Publications

Listed in reverse chronological order.

  1. Jamel Simpson and Peter M. Kasson. Structural prediction of chimeric immunogens to elicit targeted antibodies against betacoronaviruses. 2023, biorxiv doi: 10.1101/2023.01.31.526494.
  2. Dariia Yehorova, Rory Crean, Peter M. Kasson, and SCL Kamerlin. Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families. 2024, Protein Science 3(33), e4911. doi:10.1002/pro.4911
  3. Marcos Cervantes, Toby Hess, Giorgio G. Morbioli, Anjali Sengar, and Peter M. Kasson. The ACE-2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion.  2023, Chemical Science, 2023, 14, 6997-7004. doi:10.1101/2022.10.22.513347 
  4. Anjali Sengar, Marcos Cervantes, and Peter M. Kasson. Mechanistic dissection of antibody inhibition of influenza entry yields unexpected heterogeneity. 2023, Biophysical Journal. Jun 6;122(11):1996-2006. doi:10.1016/j.bpj.2022.10.026
  5. Rory M. Crean, Joanna S.G. Slusky, Peter M. Kasson, and SCL Kamerlin. KIF—Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes. J Chem Phys. 2023 Apr 14;158(14):144114. doi: 10.1063/5.0140882.
  6. Steinar Mannsverk, Ana M. Villamil Giraldo, and Peter M. Kasson. Influenza virus membrane fusion is promoted by the endosome-resident phospholipid bis(monoacylglycero)phosphate. 2022, Journal of Physical Chemistry 126, 49, 10445–10451. . doi:10.1101/2022.09.16.508338
  7. Ana M. Villamil Giraldo, Steinar Mannsverk, and Peter M. Kasson. Measuring single-virus fusion kinetics using an assay for nucleic acid exposure. 2022, Biophysical Journal. 121(23): 4467-4475. doi: 10.1016/j.bpj.2022.11.002
  8. M. Eric Irrgang, Caroline Davis, and Peter M. Kasson. gmxapi: a Gromacs-native Python interface for molecular dynamics with ensemble and plugin support. 2022, PLoS Computational Biology. Doi:10.1371/journal.pcbi.1009835
  9. Anjali Sengar, Sai T. Bondalapati, and Peter M. Kasson. Single-virus fusion measurements yield an opportunistic model for SARS-CoV-2 fusion. 2021, biorxiv. Doi: 10.1101/2021.05.04.442634
  10. Alzbeta Tuerkova and Peter M. Kasson. Computational methods to study enveloped virus entry. Biochemical Society Transactions, 2021. doi:10.1042/BST20210190
  11. Peter M. Kasson. Modeling biomolecular kinetics with large-scale simulation. Current Opinion in Structural Biology 2022, 72:95-102. doi: 10.1016/j.sbi.2021.08.009
  12. Mayuresh M Abhyankar, Barbara Mann, Jeffery Sturek, Savannah Brovero, Brett Moreau, Anjali Sengar, Sayeh Agah, Crystal M Richardson, Zach Schuhmacher, Jillian Bracaglia, Anna Pomés, Peter Kasson, Mark Tomai, Christopher Fox and William A Petri Jr. Development of COVID-19 vaccine using a dual Toll-like receptor ligand liposome adjuvant. npj Vaccines, 2021 in press.
  13. Jennifer M. Hays, Emily Boland, and Peter M. Kasson.  Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements.  J. Phys. Chem. Lett. 2021, 12, 6, 1606–1611.  doi:10.1021/acs.jpclett.0c03623
  14. Sourav Haldar, Kenta Okamoto, Rebecca A. Dunning, and Peter M. Kasson.  Precise triggering and chemical control of single-virus fusion within endosomes.  Journal of Virology, epub 2020, 95(1), e01982-20.  Preprint doi:10.1101/2020.04.12.038109
  15. Ana M. Villamil Giraldo and Peter M. Kasson. Bilayer-Coated Nanoparticles Reveal How Influenza Viral Entry Depends on Membrane Deformability but not Curvature.  Journal of Physical Chemistry Letters, 2020, 11 (17), 7190-7196. doi:10.1021/acs.jpclett.0c01778
  16. Rajasree Menon, Edgar Otto, Rachel Sealfon, Viji Nair, Aaron Wong, Chandra Theesfeld, Xi Chen, Yuan Wang, Avinash Boppana, Jinghui Luo, Yingbao Yang, Peter M. Kasson, Jennifer Schaub, Celine Berthier, Sean Eddy, Chrysta Liencezewski, Bradley Godfrey, Susan Dagenais, Ryan Sohaney, John Hartman, Damian Fermin, Lalita Subramanian, Helen Looker, Jennifer Harder, Laura Mariani, Jeffrey Hodgin, Jonathan Sexton, Christiane Wobus, Abhijit Naik, Robert Nelson, Olga Troyanskaya, Matthias Kretzler.  SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease.  Kidney International, 2020.  doi:10.1016/j.kint.2020.09.015 
  17. Shina C.L. Kamerlin and Peter M. Kasson. Managing COVID-19 spread with voluntary public-health measures: Sweden as a case study for pandemic control. Clinical Infectious Diseases, 2020.  doi:10.1093/cid/ciaa864
  18. Anna Pabis, Robert J. Rawle, and Peter M. Kasson.  Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms.  PNAS, 2020 117 (13) 7200-7207.
    doi:10.1073/pnas.1914188117
  19. Peter M. Kasson.  Infectious Disease Research in the Era of Big Data.  Annual Review of Biomedical Data Science, 2020.
    doi:10.1146/annurev-biodatasci-121219-025722
  20. Ricardo J. Ferreira and Peter M. Kasson.  Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics.  ACS Infectious Diseases, 2019, 5, 12, 2096-2104.  DOI:10.1021/acsinfecdis.9b00201
  21. Robert J. Rawle, Ana M. Villamil Giraldo, Steven G. Boxer, and Peter M. Kasson.  Detecting and controlling dye effects in single-virus fusion experiments.  Biophysical Journal, 2019.  117(3):445-452.  DOI:10.1101/646679
  22. Jennifer M. Hays, David S. Cafiso, and Peter M. Kasson.  Hybrid Refinement of Heterogeneous Conformational Ensembles using Spectroscopic Data.  Journal of Physical Chemistry Letters 2019.  10 (12):3410-3414.  preprint doi:10.1101/656595.
  23. Jennifer M. Hays; Marissa K. Kieber; Jason Z. Li; Ji In Han; Linda Columbus; Peter M. Kasson.  Refinement of highly flexible protein structures using simulation-guided spectroscopy.  Angewandte Chemie 2018.  DOI:10.1002/anie.201810462
  24. Robert J. Rawle, Elizabeth R. Webster, Marta Jelen, Peter M. Kasson*, and Steven G. Boxer*.  pH Dependence of Zika Membrane Fusion Kinetics Reveals an Off-Pathway State.  ACS Central Science 2018.  DOI: 10.1021/acscentsci.8b00494
  25. Peter M. Kasson and Shantenu Jha.  Adaptive ensemble simulations of biomolecules.  Current Opinion in Structural Biology 2018.  52:87-94.  DOI:10.1016/j.sbi.2018.09.005
  26. George A. Cortina and Peter M. Kasson.  Predicting allostery and microbial drug resistance with molecular simulations.  Current Opinion in Structural Biology 2018.  52:80-86.  DOI:10.1016/j.sbi.2018.09.001
  27. Ying Liu, Tomasz Osinski, Fengbin Wang, Mart Krupovic, Stefan Schouten, Peter Kasson, David Prangishvili, and Edward H Egelman.  Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile. Nature Communications 2018.  9(1):3360. DOI:10.1038/s41467-018-05684-6
  28. M. Eric Irrgang, Jennifer M. Hays, and Peter M. Kasson.  gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.  Bioinformatics 2018.  DOI:10.1093/bioinformatics/bty484.
  29. George A. Cortina, Jennifer M. Hays, and Peter M. Kasson.  A conformational intermediate that controls KPC-2 catalysis and beta-lactam drug resistance.  ACS Catalysis 2018.  DOI:10.1021/acscatal.7b03832
  30. Katarzyna E. Zawada, Kenta Okamoto, and Peter M. Kasson.  Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion.  Journal of Molecular Biology 2018.  DOI: 10.1016/j.jmb.2018.01.006.
  31. Isabel N. Goronzy, Robert J. Rawle, Steven G. Boxer, and Peter M. Kasson. Cholesterol enhances influenza binding avidity by promoting nanoscale receptor clustering.  Chemical Science 2018.  DOI: 10.1039/C7SC03236F.
  32. Peter M. Kasson, Frank DiMaio, Xiong Yu, Soizick Lucas-Staat, Mart Krupovic, Stefan Schouten, David Prangishvili, and Edward H Egelman.  Model for a novel membrane envelope in a filamentous hyperthermophilic virus.  Elife 2017.   DOI: 10.7554/eLife.26268.
  33. Malgorzata Latallo, George Cortina, Salem Faham, Robert Nakamoto and Peter M. Kasson.  Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme.  Chemical Science, 2017 online July 19.
  34. Marc Lipsitch, Wendy Barclay, Rahul Raman, Charles J Russell ,Jessica A Belser, Sarah Cobey, Peter M Kasson, James O Lloyd-Smith, Sebastian Maurer-Stroh, Steven Riley, Catherine AA Beauchemin, Trevor Bedford, Thomas C Friedrich, Andreas Handel, Sander Herfst, Pablo R Murcia, Benjamin Roche, Claus O Wilke, and Colin A Russell.  Viral factors in influenza pandemic risk assessment.  Elife. 2016 Nov 11;5. pii: e18491. doi: 10.7554/eLife.18491.
  35. George A. Cortina and Peter M. Kasson.  Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance.  Bioinformatics, 2016 Nov 15;32(22):3420-3427. Epub 2016 Jul 27.
  36. Katarzyna E. Zawada, Dominik Wrona, Robert J. Rawle, and Peter M. Kasson.  Influenza viral membrane fusion is sensitive to sterol concentration but surprisingly robust to sterol chemical identity.  Scientific Reports, 2016 6:29842.
  37. Robert J. Rawle, Steven G. Boxer, and Peter M. Kasson.  Disentangling viral membrane fusion from receptor binding using synthetic DNA-lipid conjugates.  Biophysical Journal, 2016 111: 123-131
  38. Marta Domanska, Rebecca Dunning, Katarzyna Zawada, Kelly Dryden, Mark Yeager, and Peter M. Kasson. Hemagglutinin spatial distribution shifts in response to cholesterol in the influenza viral envelope.  Biophysical Journal, 2015 109 (9) 1917-24
  39. Sander Pronk, Iman Pouya, Magnus Lundborg, Grant Rotskoff, Bjorn Wesen, Peter Kasson, and Erik Lindahl.  Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.  J. Chem. Theory Comput., 2015 11 (6): 2600–2608.
  40. Sander Pronk, Erik Lindahl, and Peter M. Kasson. Coupled diffusion in lipid bilayers upon close approach. Journal of the American Chemical Society. Epub Dec 23, 2014
  41. Michael D. Purdy, Brad C. Bennett, William E. McIntire, Ali Khan, Peter M. Kasson, and Mark Yeager.Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Current Opinion in Structural Biology, 2014 Aug; 27:138-48.
  42. Colin A. Russell, Peter M. Kasson, Ruben O. Donis, Steven Riley, John Dunbar, Andrew Rumbaut, Jason Asher, Stephen Burke, C. Todd Davis, Rebecca J. Garten, S. Gnanakaran, Simon I. Hay, Sander Herfst, Nicola S. Lewis, James O. Lloyd-Smith, Catherine A. Macken, Sebastian Mauerer-Stroh, ElizabethNeuhaus, Colin R. Parris, Kim M. Pepin, Daniel R. Perez, Sam Shepard, David L. Smith, David L. Suarez, Susan C. Trock, Marc-Alain Widdowson, Dylan George, Marc Lipsitch, Jesse D. Bloom. Improving pandemic influenza risk assessment. eLife, 2014 Oct 16; 3:e03883
  43. Per Larsson and Peter M. Kasson. Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations. Journal of Membrane Biology, 2014
  44. Dan A. Fox, Per Larsson, Ryan H. Lo, Brett M. Kroncke, Peter M. Kasson, and Linda Columbus. NMR and MD hybrid approach to the structure ensemble of Opa60: Insights into host interactions that induce phagocytosis. Journal of the American Chemical Society, 2014. Epub May 9.
  45. Sonia M. Gregory, Per Larsson, Elizabeth A. Nelson, Peter M. Kasson, Judith M. White, and Lukas K. Tamm.Ebolavirus entry requires a compact hydrophobic fist at the tip of the fusion loop. Journal of Virology, 2014. 88:12 6636-6649.
  46. Sander Pronk, Erik Lindahl, and Peter M. Kasson.  Dynamic heterogeneity controls diffusion and viscosity near biological interfaces.  Nature Communications, 2014 Jan 8; 5:3034.
  47. Marta K. Domanska, Dominik Wrona, and Peter M. Kasson.  Multiphasic effects of cholesterol on influenza fusion kinetics reflect multiple mechanistic roles.  Biophysical Journal, 2013 Sept 17; 105(6).
  48. Per Larsson and Peter M. Kasson.  Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models.  PLoS Computational Biology.  2013 March 7 9(3): e1002950.
  49. Sander Pronk, Szillard Pall, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, and Erik Lindahl.  GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit.  Bioinformatics.  2013.  Epub 2013 Feb 13.
  50. Peter M. Kasson*, Berk Hess, and Erik Lindahl*.  Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions.  Chemistry and Physics of Lipids.  2013. Epub 2013 Jan 12.
  51. Peter M. Kasson.  Receptor binding by influenza virus:  using computational techniques to extend structural data.  Biochemistry.  2012 Mar 27; 51(12): 2359-65.
  52. Sander Pronk, Per Larsson, Iman Pouya, Gregory Bowman, Imran Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande*, Peter M. Kasson*, and Erik Lindahl*.  Copernicus: a new paradigm for parallel adaptive molecular dynamics. Supercomputing 2011.
  53. Peter M. Kasson and Vijay S. Pande.  A bundling of viral fusion mechanisms.  Proceedings of the National Academy of Sciences.  2011 Feb 28.
  54. Peter M. Kasson, Erik Lindahl, and Vijay S. Pande.  Water ordering at membrane interfaces controls fusion dynamics.  J Am Chem Soc. 2011; 133(11):3812-15.
  55. Peter M. Kasson, Erik Lindahl, and Vijay S. Pande. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.  PLoS Computational Biology, 2010 June 24; 6(6)e1000829.
  56. Peter M. Kasson and Vijay S. Pande.  “Cross-graining.”  Efficient multi-scale simulation via Markov State Models.  Pacific Symposium on Biocomputing.  2010:260-8.
  57. Peter M. Kasson, Daniel L. Ensign, and Vijay S. Pande.  Combining molecular dynamics with Bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.  J Am Chem Soc. 2009 Aug 19;131(32):11338-40.  Epub 2009 July 28.
  58. Peter M. Kasson and Vijay S. Pande.  Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin.  Pac Symp Biocomput. 2009:492-503.
  59. Peter M. Kasson and Vijay S. Pande.  Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.  Biophys J. 2008 Oct;95(7):L48-50.  Epub 2008 July 18.
  60. Peter M. Kasson and Vijay S. Pande.  Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics.  PLoS Computational Biology, 2007 Nov; 3(11)e220.  Epub 2007 Sept 26.
  61. Daniel L. Ensign, Peter M. Kasson, and Vijay S. Pande.  Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.  J. Mol. Biol., 2007 Nov 30; 374(3):806-16.  Epub 2007 Oct 1.
  62. Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, and Vijay S. Pande. Persistent voids:  a new structural metric for membrane fusion.  Bioinformatics. 2007 Jul 15;23(14):1753-9. Epub 2007 May 8.
  63. Peter M. Kasson and Vijay S. Pande.  Predicting structure and dynamics of loosely-ordered protein complexes:  influenza hemagglutinin peptide.  Pacific Symposium on Biocomputing. 2007 12:40-50.
  64. Peter M. Kasson, Nicholas W. Kelley, Nina Singhal, Marija Vrljic, Axel T. Brunger, and Vijay S. Pande. Ensemble molecular dynamics yields sub-millisecond kinetics and intermediates of membrane fusion.  Proceedings of the National Academy of Sciences. 2006 Aug 8;103(32):11916-21. Epub 2006 Jul 31.
  65. Peter M. Kasson, Johannes B. Huppa, Mark M. Davis, and Axel T. Brunger.  A hybrid machine-learning approach for segmentation of protein localization data.  Bioinformatics. 2005 Oct 1;21(19):3778-86. Epub 2005 Aug 9.
  66. Peter M. Kasson, Mark M. Davis, and Axel T. Brunger.  Deformable modeling for improved calculation of molecular velocities from single-particle tracking.  2005 EEE Computational Systems Bioinformatics Conference 8-11 Aug. 2005.
  67. Peter M. Kasson, Johannes B. Huppa, Michelle Krogsgaard, Mark M. Davis, and Axel T. Brunger. Quantitative imaging of lymphocyte membrane protein reorganization and signaling.  Biophys J. 2005 Jan;88(1):579-89.
  68. Peter M. Kasson, Johannes B. Huppa, Mark M. Davis, and Axel T. Brunger.  Quantitative analysis of lymphocyte membrane protein redistribution from fluorescence microscopy.  Proceedings – International Conference on Image Processing.  2004; v.2, p.2933-2936.
  69. Peter M. Kasson and Vijay S. Pande.  Molecular dynamics simulation of lipid reorientation at bilayer edges.  Biophys J. 2004 Jun;86(6):3744-9.
  70. Peter M. Kasson, Joshua D. Rabinowitz, Lutz Schmitt, Mark M. Davis, and Harden M. McConnell.  Kinetics of Peptide Binding to the class II MHC protein I-Ek.  Biochemistry, 2000 Feb 8;39(5):1048-58.
  71. Joshua D. Rabinowitz, Maria Vrljic, Peter M. Kasson, Michael N. Liang, Robert Busch, J.J Boniface, Mark M. Davis, and Harden M. McConnell.  Formation of a Highly Peptide-Receptive State of Class II MHC.  Immunity, 1998 Nov;9(5):699-709.