Cellular environments

Cellular environments

Biological environments present a very crowded, highly complex environment in which proteins and nucleic acids have to maintain their structure and carry out their function. If and how exactly such an environment affects biomolecules compared to dilute solvent or crystal conditions under which biomolecules are often studied remains largely unclear. The reduction of space leads to the well-known volume exclusion effect that generally favors more compact states under crowded conditions. But recent experiments and computer simulations suggest that non-specific protein-protein interactions, altered solvent properties, and high effective metabolite concentrations may have equally important effects on biomolecular stability and dynamics.

In collaboration with the Sugita group (RIKEN, Japan) we are carrying out molecular dynamics simulations of dense protein and nucleic acid systems ranging from simple models to highly complex, realistic models of bacterial cytoplasms.

 

Related Publications:

2021
  32. Natalia Ostrowska, Michael Feig, Joanna Trylska: Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex Biophysical Journal (2021) 120, 3795-3806 Abstract PDF
  31. Michael Feig: Virtual Issue on Protein Crowding and Stability Journal of Physical Chemistry B (2021) 125, 10649-10651 Abstract PDF
  30. Kento Kasahara, Suyong Re, Grzeogorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita: Reduced Efficacy of Src Kinase Inhibitor in Crowded Protein Solution Nature Communications (2021) 12, 4099 Abstract PDF
  29. Bercem Dutagaci, Grzegorz Nawrocki, Joyce Goodluck, Ali Akbar Ashkarran, Charles G. Hoogstraten, Lisa J. Lapidus, Michael Feig: Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments eLife (2021) 10, e64004 Abstract PDF
  28. Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita: New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems Journal of Computational Chemistry (2021) 42, 231-241 Abstract PDF
2020
  27. Agnieszka Popielec, Natalia Ostrowska, Monika Wojciechowska, Michael Feig, Joanna Trylska: Crowded environment affects the activity and inhibition of the NS3/4A protease Biochimie (2020) 176, 169-180 Abstract PDF
  26. Yuji Sugita, Michael Feig: All-atom Molecular Dynamics Simulation of Proteins in Crowded Environments In-cell NMR Spectroscopy: From Molecular Sciences to Cell Biology, eds. Yutaka Ito, Volker Dötsch, Masahiro Shirakawa, Royal Society of Chemistry (2020) Chapter 14, 228-248 Abstract PDF
2019
  25. Grzegorz Nawrocki, Wonpil Im, Yuji Sugita, Michael Feig: Clustering and Dynamics of Crowded Proteins near Membranes and Their Influence on Membrane Bending Proceedings of the National Academy of Sciences, USA (2019) 116, 24562-24567 Abstract PDF
  24. Natalia Ostrowska, Michael Feig, Joanna Trylska: Modeling crowded environment in molecular simulations Frontiers in Molecular Biosciences (2019) 6, 86 Abstract PDF
  23. Michael Feig, Yuji Sugita: Whole-Cell Models and Simulations in Molecular Detail Annual Reviews of Cell and Developmental Biology (2019) 35, 191-211 Abstract PDF
  22. Grzegorz Nawrocki, Alp Karaboga, Yuji Sugita, Michael Feig: Effect of Protein-Protein Interactions and Solvent Viscosity on the Rotational Diffusion of Proteins in Crowded Environments Physical Chemistry Chemical Physics (2019) 21, 876-883 Abstract PDF
2018
  21. Asli Yildirim, Nathalie Brenner, Robert Sutherland, Michael Feig: Role of Protein Interactions in Stabilizing Canonical DNA Features in Simulations of DNA in Crowded Environments BMC Biophysics (2018) 11, 8 Abstract PDF
  20. Asli Yildirim, Michael Feig: High-Resolution 3D Models of Caulobacter crescentus Chromosome Reveal Genome Structural Variability and Organization Nucleic Acids Research (2018) 46, 3937-3952 Abstract PDF
  19. Isseki Yu, Michael Feig, Yuji Sugita: High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations Journal of Physics, Conference Series (2018) 1036, 012009 Abstract PDF
  18. Michael Feig, Grzegorz Nawrocki, Isseki Yu, Po-hung Wang, Yuji Sugita: Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments Journal of Physics, Conference Series (2018) 1036, 012010 Abstract PDF
2017
  17. Grzegorz Nawrocki, Po-hung Wang, Isseki Yu, Yuji Sugita, Michael Feig: Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation Journal of Physical Chemistry B (2017) 121, 11072-11084 Abstract PDF
  16. Yuji Sugita, Isseki Yu, Michael Feig: Molecular Dynamics Simulations of Biomolecules in Cellular Environments Molecular Science (2017) 11, A0094 Abstract PDF
  15. Michael Feig, Isseki Yu, Po-hung Wang, Grzegorz Nawrocki, Yuji Sugita: Crowding and Interactions in Cellular Environments at an Atomistic Level from Computer Simulations Journal of Physical Chemistry B (2017) 121, 8009-8025 Abstract PDF
  14. Po-hung Wang, Isseki Yu, Michael Feig, Yuji Sugita: Influence of Protein Crowder Size on Hydration Structure and Dynamics in Macromolecular Crowding Chemical Physics Letters (2017) 671, 63-70 Abstract PDF
2016
  13. Tadashi Ando, Isseki Yu, Michael Feig, Yuji Sugita: Thermodynamics of macromolecular association in heterogeneous crwoding environments: Theoretical and simulation studies with a simplified model Journal of Physical Chemistry B (2016) 120, 11856-11865 Abstract PDF
  12. Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig: Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm eLife (2016) 5, e19274 Abstract PDF
2015
  11. Jaewoon Jong, Takakaru Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita: GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations WIREs Computational Molecular Science (2015) 5, 310-323 Abstract PDF
  10. Michael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koichi Takahashi, Yuji Sugita: Complete Atomistic Model of a Bacterial Cytoplasm Integrates Physics, Biochemistry, and Systems Biology Journal of Molecular Graphics and Modeling (2015) 58, 1-9 Abstract PDF
2014
  9. Asli Yildirim, Monika Sharma, Bradley Varner, Liang Fang, Michael Feig: Conformational Preferences of DNA in Cellular Environments Journal of Physical Chemistry B (2014) 118, 10874-10881 Abstract PDF
2013
  8. Michael Feig, Yuji Sugita: Reaching New Levels of Realism in Modeling Biological Macromolecules in Cellular Environments Journal of Molecular Graphics and Modeling (2013) 45, 144-156 Abstract PDF
  7. Ryuhei Harada, Naoya Tochio, Takanori Kigawa, Yuji Sugita, Michael Feig: Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions Journal of the American Chemical Society (2013) 135, 3696-3701 Abstract PDF
2012
  6. Ryuhei Harada, Yuji Sugita, Michael Feig: Protein crowding affects hydration structure and dynamics Journal of the American Chemical Society (2012) 134, 4842-4849 Abstract PDF
  5. Alexander Predeus, Seref Gul, Srinivasa Gopal, Michael Feig: Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations Journal of Physical Chemistry B (2012) 116, 8610-8620 Abstract PDF
  4. Michael Feig, Yuji Sugita: Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding Journal of Physical Chemistry B (2012) 116, 599-605 Abstract PDF
2008
  3. Michael Feig, Seiichiro Tanizaki, Maryam Sayadi: Implicit solvent simulations of biomolecules in cellular environments Annual Reviews in Computational Chemistry, Elsevier, Oxford (2008) 4,
  2. Michael Feig, Seiichiro Tanizaki, Jana Chocholousova, Maryam Sayadi, Jacob Clifford, Brian Connelly, Shayantani Mukherjee, Sean Law: Simulating Biomolecules in Cellular Environments From Computational Biophysics to Systems Biology (CBSB08) Proceedings, John von Neumann Institute for Computing (NIC) Series, ed. Ulrich Hansmann et al. (2008) 40, 23-30
  1. Seiichiro Tanizaki, Jacob W. Clifford, Brian D. Connelly, Michael Feig: Conformational Sampling of Peptides in Cellular Environments Biophysical Journal (2008) 94, 747-759 Abstract PDF