đ Publications
Protein Self-assembly
Parallelization of particle-based reaction-diffusion simulations using MPI
Sikao Guo, Korolija Nenad, Milfeld Kent, Jhaveri Adip, Sang Mankun, Ying M Yue, Margaret E Johnson, bioRxiv. 2024.12.06.627287 (2024).
By developing a parallel implementation of NERDSS using MPI-based domain decomposition, We have achieved near-linear scaling on large computing clusters. This enables the simulation of complex, biologically relevant self-assembly processesâsuch as protein lattice formation and the organization of multimeric complexes. Although performance depends on system size, reaction networks, and timescales, our open-source, parallelized code significantly improves the speed and accessibility of structure-resolved reaction-diffusion simulations, providing a powerful resource for researchers studying molecular assembly.
Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions
Sikao Guo, Ipsita Saha, Saveez Saffarian, Margaret E Johnson, eLife. 12:e84881 (2023).
âThis fundamental work substantially advances our understanding of the maturation of retroviruses, a key step in understanding the formation of infectious viruses. The evidence supporting the conclusions is compelling, with rigorous computational simulations. The work will be of broad interest to the community of virologists worldwide.â â Editorâs evaluation
Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins
Si-Kao Guo, Alexander J Sodt, Margaret E Johnson, PLOS Computational Biology. 18, e1009969 (2022).
We explore how clathrin-coated structures assemble and disassemble on cell membranes, a key process in cellular transport. By integrating in vitro kinetic data with detailed reaction-diffusion simulations and membrane modeling, We show that stable nucleation of these lattices requires a greater-than-1:1 ratio of adaptor proteins to clathrin. Under more physiologically relevant conditions, insufficient adaptor abundance leads to spontaneously forming but ultimately transient assemblies, explaining why so many clathrin structures fail to mature into vesicles. This work provides a quantitative framework for understanding how cellular conditions govern the transition from transient clathrin-coated structures to productive vesicle formation.
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Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters, 1. Jiang A., Kudo, K., Gormal R. S., Ellis S., Sikao Guo, Wallis T. P., Longfield S. F., Robinson P. J., Johnson M. E., Joensuu M., Meunier F. A., Nature Communications, 15: 4060, DOI: https://doi.org/10.1038/s41467-024-47677-8 (2024).
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Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly, Yian Qian, Daniel Evans, Bhavya Mishra, Yiben Fu, Zixiu Hugh Liu, Sikao Guo, Margaret E Johnson, Biophysical Journal DOI:https://doi.org/10.1016/j.bpj.2023.06.021 (2023).
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Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface, Qi Xie, Sea On Lee, Nitya Vissamsetti, Sikao Guo, Margaret E. Johnson, Stephen D. Fried, Angewandte Chemie DOI:https://doi.org/10.1002/ange.202305178 (2023).
Molecular motor: Kinesin
- A common chemomechanical coupling model for orphan and conventional kinesin molecular motors, Si-Kao Guo, Ping Xie, Biophysical Chemistry 264, 106427 (2020).
- Allâatom molecular dynamics simulations reveal how kinesin transits from oneâheadâbound to twoâheadsâbound state, XiaoâXuan Shi, SiâKao Guo, PengâYe Wang, Hong Chen, Ping Xie, Proteins: Structure, Function, and Bioinformatics 88 (4), 545-557 (2020).
- Run length distribution of dimerized kinesin-3 molecular motors: comparison with dimeric kinesin-1, Si-Kao Guo, Xiao-Xuan Shi, Peng-Ye Wang, Ping Xie, Scientific reports 9, 16973 (2019).
- Force dependence of unbinding rate of kinesin motor during its processive movement on microtubule, Si-Kao Guo, Xiao-Xuan Shi, Peng-Ye Wang, Ping Xie, Biophysical Chemistry 253, 106216 (2019).
- Dynamics of cooperative cargo transport by two elastically coupled kinesin motors, Yi-Ben Fu, Si-Kao Guo, Peng-Ye Wang, Ping Xie, The European Physical Journal E 42 (4), 1-13 (2019).
- A generalized kinetic model for coupling between stepping and ATP hydrolysis of kinesin molecular motors, Ping Xie, Si-Kao Guo, Hong Chen, International journal of molecular sciences 20 (19), 4911 (2019).
- Force dependence of velocity and run length of kinesin-1, kinesin-2 and kinesin-5 family molecular motors, Si-Kao Guo, Wei-Chi Wang, Peng-Ye Wang, Ping Xie, Molecules 24 (2), 287 (2019).
- ATP-concentration-and force-dependent chemomechanical coupling of kinesin molecular motors, Ping Xie, Si-Kao Guo, Hong Chen, Journal of Chemical Information and Modeling 59 (1), 360-372 (2018).
- Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by allâatom molecular dynamics simulation, XiaoâXuan Shi, YiâBen Fu, SiâKao Guo, PengâYe Wang, Hong Chen, Ping Xie, Proteins: Structure, Function, and Bioinformatics 86 (11), 1127-1139 (2018).
- Processivity of dimeric kinesinâ1 molecular motors, SiâKao Guo, XiaoâXuan Shi, PengâYe Wang, Ping Xie, FEBS Open Bio 8 (8), 1332-1351 (2018).
- Dynamics of dimeric kinesins: Limping, effect of longitudinal force, effects of neck linker extension and mutation, and comparison between kinesin-1 and kinesin-2, Si-Kao Guo, Peng-Ye Wang, Ping Xie, International journal of biological macromolecules 105, 1126-1137 (2017).
- A model of processive movement of dimeric kinesin, Si-Kao Guo, Peng-Ye Wang, Ping Xie, Journal of Theoretical Biology 414, 62-75 (2017).