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Topic Review
Debugging the Center-of-mass Distance Method
The paper "On the in silico application of the center-of-mass distance method", introduces a protocol for utilizing the center-of-mass (CoM) distance method within GROMACS molecular dynamics (MD) simulation software. This method is valuable for assessing changes in binding affinity in heterodimeric proteins resulting from modifications in one of the monomer units. The study hypothesizes that an increase in binding affinity correlates with a reduction in the relative CoM distance between monomers, while a decrease in binding affinity corresponds to an increase in this distance. A key finding of the research is that CoM distance analysis should be conducted during the convergent phase of the system's dynamics, once the monomers have adopted a stable conformation—a factor that is often overlooked in similar studies. The method was applied to investigate the impact of the K417Y mutation in the SARS-CoV-2 surface glycoprotein (S-protein).
  • 287
  • 03 Mar 2025
Topic Review
A New Paradigm for Bio-osmotic Pressure
Osmotic pressure (OP) is widely recognized as a crucial driving force for the flow of body fluids. To provide a reasonable explanation for osmosis-dependent pathophysiological phenomena in live cells, we establish fluorescence resonance energy transfer (FRET)-based intermediate filament (IF) tension probes, converting the osmotic effect into optical signals. We then propose the theory of bio-osmotic pressure (bio-OP), which relies on the selective permeability of ion channels and water flux. Protein nanoparticles (PNs) play a crucial role in modulating transmembrane osmotic gradient by regulating the electrical activity of plasma membrane and voltage-dependent ion channels. Different ion compositions exhibit synergistic or antagonistic effects on PNs-induced electrical activity. As a result, PNs are crucial for maintaining intracellular osmotic effect. PNs, in collaboration with changes in ions and water, establish a new homeostasis in membrane potential and bio-OP. This collaboration leads to the synergistic regulation of electromechanical activity involved in the occurrence and development of various diseases associated with bio-OP, such as brain edema. 
  • 54
  • 14 Jan 2026
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