ArticleBiophysical journal2009
REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Advances in coarse-grained modeling of macromolecular complexes.Current opinion in structural biology · 2018Review
- Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.Protein science : a publication of the Protein Society · 2018Article
- Dynamic features of homodimer interfaces calculated by normal-mode analysis.Protein science : a publication of the Protein Society · 2012Article
- Combining NMR and molecular dynamics studies for insights into the allostery of small GTPase-protein interactions.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.Biophysical journal · 2010Article
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3 authors.
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Abstract
The REACH (realistic extension algorithm via covariance Hessian) coarse-grained biomolecular simulation method is a self-consistent multiscale approach directly mapping atomistic molecular dynamics simulation results onto a residue-scale model. Here, REACH is applied to calculate the dynamics of protein-protein interactions. The intra- and intermolecular fluctuations and the intermolecular vibrational densities of states derived from atomistic molecular dynamics are well reproduced by the REACH normal modes. The phonon dispersion relations derived from the REACH lattice dynamics model of crystalline ribonuclease A are also in satisfactory agreement with the corresponding all-atom results. The REACH model demonstrates that increasing dimer interaction strength decreases the translational and rotational intermolecular vibrational amplitudes, while their vibrational frequencies are relatively unaffected. A comparative study of functionally interacting biological dimers with crystal dimers, which are formed artificially via crystallization, reveals a relation between their static structures and the interprotein dynamics: i.e., the consequence of the extensive interfaces of biological dimers is reduction of the intermonomer translational and rotational amplitudes, but not the frequencies.
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