Dataset Information

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.

ABSTRACT: A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force-extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT14 fragment via FRET while stretching the molecules using optical tweezers. The model offers straightforward generalization to systems containing double-stranded DNA and DNA binding proteins.

SUBMITTER: Maffeo C

PROVIDER: S-EPMC4132850 | biostudies-other | 2014 Aug

REPOSITORIES: biostudies-other

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A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.

Maffeo Christopher C Ngo Thuy T M TT Ha Taekjip T Aksimentiev Aleksei A

Journal of chemical theory and computation 20140603 8

A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to ...[more]

PMID: 25136266

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Project description:Using both atomistic and coarse-grained (CG) models, we compute the three-dimensional stress field around a gramicidin A (gA) dimer in lipid bilayers that feature different degrees of negative hydrophobic mismatch. The general trends in the computed stress field are similar at the atomistic and CG levels, supporting the use of the CG model for analyzing the mechanical features of protein/lipid/water interfaces. The calculations reveal that the stress field near the protein-lipid interface exhibits a layered structure with both significant repulsive and attractive regions, with the magnitude of the stress reaching 1000 bar in certain regions. Analysis of density profiles and stress field distributions helps highlight the Trp residues at the protein/membrane/water interface as mechanical anchors, suggesting that similar analysis is useful for identifying tension sensors in other membrane proteins, especially membrane proteins involved in mechanosensation. This work fosters a connection between microscopic and continuum mechanics models for proteins in complex environments and makes it possible to test the validity of assumptions commonly made in continuum mechanics models for membrane mediated processes. For example, using the calculated stress field, we estimate the free energy of membrane deformation induced by the hydrophobic mismatch, and the results for regions beyond the annular lipids are in general consistent with relevant experimental data and previous theoretical estimates using elasticity theory. On the other hand, the assumptions of homogeneous material properties for the membrane and a bilayer thickness at the protein/lipid interface being independent of lipid type (e.g., tail length) appear to be oversimplified, highlighting the importance of annular lipids of membrane proteins. Finally, the stress field analysis makes it clear that the effect of even rather severe hydrophobic mismatch propagates to only about two to three lipid layers, thus putting a limit on the range of cooperativity between membrane proteins in crowded cellular membranes.

Dataset Information

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.

Publications

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.

Similar Datasets

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