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REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

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.

SUBMITTER: Moritsugu K

PROVIDER: S-EPMC2726322 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature

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REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

Moritsugu Kei K Kurkal-Siebert Vandana V Smith Jeremy C JC

Biophysical journal 20090801 4

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 ...[more]

PMID: 19686664

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Project description:Microtubules are long polymers of alphabeta-tubulin heterodimers. They undergo a process known as dynamic instability, in which the ends of a microtubule switch stochastically between phases of slow growth and rapid shrinkage. The molecular mechanisms inducing the depolymerization of microtubules were attributed to the hydrolysis of the guanosine triphosphate (GTP) nucleotide bound to the beta-tubulin. The hydrolysis of GTP is thought to cause microtubule instability by promoting outward curving of the protofilaments constituting the microtubule lattice. The bending of protofilaments is associated with the structural transformation of a tubulin dimer from straight to curved conformations. However, the nature of intrinsic bending of the dimer remains elusive. This study uses molecular dynamics (MD) simulations and coarse-grained analysis to reveal the intrinsic bending, as well as the local structural rearrangements, of the unassembled tubulin dimer as the dimer relaxes from its lattice-constrained, straight conformation of a zinc-induced tubulin sheet. The effect of the nucleotide state on dimer-bending is investigated by the introduction of gamma-phosphate into the beta-tubulin to form GTP-bound tubulin. In agreement with recent experimental studies that proposed nucleotide-independent curved conformations, both guanosine diphosphate (GDP)-bound and GTP-bound tubulin dimers were found to have curved conformations, but with a tendency toward smaller bending in the GTP-tubulin than in the GDP-tubulin. The perturbation induced through the introduction of gamma-phosphate is posited to play a role in straightening the intradimer bending. The local structural rearrangements of GDP-tubulin because of the bending mode of motion of the dimer reveal that one of the three functional domains, the intermediate domain, exhibits significantly lower bending deformation compared with the others, signifying a dynamic connection to the functionally defined domains.

Dataset Information

REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

Publications

REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

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