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).
- simulation
- center of mass distance
- center-of-mass
- distance
- debugging
- application
- K417Y
- Gromacs
The key findings of the article "On the in silico application of the center-of-mass distance method" are:
- Application of the Center-of-Mass (CoM) Distance Method: The paper demonstrates the use of the CoM distance method in molecular dynamics simulations, specifically within the GROMACS software, for assessing changes in binding affinity in heterodimeric proteins.
- Correlation Between CoM Distance and Binding Affinity: The research hypothesizes that a decrease in the CoM distance between monomers corresponds to an increase in binding affinity, while an increase in CoM distance reflects a decrease in binding affinity.
- Timing of CoM Distance Analysis: The study emphasizes the importance of conducting CoM distance analysis during the convergent phase of the simulation, when the monomers have reached a stable conformation. This step is often overlooked in similar studies.
- Application to SARS-CoV-2: The method was applied to investigate the effect of the K417Y mutation in the SARS-CoV-2 surface glycoprotein (S-protein), highlighting the utility of CoM distance in evaluating mutations related to protein interactions and stability.
These findings underscore the CoM distance method as a useful tool in computational biology for understanding protein interactions and predicting the effects of mutations.
This entry is adapted from: https://doi.org/10.36922/gpd.2657
References
- Done Stojanov; Structural implications of SARS-CoV-2 Surface Glycoprotein N501Y mutation within receptor-binding domain [499-505] – computational analysis of the most frequent Asn501 polar uncharged amino acid mutations. Biotechnol. Biotechnol. Equip. 2023, 37, 1, .
- Done Stojanov; Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Meta Gene 2021, 30, 100967-100967, .