Jakob P. Ulmschneider - 上海交通大学

个人简介

1998 – 2004 PhD in Physics, Yale University 2005 – 2007 Emmy Noether Fellow, University of Rome 2008 Research Associate, University of Oxford 2008 – 2011 BIOMS Fellow, University of Heidelberg 2011 – 2018 　Assoc. Prof., SJTU 2018 – Prof., SJTU Our research is focused on studying and computationally modeling the protein machinery that drives membrane biology. Lipid bilayer membranes are bi-molecular lipid sheets, roughly 3-6 nanometers thick, that protect and compartmentalize the cellular machinery. Communication and transport across lipid bilayers is achieved by proteins associated with or embedded into the bilayer.

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40. Chen CH, Yu-Han Liu, Arvin Eskandari, Jenisha Ghimire, Leon Chien-Wei Lin, Zih-Syun Fang, William C. Wimley, Ulmschneider JP, Kogularamanan Suntharalingam, Che-Ming Jack Hu, and Martin B. Ulmschneider. Integrated Design of a Membrane-Lytic Peptide-Based Intravenous Nanotherapeutic Suppresses Triple-Negative Breast Cancer, Advanced Science 2022, 2105506 39. Chen CH*, Charles G. Starr, Shantanu Guha, William C. Wimley, Martin B. Ulmschneider*, Ulmschneider JP*, Tuning of a membrane-perforating antimicrobial peptide to selectively target membranes of different lipid composition The Journal of Membrane Biology 2021, 254, 75-96 38. Chen CH, Ulmschneider JP*, Ulmschneider MB: Mechanisms of a Small Membrane-Active Antimicrobial Peptide from Hyla punctata. Australian Journal of Chemistry 2020, 73:236-245. 37. Chen CH, Melo MCR, Berglund N, Khan A, de la Fuente-Nunez C, Ulmschneider JP*, Ulmschneider MB: Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly. Current Opinion in Structural Biology 2020, 61:160-166 36. C.H. Chen, C.G. Starr, E. Troendle, G. Wiedman, W.C. Wimley, J.P. Ulmschneider*, M.B. Ulmschneider. Simulation-guided rational de novo design of a small pore-forming antimicrobial peptide, J. Am. Chem. Soc. 2019, 141, 12, 4839-4848 35. Song Ke, M. B. Ulmschneider, A. Wallace, Ulmschneider, J. P*., Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel Biophysical Journal 2018, 115, 1920-193 34. Ulmschneider, J. P.*, J. C. Smith, S. H. White, and M. B. Ulmschneider. The importance of the membrane interface as the reference state for membrane protein stability. Biochim. Biophys. Acta Biomem. 2018, 1860(12):2539-2548. 33. Ulmschneider, J. P.*, & Ulmschneider, M. B. Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes. Accounts of Chemical Research 2018. doi: 10.1021/acs.accounts.7b00613 32. Gumbart, J. C., Ulmschneider, M. B., Hazel, A., White, S. H., & Ulmschneider, J. P.* Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. The Journal of Membrane Biology 2018. doi: 10.1007/s00232-018-0026-y 31. Ulmschneider, J. P.* Highly charged antimicrobial peptides can permeabilize and translocate across lipid bilayers without forming channel-like pores. Biophysical Journal 2017, 113(1), 73-81 30. Ulmschneider, M. B., Ulmschneider, J. P., Freites, J. A., von Heijne, G., Tobias, D. J., & White, S. H. Transmembrane helices containing a charged arginine are thermodynamically stable. European Biophysics Journal, 2017, 1-11 29. Wang, Y., Chen, C. H., Hu, D., Ulmschneider, M. B. & Ulmschneider, J. P.* Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide. Nature Communications 2016, 7, 13535 28. S. Upadhyay, Y. Wang, T. Zhao, J.P. Ulmschneider*, Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers. J Membrane Biol 2015, 248, 497-503 27. M. B.Ulmschneider, J. P. Ulmschneider, N. Schiller, B.A. Wallace, G. von Heijne & S. H. White Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion Nature Communications 2014, 5:4863 26. Y. Wang, T. Zhao, D. Wei, E. Strandberg, A. S. Ulrich, J. P. Ulmschneider* How reliable are molecular dynamics simulations of membrane active antimicrobial peptides? BBA Biomembranes, 2014, 1838, 2280 25. J. P. Ulmschneider* New Insights into the Peptide-Membrane Partitioning Equilibrium from in Silico Free Surface-to-Bilayer Peptide Insertion. Chap. 5 In Liposomes, Lipid Bilayers and Model Membranes: From Basic Research to Application, edited by N. Kučerka G. Pabst, M.-P. Nieh, J. Katsaras CRC Press, 2014 24. R. McNulty, J. P. Ulmschneider, H. Luecke, M. B. Ulmschneider Mechanisms of molecular transport through the urea channel of Helicobacter pylori Nature Communications 2013, 4:2900 23. M. Andersson, J. P. Ulmschneider, M. B. Ulmschneider, S. H. White Conformational states of melittin at a bilayer interface, Biophysical Journal 2013, 104, L12 22. M.B. Ulmschneider, C. Bagn�ris, E.C. McCusker, P. DeCaen, M. Delling, D.E. Clapham, J.P. Ulmschneider*, B. A. Wallace, Molecular Dynamics of Ion Transport through the Open Conformation of a Bacterial Voltage-gated Sodium Channel, Proc. Nat. Acad. Sci. 2013, 110, 6364 21. Y. Wang, D-Q. Wei, R. Gu, H. Fan, J. P. Ulmschneider*, Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems, Canadian Journal of Chemistry 2013, 91(9): 769-774 20. J. P. Ulmschneider*, Jeremy C. Smith, Martin B. Ulmschneider, Anne S. Ulrich, Erik Strandberg, Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations, Biophysical Journal 2012, (103), Issue 3, 472-482 19. J.P. Ulmschneider*, J.C. Smith, S. H. White, M. B. Ulmschneider, In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides Under Equilibrium Conditions, J. Am. Chem. Soc. 2011, 133(39):15487-15495. 18. J.P. Ulmschneider*, M. Anderson, M.B. Ulmschneider, Peptide partitioning properties from direct insertion via molecular mechanics simulation, J. Membr. Biol. 2011, 239, 15–26. 17. M.B. Ulmschneider, J.C. Smith, J.P. Ulmschneider*, Peptide partitioning properties from direct insertion studies, Biophys J., 2010, 98, L60–L62. 16. M.B. Ulmschneider, J. P. F. Doux, J. A. Killian, J.C. Smith, J.P. Ulmschneider*, Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides, J. Am. Chem. Soc., 2010, 132, 3452–3460. 15. M.B. Ulmschneider, J.P. Ulmschneider*, Implicit membrane models for peptide folding and insertion studies. In: Molecular Simulations and Biomembranes: From Biophysics to Function, Royal Society of Chemistry, 2010. 14. J. P. Ulmschneider*, J. P. F. Doux, J. A. Killian, J. C. Smith, M. B. Ulmschneider, Peptide Partitioning and Folding into Lipid Bilayers, J. Chem. Theory Comput. 2009, 5, 2202-2205. 13. J.P. Ulmschneider*, M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field. J. Chem. Theory Comput. 2009, 5, 1803-1813. 12. J.P. Ulmschneider*, M.B. Ulmschneider, Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations. Proteins 2009, 75, 586-597. 11. M.B. Ulmschneider, J.P. Ulmschneider*, Folding peptides into lipid bilayers. J. Chem. Theory Comput. 2008, 4, 1807-1809. 10. M.B. Ulmschneider, J.P. Ulmschneider*, Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides, Mol. Mem. Biol. 2008, 25, 245-257. 9. J.P. Ulmschneider*, M.B. Ulmschneider, Folding simulations of the trans-membrane helix of virus protein U in an implicit membrane model. J. Chem. Theory Comput. 2007, 3, 2335-2346. 8. J.P. Ulmschneider*, M.B.Ulmschneider, A. Di Nola, Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane, Proteins 2007, 69, 297-308. 7. M.B.Ulmschneider, J.P. Ulmschneider*, A. Di Nola, M.S.P. Sansom, A generalized Born implicit membrane representation based on experimental insertion free energies. Biophys. J. 2007, 92, 2338–2349. 6. J.P. Ulmschneider*, M.B. Ulmschneider, A. Di Nola, Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding Simulations, J. Phys. Chem. B 2006, 110, 16733-16742. 5. J.P. Ulmschneider, W.L. Jorgensen, Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation, Yale Univ. Ph.D. Thesis, Dec. 2004. 4. W.L. Jorgensen, J.P. Ulmschneider, J. Tirado-Rives, Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field, J. Phys. Chem. B 2004, 108, 16264-16270. 3. J.P. Ulmschneider, W.L. Jorgensen, Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation, J. Am. Chem. Soc. 2004, 126, 1849-1857. 2. J.P. Ulmschneider, W.L. Jorgensen, Monte Carlo Backbone Sampling for Nucleic Acids using Concerted Rotations including Variable Bond Angles, J. Phys. Chem. B 2004, 108, 16883-16892. 1. J.P. Ulmschneider, W.L. Jorgensen, Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias, J. Chem. Phys. 2003, 118, 4261-4271.