报告题目：DNA packing in viral capsids
报告人：Jure Dobnikar 教授CECAM-CN主任中国科学院物理研究所
报告时间：2025年11月14日（周五）下午2:00-3:00
报告地点：物理科技楼 101室
报告摘要：Assembly of viral capsidscontaining genetic material, is a key process in viral reproduction cycle. The bacteriophages and double strandedDNA viruses assemble their capsids prior togenome packaging and actively push DNA inside by ATP-driven packaging motors. The genome is typically densely packed in the capsid and understanding its spatial configuration presents a challenging problem, which is not completely understood despite its obvious importance.
To elucidate the mechanism of DNA packing, we first explored a simple model of elastic filament confined to a sphere with three competing interactions [1]. The simple phenomenological theory supported by extensive parallel tempering MD simulations of the wormlike chain (WLC) model show that the optimal ground state packing is not an inverse spool configuration as previously assumed; it is a more complex structure where the filament is compartmentalized into multiple domains, resembling nested tori or topological links. While this suggests that DNA will also form multidomain structures in a viral capsid, it is important to realize that DNA cannot be completely described by the linear elastic model. Under sufficient local torsion, the base pairs of the double helix can locally melt creating regions with large flexibility that can easily form kinks. We incorporated this effect into a meltable WLC model and explored nonequilibrium process of pushing such kinkable chains into a capsid by molecular motors [3]. It turns out that the kink formation crucially affects the structure: for sufficiently slow packing process we observe a coexistence of outer spool domain and a twisted nematic core – in a perfect agreement with available cryo-EM experimental observations. Our findings suggest that the nonlinear elasticity of biological molecules plays an important role in their spatial structuring in confined biological systems.
References
[1] T. Curk, J.D. Farrell, J. Dobnikar, R. Podgornik, Spontaneous Domain Formation in Spherically Confined Elastic Filaments, Phys. Rev. Lett.123 047801 (2019)
[2] J.D. Farrell, J. Dobnikar, R. Podgornik, T. Curk: Spool-nematic ordering of dsDNA and dsRNA under confinement,Phys. Rev. Lett.133 148101 (2024)
报告人简介：
2001 PhD degree in Physics at University of Ljubljana, Slovenia
2001-2004 Post doctoral fellow: University Konstanz, Germany
2004-2006 Marie-Curie fellow at University of Graz, Austria
2006-2015 Senior Researcher: Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
2008-2015 Senior Research Associate: Department of Chemistry, University of Cambridge, UK
2014-2016 Assistant Director: International Center for Soft Matter Research, BUCT, Beijing
2016-20xx Full Professor, Institute of Physics, CAS, Beijing
Jure Dobnikar graduated in theoretical physics from University of Ljubljana in 2001. He worked as a postdoctoral fellow at University of Konstanz and University of Graz, and later as a senior researcher at Jožef Stefan Institute in Ljubljana and at University of Cambridge. In 2014, he moved to Beijing to manage the International Soft Matter Research Center at BUCT and in 2016 he accepted a permanent position at the Institute of Physics, Chinese Academy of sciences, where he is currently a full professor and the leader of the SM9 research group. His research interests are in physical modelling of soft and biological matter, particularly colloidal interactions, self-assembly, non-equilibrium phenomena, active matter, bacterial motility, and multivalent binding in cellular targeting and activation processes. He is also the director of the CECAM-CN node with a mission to bring high quality scientific event organization and international exchange possibilities to China.
