Publications

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      2016

  1. H. Zhao, D. Winogradoff, M. Bui, Y. Dalal, and G. A. Papoian* "Promiscuous histone mis-assembly is actively prevented by chaperones"; JACS; 2016, 10.1021/jacs.6b05355 [Article]

  2. B. Zhang, W. Zheng, G. A. Papoian, and P. G. Wolynes* "Exploring the Free Energy Landscape of Nucleosomes"; JACS; 2016, 10.1021/jacs.6b02893 [Article]

  3. K. Popov, J. Komianos, and G. A. Papoian* "MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks"; PLoS Comp Bio; 2016, doi:10.1371/journal.pcbi.1004877 [Article]

  4. U. Dobramysl, G. A. Papoian*, and R. Erban*, "Steric Effects Induce Geometric Remodeling of Actin Bundles in Filopodia"; Biophys J; 2016, doi:10.1016/j.bpj.2016.03.013 [Article]

  5. A. Davtyan, M. Platkov, M. Gruebele*, G. A. Papoian*, "Stochastic Resonance in Protein Folding Dynamics"; ChemPhysChem; 2016, doi:10.1002/cphc.201501125 [Article]

  6. K. Dave, A. Davtyan, G. A. Papoian*, M. Gruebele*, M. Platkov, "Environmental Fluctuations and Stochastic Resonance in Protein Folding"; ChemPhysChem; 2016, doi:10.1002/cphc.201501041 [Article]


    2015


  7. D. Winogradoff, H. Zhao, Y. Dalal*, G. A. Papoian*, "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome"; Sci Rep; 2015, 5, 17038 DOI: 10.1038/srep17038 [PDF]

  8. D. Winogradoff, I. Echeverria, D. A. Potoyan, G A. Papoian*, "The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects"; J Am Chem Soc; 2015,137, 6245-6253 [PDF]

  9. I. Echeverria and G. A. Papoian* "DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates" PLOS Comp. Bio.; 2015, DOI: 10.1371/journal.pcbi.1003980 [PDF]


    2014


  10. I. Echeverria and G. A. Papoian* "Structural Heterogeneity and Dynamics of the Unfolded Ensemble" Israel J. Chem.; 2014, 54, 1293–1301 [PDF]

  11. I. Echeverria, D. E. Makarov* and G. A. Papoian* "Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins" J. Am. Chem. Soc.; 2014, 136, 8708–8713 [PDF]

  12. R. Erban*, M. Flegg and G. A. Papoian* "Multiscale Stochastic Reaction-Diffusion Modeling: Application to Actin Dynamics in Filopodia" Bulletin of Mathematical Biology; 2014, 76, 799–818 [PDF]


    2013


  13. K. Popov and G. A. Papoian* "Capsid Deformations Reveal Complex Mechano-Chemistry" Biophysical Journal; 2013, 105, 2233–2234 [PDF]

  14. L. Hu and G. A. Papoian* "Molecular Transport Modulates the Adaptive Response of Branched Actin Networks to an External Force" J. Phys. Chem. B.; 2013, 117, 13388–13396 [PDF]

  15. D. Ma, S. Bettis, K. Hanson, M. Minakova, L. Alibabaei, W. Fondrie, D. Ryan, G. A. Papoian, T. J. Meyer, M. L. Waters and J. M. Papanikolas,  "Interfacial Energy Conversion in RuII Polypyridyl-Derivatized Oligoproline Assemblies on TiO2" J. Am. Chem. Soc.; 2013, 135, 5250–5253 [PDF]

  16. D. A. Potoyan, A. Savelyev and G. A. Papoian*"Recent successes in coarse-grained modeling of DNA"WIREs Comput. Mol. Sci.; 2013, 3, 69–83 [PDF]


    2012


  17. W. Zheng, N. Schafer, A. Davtyan, G. A. Papoian* and P. G. Wolynes*"Predictive Energy Landscapes for Protein-Protein Association"Proc. Natl. Acad. Sci. USA; 2012, 109, 19244–19429 [PDF]

  18. D. A. Potoyan and G. A. Papoian* "Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation" Proc. Natl. Acad. Sci. USA; 2012, 109, 17857-17862 [PDF]

  19. P. I. Zhuravlev, Y. Lan, M. S. Minakova and G. A. Papoian* "Theory of active transport in filopodia and stereocilia" Proc. Natl. Acad. Sci. USA; 2012, 109, 10849–10854 [PDF]

  20. M. Rubinstein and G. A. Papoian* "Polyelectrolytes in biology and soft matter" Soft Matter; 2012, 8, 9265–9267 [PDF]

  21. D. J. Wilger, S. E. Bettis, C. K. Materese, M. S. Minakova, G. A. Papoian*, J. M. Panpanikolas and M. L. Waters, "Tunable Energy Transfer Rates via Control of Primary, Secondary, and Tertiary Structure of a Coiled Coil Peptide Scaffold"Inorganic Chemistry; 2012, 51, 11324 [PDF]

  22. A. Davtyan, W. Zheng, N. Schafer, C. Clementi, P. G. Wolynes* and G. A. Papoian*"AWSEM-MD: Protein Structure Prediction Using Coarse-grained Physical Potentials and Bioinformatically Based Local Structure Biasing"J. Phys. Chem. B.; 2012,116, 8494–8503 [PDF]

  23. D. A. Potoyan, P. I. Zhuravlev and G. A. Papoian*"Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase using All Atom Explicit Solvent Simulations"J. Phys. Chem. B.; 2012,116, 1709–1715 [PDF]


  24. P. I. Zhuravlev, L. Hu, and G. A. Papoian*"Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility"Contributed Book Chapter in “Computational Modeling of Biological Systems: From Molecules to Pathways”, Publisher: Springer, edited by N. Dokholyan; 2012, ISBN-10: 1461421454 [Publisher's Site][Amazon]


    2011


  25. A. Savelyev, C. K. Materese and G. A. Papoian*"Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?"J. Am. Chem. Soc.; 2011, 133, 19290–19293 [PDF]
    (This work was highlighted by "Chemistry World", which is an RSC publication)

  26. P. I. Zhuravlev and G. A. Papoian* "Protein fluxes along the filopodium as a framework for understanding the growth-retraction dynamics: The interplay between diffusion and active transport"Cell Adhesion & Migration; 2011, 5, 448–456 [Article][PDF] (Note: Special Issue on Filopodia- This article has a review section summarizing our recent works on modeling filopodia)

  27. L. Hu and G. A. Papoian*"How does the Antagonism Between Capping and Anti-Capping Proteins Control Actin Network Dynamics?"; J. Phys.: Condens. Matter (Special Issue on “Cooperative dynamics in cells)”; 2011, 23, 374101 [PDF]

  28. M. Minakova, A. Savelyev and G. A. Papoian*"Non-equilibrium Water Transport in a Nonionic Microemulsion System"J. Phys. Chem. B.; 2011, 115, 6503-6508 [PDF]

  29. D. A. Potoyan and G. A. Papoian*"Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics"J. Am. Chem. Soc.; 2011,133,7405-7415 [PDF]


    2010


  30. A. Savelyev and G. A. Papoian*"Chemically accurate coarse graining of double-stranded DNA"Proc. Natl. Acad. Sci. USA; 2010, 107, 20340–5 [PDF]

  31. V. Oklejas, C. Zong, G. A. Papoian, P. G. Wolynes*"Protein structure prediction: Do hydrogen bonding and water-mediated interactions suffice?"Methods; 2010, 52, 84–90 [PDF]

  32. P. I. Zhuravlev and G. A. Papoian* "Protein functional landscapes, dynamics, allostery : a tortuous path towards a universal theoretical framework"Q Rev. Biophys.; 2010, 43(3),295–332 [PDF]

  33. P. I. Zhuravlev, S. Wu, D. A. Potoyan, M. Rubinstein and G. A. Papoian* "Computing free energies of protein conformations from explicit solvent simulations"Methods; 2010, 52, 115–121[PDF]

  34. P. I. Zhuravlev, B. Der and G. A. Papoian* "Design of Active Transport Must Be Highly Intricate: a Possible Role of Myosin and Ena/Vasp for G-Actin Transport in Filopodia"Biophys. J.; 2010, 98, 1439–1448 [PDF]

  35. L. Hu and G. A. Papoian* "Mechano-Chemical Feedbacks Regulate Actin Mesh Growth in Lamellipodial Protrusions"Biophys. J.; 2010, 98,1375–1384 [PDF]

  36. N. Tanaka and G. A. Papoian* "Reverse-Engineering of Biochemical Reaction Networks from Spatio-Temporal Correlations of Fluorescence Fluctuations"J. Theor. Biol.; 2010, 264, 490–500 [PDF]

  37. P. I. Zhuravlev and G. A. Papoian* "Functional vs. Folding Landscapes: The Same yet Different"Curr. Opin. Struct. Biol.; 2010, 20, 16–20 [PDF]


    2009


  38. C. K. Materese, A. Savelyev and G. A. Papoian* "Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle"J. Am. Chem. Soc.; 2009, 131, 15005–15013 [PDF]

  39. P. I. Zhuravlev and G. A. Papoian* "Molecular Noise of Capping Protein Binding Induces Macroscopic Instability in Filopodial Dynamics" Proc. Natl. Acad. Sci. USA; 2009, 106 (28), 11570-11575 [PDF]

  40. P. I. Zhuravlev, C. K. Materese and G. A. Papoian* "Deconstructing the Native State: Energy Landscapes, Function and Dynamics of Globular Proteins" J. Phys. Chem. B (Feature Article; July 2 2009 Journal Cover); 2009, 113, 8800–8812 [PDF]

  41. A. Savelyev and G. A. Papoian* "Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl"J. Phys. Chem. B.;2009, 113, 7785–7793 [PDF]

  42. A. Savelyev and G. A. Papoian* "Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA" Biophys. J.; 2009, 96, 4044-4052 [PDF]


    2008


  43. S. Wu, P. I. Zhuravlev and G. A. Papoian* "High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics" Biophysical J.; 2008, 95, 5524-5532 [PDF]

  44. Y. Lan, T. Elston*, and G. A. Papoian* "Elimination of Fast Variables in Chemical Langevin Equations" J. Chem. Phys.; 2008, 129, 214115 [PDF]

  45. G. A. Papoian* "Proteins with Weakly Funneled Energy Landscapes Challenge the Classical Structure–Function Paradigm" Proc. Natl. Acad. Sci. USA; 2008, 105 , 14237–14238 [PDF]

  46. A. Savelyev and G. A. Papoian* "Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers" The Journal of Physical Chemistry B; 2008, 112, 9135–9145[PDF]

  47. C. K. Materese, C. C. Goldmon and G. A. Papoian* "Hierarchical Organization of Eglin C Native State Dynamics Is Shaped by Competing Direct and Water-Mediated Interactions" Proc. Natl. Acad. Sci. USA; 2008, 105 , 10659 –10664 [PDF]
    (This article accompanied by V. Lubchenko's Commentary and highlighted on the Cover of August 5th issue of PNAS.)

  48. Y. Lan and G. A. Papoian* "The Stochastic Dynamics of Filopodial Growth", Biophysical Journal; 2008, 94, 3839-3852[PDF]


    2007


  49. Y. Lan and G. A. Papoian* "Stochastic Resonant Signaling in Enzyme Cascades", Physical Review Letters; 2007, 98 , 228301 [PDF]

  50. A. Savelyev and G. A. Papoian* "Inter-DNA Electrostatics from Explicit Solvent Molecular Dynamics Simulations" Journal of the American Chemical Society; 2007, 129 , 6060-6061 [PDF]

  51. Y. Lan and G. A. Papoian* "Evolution of Complex Probability Distributions in Enzyme Cascades", Journal of Theoretical Biology; 2007, 248, 537-545 [PDF]

  52. J. Latzer, G. A. Papoian, M. C. Prentiss, E. A. Komives, and P. G. Wolynes*"Induced Fit, Folding, and Recognition of the NF-κB-Nuclear Localization Signals by IκBα and IκBβ"; Journal of Molecular Biology; 2007, 367, 262-274 [PDF]

  53. A. Savelyev and G. A. Papoian* "Free Energy Calculations of Na+ and K+ Partitioning between DNA and Chloride Solutions" Mendeleev Communications 2007, 17, 97-99 [PDF]


    2006


  54.  A. Savelyev and G. A. Papoian* "Electrostatic, Steric, and Hydration Interactions Favor Na+ Condensation around DNA Compared with K+" Journal of the American Chemical Society 2006, 128 , 14506-14518 [PDF]

  55. Y. Lan, P. G. Wolynes, and G. A. Papoian*"A Variational Approach to the Stochastic Aspects of Cellular Signal Transduction", Journal of Chemical Physics; 2006, 125, 124106, [PDF]

  56. Y. Lan and G. A. Papoian* "The Interplay between Discrete Noise and Nonlinear Chemical Kinetics in a Signal Amplification Cascade", Journal of Chemical Physics; 2006125, 154901, [PDF]

    UCSD & UPenn

  57. C. Zong, G. A. Papoian, J. Ulander, and P. G. Wolynes "The Role of Topology, Nonadditivity and Water Mediated Interactions in Predicting the Structures of α/β Proteins" Journal of the American Chemical Society; 2006, 128 , 281-297 [PDF]

    2004

  58. G. A. Papoian, J. Ulander, M. E. Eastwood, Z. Luthey-Schulten, and P. G. Wolynes "Water in Protein Structure Prediction" ; Proc. Natl. Acad. Sci. USA; 2004, 101 , 3352-3357 [PDF][Commentary PDF]

  59. Y. Levy, G. A. Papoian, J. N. Onuchic, and P. G. Wolynes "The Energy Landscape Analysis of Protein Dimers" ; Israel J. Chem.; 2004 , 44 , 281-297 [PDF]

  60. G. A. Papoian, J. Ulander, and P. G. Wolynes "The Role of Water Mediated Interactions in Protein-Protein Recognition Landscapes." ; Journal of the American Chemical Society ; 2003 , 125 , 9170-9178 [PDF]

    2003

  61. G. A. Papoian and P. G. Wolynes "The Physics and Bioinformatics of Binding and Folding - an Energy Landscape Perspective" ; Biopolymers; 2003, 68 , 333-349 [PDF]

  62. G. A. Papoian, W. F. DeGrado, and M. L. Klein "Probing the Configurational Space of a Metalloprotein Core: An ab Initio Molecular Dynamics Study of Duo Ferro 1 binuclear Zn Cofactor."; Journal of the American Chemical Society; 2003 , 125, 560-569 [PDF]

    Cornell University

  63. G. A. Papoian and R. Hoffmann "Electron-rich Rods as Building Blocks for Sb Strips and Te sheets" ; Journal of the American Chemical Society; 2001 , 123 , 6600-6608 [PDF]

  64. A. Ienco, R. Hoffmann and G. A. Papoian "Electron-rich bonding and the Importance of s,p mixing as One Moves Across a Period: A Lesson from the LiSn System." Journal of the American Chemical Society; 2001 , 123 , 2317-2325 [PDF]

  65. G. A. Papoian and R. Hoffmann "Hypervalent Bonding in One, Two and Three Dimensions: Extending the Zintl-Klemm Concept to Nonclassical Electron-Rich Networks." Angewandte Chemie International Edition; 2000, 39 , 2408-2448 [PDF][Popular Press: Science Daily]

  66. G. A. Papoian, J. K. NÝrskov, and R. Hoffmann "A comparative study of hydrogen, methyl, and ethyl chemisorption on the Pt (111) surface." Journal of the American Chemical Society; 2000 , 122 , 4129-4144 [PDF]

  67. D. -K. Seo, G. A. Papoian, and R. Hoffmann. "Generalized Perturbational Molecular Orbital (PMO) Theory." International Journal of Quantum Chemistry; 2000 , 77 , 408-420 [PDF]

  68. W. V. Glassey, G. A. Papoian and R. Hoffmann "Total energy partitioning within an extended Huckel framework: a Hamilton Population study of surface --- CO interaction in the c(2x2) --- CO/Ni(100) chemisorption system." Journal of Chemical Physics; 1999, 111 , 893-910 [PDF]

  69. G. A. Papoian and R. Hoffmann "Building up complexity from strips and sheets --- the electronic structure of the La12Mn2Sb30 alloy." Journal of Solid State Chemistry; 1998 , 139 , 8-21 [PDF]

  70. G. A. Papoian, K.P. Butin, R. Hoffmann, and V.I Rozenberg "Theoretical investigation of [2.2]paracyclophane as a donor toward Cr(CO)3 group." Russian Chemical Bulletin; 1998 , 47 , 153-159

    University of Kansas

  71. G. A. Papoian, K. Gu, J. Wiorkiewicz-Kuczera, K. Kuczera, and K. Bowman-James. "Molecular dynamics simulations of nitrate complexes with polyammonium macrocycles: insight on phosphoryl transfer catalysis." Journal of the American Chemical Society; 1996, 118 , 1354-64 [PDF]

    Russian Academy of Sciences, Higher Chemical College

  72. S. Nefedov, A. Pasynskii, I. Eremenko, G. A. Papoian, L. Rubinstein, A. Yanovskii, and Yu. Struchkov. "Electron control of metal-metal bond multiplicity in binuclear thiolate-bridged rhenium-molybdenum complexes." Russian Journal of Inorganic Chemistry; 1993 , 38 , 69-7 
Last updated:   March 16, 2016