-interfering agents with enhanced antiproliferative activity. Biochemical Pharmacology, 92, 192–205

  21. Zhang C., Huang Y., Jiang Y., Mulpuri N., Wei L., Hamelberg D., Brown E. M., Yang J. J., (2014). Identification of an L-Phenylalanine Binding Site Enhancing The Cooperative Responses of The Calcium Sensing Receptor to Calcium. Journal of Biological Chemistry, 289, 5296-5309

  22. Jiang J. Y., Nagaraju M., Meyer R. C., Zhang L., Hamelberg D., Hall R. A., Brown E. M., Conn P. J., Yang J. J. (2014). Extracellular calcium modulates actions of orthosteric and allosteric ligands on metabotropic glutamate receptor 1α. Journal of Biological Chemistry, 289, 1649-1661

  23. Levitz A., Tork-Ladani S., Hamelberg D., Henary M., (2014). Synthesis and effect of heterocycle modification on the spectroscopic properties of a series of unsymmetrical trimethine cyanine dyes. Dyes and Pigments, 105, 238–249

  24. Doshi U., Hamelberg D., (2014). The Dilemma of Conformational Dynamics in Enzyme Catalysis: Perspectives from Theory and Experiment. in Protein Conformational Dynamics: Advances in Experimental Medicine and Biology, Han, K.-l.; Zhang, X.; Yang, M.-j., Eds. Springer International Publishing, 805, 221-243

  25. Velazquez H. A., Hamelberg D., (2013). Conformation-Directed Catalysis and Coupled Enzyme–Substrate Dynamics in Pin1 Phosphorylation-Dependent Cis–Trans Isomerase. Journal of Physical Chemistry B, 117, 11509–11517

  26. Nagaraju M., McGowan L. C., Hamelberg D., (2013). Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design. Journal of Chemical Information and Modeling, 53, 403–410

  27. McGowan L. C., Hamelberg D., (2013). Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover Biophysical Journal, 104, 216-226

  28. Doshi U., Hamelberg D., (2012). Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. Journal of Chemical Theory and Computation, 8, 4004–4012

  29. Tork-Ladani S., Hamelberg D., (2012). Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A. Journal of Physical Chemistry B, 116, 10771–10778

  30. Doshi U., McGowan L. C., Tork-Ladani S., Hamelberg D., (2012). Resolving the complex role of enzyme conformational dynamics in catalytic function Proceedings of the National Academy of Sciences of the United States of America, 109, 5699-5704

  31. Madan J., Baruah B., Nagaraju M., Abdalla M. O., Yates C., Turner T., Rangari V., Hamelberg D., Aneja R., (2012). Molecular Cycloencapsulation Augments Solubility and Improves Therapeutic Index of Brominated Noscapine in Prostate Cancer Cells Molecular Pharmaceutics, 9, 1470-1480

  32. Nellas R. B., Glover M. M., Hamelberg D., Shen T., (2012). High-pressure effect on the dynamics of solvated peptides Journal of Chemical Physics, 136, 145103

  33. Doshi U., Kelley J. M., Hamelberg D., (2012). Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch RNA, 18, 300-307

  34. Chen W., Wang D., Dai C., Hamelberg D., Wang B., (2012). Clicking 1,2,4,5-tetrazine and cyclooctynes with tunable reaction rates Chemical Communications , 48, 1736-1738

  35. Torbeeva V. Y., Raghuraman H., Hamelberg D., Tonellie M., Westlere W. M., Perozoa E., Kent S. B. H., (2011). Protein conformational dynamics in the mechanism of HIV-1 protease catalysis Proceedings of the National Academy of Sciences of the United States of America, 108, 20982-20987

  36. Yuan H., Xin Y., Hamelberg D., Gadda G., (2011). Insights on the Mechanism of Amine Oxidation Catalyzed by d-Arginine Dehydrogenase Through pH and Kinetic Isotope Effects Journal of the American Chemical Society, 133, 18957–18965

  37. Velazquez H. A., Hamelberg D., (2011). Conformational Selection in the Recognition of Phosphorylated Substrates by the Catalytic Domain of Human Pin1 Biochemistry, 50, 9605–9615

  38. Doshi U., Hamelberg D., (2011). Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers’ Theory Journal of Chemical Theory and Computation, 7, 575–581

  39. Velazquez H. A., Hamelberg D., (2011). Ionic, Hydrogen Bond, and π–Cation Interactions in Chemosensors: Principles, Strategies, and Applications (eds B. Wang and E. V. Anslyn), John Wiley & Sons, Inc., Hoboken, NJ, USA

  40. Xin Y., Hamelberg D., (2010). Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme RNA, 16, 2455-2463

  41. Johnson Q., Doshi U., Shen T., Hamelberg D., (2010). Water’s Contribution to the Energetic Roughness from Peptide Dynamics Journal of Chemical Theory and Computation, 6, 2591–2597

  42. Xin Y., Doshi U., Hamelberg D., (2010). Examining the limits of time reweighting and Kramers’ rate theory to obtain correct kinetics from accelerated molecular dynamics Journal of Chemical Physics, 132, 224101

  43. Kelley J. M., Hamelberg D., (2010). Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch Nucleic Acids Research, 38, 1392-1400

  44. Doshi U., Hamelberg D., (2009). Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics Journal of Physical Chemistry B, 113, 16590-16595

  45. Xin Y., Gadda G., Hamelberg D., (2009). Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase Biochemistry, 48, 9599-9605

  46. Knight J. D. R., Hamelberg D., McCammon J. A., Kothary R., (2009). The role conserved water molecules in the catalytic domain of protein kinases Proteins: Structure, Function, and Bioinformatics, 76, 527-535

  47. Hamelberg D., McCammon J. A., (2009). Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A. Journal of the American Chemical Society, 131, 147-152

  48. Shen T., Hamelberg D., (2008). A statistical analysis of the precision of reweighting-based simulations Journal of Chemical Physics, 129, 034103

  49. Fajer M., Hamelberg D., McCammon J. A., (2008). Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. Journal of Chemical Theory and Computation, 4, 1565-1569

  50. de Oliveira C. A. F., Hamelberg D., McCammon J. A., (2008). Coupling accelerated molecular dynamics methods with thermodynamic integration simulations. Journal of Chemical Theory and Computation, 4, 1516-1525

  51. Qvist J., Davidovic M., Hamelberg D., Halle B., (2008). A dry ligand-binding cavity in a solvated protein. Proceedings of the National Academy of Sciences of the United States of America, 105, 6296-6301(Cover Issue)

  52. Hamelberg D., Shen T., McCammon J. A., (2007). A proposed signaling motif for nuclear import in mRNA processing via the formation of Arginine Claw. Proceedings of the National Academy of Sciences of the United States of America, 104, 14947-14951

  53. Minh D., Hamelberg D., McCammon J. A., (2007). Accelerated entropy estimates with accelerated dynamics. Journal of Chemical Physics, 127, 154105

  54. Hamelberg D., de Oliveira C. A. F., McCammon J. A., (2007). Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. Journal of Chemical Physics, 127, 155102

  55. de Oliveira C. A. F., Hamelberg D., McCammon J. A., (2007). Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine Dipeptide in explicit solvent as a case study. Journal of Chemical Physics, 127, 175105

  56. Hamelberg D., McCammon J. A., (2007). Dealing with bound waters in a site: Do they leave or stay? In "Computational and Structural Approaches to Drug Discovery," R.M. Stroud, Ed., Royal Society of Chemistry, Ch. 5, pp. 95-110

  57. Sørensen J., Hamelberg D., Schiøtt B., McCammon, J. A. (2007). Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers, 86, 73-82 (Cover Issue)

  58. Hamelberg D., McCammon J. A., (2006). Accelerating conformational transitions in biomolecular systems. Annual Reports in Computational Chemistry, 2, 221-232

  59. de Oliveira C. A. F., Hamelberg D., McCammon J. A., (2006). On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations. Journal of Physical Chemistry B, 110, 22695-22701

  60. Hamelberg D., Shen T., McCammon J. A., (2006). Insight into the role of hydration on protein dynamics. Journal Chemical Physics, 125, 094905

  61. Shen T., Hamelberg D., McCammon J. A., (2006). Elasticity of peptide omega bonds. Physical Review E, 73, 041908

  62. Vera C., Lao J., Hamelberg D., Sung L. A., (2005). Mapping the tropomyosin isoform 5 binding site on human erythrocyte tropomodulin: Further insights into E-Tmod/TM5 interaction. Archives of Biochemistry and Biophysics, 444, 130-138 (Cover Issue)

  63. Hamelberg D., McCammon J. A., (2005). Fast Peptidyl cis-trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 Protease. Journal of the American Chemical Society, 127, 13778-13779

  64. Shen TY, Zong CH, Hamelberg D., McCammon J. A., Wolynes, P. G, (2005). The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB Journal, 19, 1389-1395

  65. Hamelberg D., Shen T., McCammon J. A., (2005). Relating kinetic rates and local energetic roughness byaccelerated molecular-dynamics simulations. Journal of Chemical Physics, 122, 241103

  66. Hamelberg D., Shen T., McCammon J. A., (2005). Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: Accelerated molecular dynamics analysis. Journal of the American Chemical Society, 127, 1969-1974

  67. Chaires J. B., Ren .J, Hamelberg D., Kumar A., Pandya V., Boykin D. W., Wilson W. D., (2004). Structural selectivity of aromatic diamidines. Journal of Medicinal Chemistry, 47, 5729-5742

  68. Hamelberg D., McCammon J. A., (2004). Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. Journal of the American Chemical Society, 126, 7683-7689

  69. Hamelberg, D., Mongan J., McCammon J. A., (2004). Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. Journal of Chemical Physics, 120 (24), 11919-11929

  70. Grossman R., Kasturi, P., Hamelberg, D., Liu, B. (2004). An empirical study of the universal chemical key algorithm for assigning unique keys to chemical compounds. Journal of Bioinformatics and Computational Biology, 2, 155-171

  71. Tanious F. A., Hamelberg D., Bailly C., Czarny, A., Boykin D. W., Wilson, W. D., (2004). DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives. Journal of the American Chemical Society, 126, 143-153

  72. Nguyen B, Hamelberg D., Bailly C., Colson P., Stanek J., Brun R., Neidle S., Wilson W. D. (2004). Characterization of Novel DNA minor-groove complex. Biophysical Journal. 82, 1028-1041

  73. Grossman R. L., Gu Y. H., Hamelberg D., Hanley D., Hong X. W., Levera J., Lillethun D., Mazzucco M., Mambretti J., Weinberger J., (2003). Experimental studies using photonic data services at IGrid 2002. Future Generation Computer Systems 19, 945-955

  74. Nguyen B, Lee M. P. H., Hamelberg D., Joubert A., Bailly C., Brun R., Neidle S., Wilson W. D. (2002). Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove. Journal of the American Chemical Society. 124, 13680-13681

  75. Hamelberg D., Williams, L. D., Wilson, W. D., (2002). The Effect of Neutralized Phosphate Backbone on the Minor Groove Structure of B-DNA: Molecular Dynamics Simulation Studies. Nucleic Acid Research, 30, 3615-3623

  76. Hamelberg D., Williams, L. D., Wilson, W. D., (2001). Influence of the Dynamic Positions of Cations onthe Structure of the DNA Minor: Sequence Dependent Effects. Journal of the American Chemical Society, 123, 7745-7755

  77. Hamelberg D., McFail-Isom, L., Williams, L. D., Wilson, W. D., (2000). Flexible Structure of DNA: Ion Dependence of Minor-Groove Structure and Dynamics. Journal of the American Chemical Society, 122, 10513-10520