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:

2017
  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) in press, 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