Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 Å Resolution

Water is essential for life in many ways, and without it biomolecules might no longer truly be biomolecules. In particular, water is important to the structure, stability, dynamics, and function of biological macromolecules. In protein folding, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. Water actively participates in molecular recognition by mediating the interactions between binding partners and contributes to either enthalpic or entropic stabilization. Accordingly, water must be included in recognition and structure prediction codes to capture specificity. Thus water should not be treated as an inert environment, but rather as an integral and active component of biomolecular systems, where it has both dynamic and structural roles. Focusing on water sheds light on the physics and function of biological machinery and self-assembly and may advance our understanding of the natural design of proteins and nucleic acids.

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Water mediation in protein folding and molecular recognition

Molecular dynamics simulations based on empirical force fields can greatly enhance knowledge of DNA and RNA structure and dynamics in solution. Presented are results on simulations of three DNA sequences and one RNA sequence using the new all-atom CHARMM27 force field for nucleic acids presented in the accompanying manuscript (Foloppe, MacKerell, J Comput Chem, this issue). Data are reported on structural, dynamic, and hydration properties including dihedral angle, sugar puckering, and helicoidal parameter probability distributions. Also presented are calculations of a DNA hexamer in 0 and 75% ethanol starting from both the canonical A and B forms. Analysis of RMS differences with respect to the canonical A and B forms of DNA show a highly anticorrelated behavior indicating that the force field samples the equilibrium between the A and B forms of DNA. Proper stabilization of B form DNA in aqueous solution and A form DNA in 75% ethanol show that this equilibrium can be perturbed by environmental contributions. Success of the force field in reproducing a variety of experimental data for duplex DNA and RNA indicates that it is of general use for computational investigations of nucleic acids as well as nucleic acids in complexes with proteins and lipids. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 105–120, 2000

All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases and so on. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.

/pdf/3dna-a-versatile-integrated-software-system-for-the-analysis-1jvfgs29j2.pdf

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

http://pubs.acs.org/doi/pdf/10.1021/acs.chemrev.6b00765

Water Dynamics in the Hydration Shells of Biomolecules

Hydration of the phosphate group in double-helical DNA

https://www.cell.com/biophysj/pdf/S0006-3495(98)77660-X.pdf

Ketan Patel

Papers

Hydration of the phosphate group in double-helical DNA

An analysis of the relationship between hydration and protein-DNA interactions