I work at Johnson Lab as a postdoc now. I develop model techniques to study how protein assembly control the biological processes such as endocytosis and viral exit. If interested, feel free to email me at sikaoguo@gmail.com. Here is my most update CV.

I graduated from School of Physics, Nankai University with a bachelor’s degree and from Institute of Physics, Chinese Academy of Sciences with a PhD degree, advised by Ping Xie.

My research interest is computational biophysics. The transport of nutrients into our cells and the viral budding out of the cell both require to cross the membrane. In both cases the membrane will be reshaped to a vesicle because of the self-assembly of the different protein components. The dynamics of self-assembly in the cell are challenging to simulate because it involves both fast molecule motion and slow collective dynamics. I developed model techniques to study the control and spatio-temporal dynamics of these assembly problems. I am broadly interested in how key features of dimensionality and component stoichiometry controls assembly in these cellular pathways, such as endocytosis and infectious viral formation.

🔥 News

• 2023.07: Our paper “Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions” has been published in eLife!
• 2022.12: 🎉🎉 My google scholar citations have reached 200!
• 2022.03: Our paper “Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins” has been published in PLoS computational biology!

📝 Publications

Protein Self-assembly

Gag 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).

Poster

For the immature Gag lattice to become mature, a pair of protease within the lattice need to form a dimer. We studied the mechanism of protease dimerization within the immature lattice.

Clathrin assembly on membrane

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).

Poster

Stochastic self-assembly of clathrin-coated structures on the membrane is essential for transport into cells. These structures can grow large, yet they often fail to form productive versicles, instead disassembling. We studied the mechanisms of stable vs unstable clathrin assembly on membranes.

• 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).

• 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).
• All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state, Xiao‐Xuan Shi, Si‐Kao Guo, Peng‐Ye 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 all‐atom molecular dynamics simulation, Xiao‐Xuan Shi, Yi‐Ben Fu, Si‐Kao Guo, Peng‐Ye Wang, Hong Chen, Ping Xie, Proteins: Structure, Function, and Bioinformatics 86 (11), 1127-1139 (2018).
• Processivity of dimeric kinesin‐1 molecular motors, Si‐Kao Guo, Xiao‐Xuan Shi, Peng‐Ye 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).

Professional Experience

01/2020 - present

Postdoctoral Research, Johns Hopkins University, Department of Biophysics

Research Advisor: Professor Margaret E. Johnson

Educations

09/2014 - 12/2019

Ph.D. in Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China

Research Advisor: Professor Ping Xie

Graduate Thesis Title: “Studying the movement mechanism of dimer kinesin through theoretical modeling and numerical simulation”

09/2010 - 06/2014

B.S. in Physics, Nankai University, Tianjin, China

Conference Presentations

• Defects Within the HIV-1 Immature Lattice Support Dynamic Remodeling and Protease Dimerization, Cell Bio 2022, Washington, DC, USA, December 4, 2022.
• Large Self-assembled Clathrin Lattices Spontaneously Disassemble Without Sufficient Adaptor Proteins, Biophysical Society 66th Annual Meeting, San Francisco, CA, USA, February 19, 2022.
• Self-assembled clathrin lattices spontaneously disassemble without sufficient links to the plasma membrane, Stochastic Physics in Biology (Gordon Research Conference), Ventura, CA, USA, October 10, 2021.
• Modeling Nucleation and Kinetics of Clathrin Assembly by Membrane Localization, Biophysical Society 65th Annual Meeting, Virtual, February 22, 2021.
• Molecular mechanism of dimeric kinesin, 2018 Annual Summary Report, Institute of Physics, Chinese Academy of Sciences, Beijing, China, November 25, 2018.
• A model of processive movement of dimeric kinesin, Year-end Meeting and Exhibition of IOP, Institute of Physics, Chinese Academy of Science, Beijing, China, January 5, 2018.

Academic Service

• Reviewer of The Journal of Physical Chemistry, PROTEINS: Structure, Function, and Bioinformatics, PLOS Computational Biology, International Journal of Molecular Sciences, Cells, Applied Sciences, Biophysica, Biochemistry and Biophysics Reports, Entropy.
• Guest Editor of Biology, Special Issue: “Microtubule Network: Role in Cell Development and Disease”.
• Guest Editor of Biomedicines, Special Issue: “Molecular Mechanisms and Regulation of Self-Assembly Pathways in the Cell”.

Open-Source Software

• Developer of a simulator for self-assembly at the cellular scale – NERDSS.
• Creator and developer of the simulation kit for molecular motor – kinesin.

Contact

Department of Biophysics, Johns Hopkins University Baltimore, MD 21218

sikaoguo@gmail.com