Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations

Abstract

BackgroundHow proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. The enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the molecular basis of this finding has not been fully established. Recently, it has been suggested that hydration dynamics play a predominant role in controlling the distribution of hot spots on surface of proteins.ResultsIn the present study, the hydration of the archaeal multifunctional protein Sso7d from Solfolobus solfataricus was investigated using a combination of computational and experimental data derived from molecular dynamics simulations and ePHOGSY NMR spectroscopy.ConclusionsWe obtained a convergent protein hydration landscape that indicated how the shape and stability of the Sso7d hydration shell could modulate the function of the protein. The DNA binding domain overlaps with the protein region involved in chaperon activity and this domain is hydrated only in a very small central region. This localized hydration seems to favor intermolecular approaches from a large variety of ligands. Conversely, high water density was found in surface regions of the protein where the ATP binding site is located, suggesting that surface water molecules play a role in protecting the protein from unspecific interactions.

Water-Peptide Site-Specific Interactions: A Structural Study on the Hydration of Glutathione

“…A description at the atomic scale of water hydration can provide insights on still open and important issues such as protein folding and association as well as protein-ligand binding, where water-related interactions have been proposed to dominate the thermodynamic signature of molecular recognition in ligand binding (6). To date, investigations concerning site-specific water-protein interactions in solution at the atomic length scale have coupled spectroscopic measurements with computation to understand which residues are preferentially interacting with the surrounding water solvent (3,4). Although NMR is a powerful tool for probing the structure of small peptides in solution, important details of the water hydration are lost on the time scale of NMR as it gives a spectral average of the water signal or any hydrogen binding site that is in fast exchange with the surrounding water solvent.…”

Urea–Water Solvation Forces on Prion Structures

“…45 The solvent interaction forces of individual atom types could be converted to solvation parameters and embedded in an implicit solvation model for urea–water mixtures. Another, more challenging, perspective is the combination of the observed surface site interactions in MD simulations with a thermodynamic site model.…”

“…Protein simulations in urea–water mixtures provide a rich source of information about solvation effects that can be used to detect potential structural defects and interaction sites. 45 The solvent interaction forces of individual atom types could be converted to solvation parameters and embedded in an implicit solvation model for urea–water mixtures. Another, more challenging, perspective is the combination of the observed surface site interactions in MD simulations with a thermodynamic site model.…”

NMR techniques in studying water in biotechnological systems

“…Many other questions including the function of the biomolecules, secondary structures, and folding biomacromolecules are depending on hydration water (Henkelman et al 1994;Zhang et al 2013;Nooeaid et al 2012;Bouazizi and Guillot 2019;Hoffmann et al 2019). Mostly, much slower dynamics of molecules has a place in the hydration layers (Blinc et al 1995;Rodin 2004;Belton 2011;Bernini et al 2011). NMR relaxation in combination with molecular dynamics simulations offers unique opportunities to test the internal dynamics of proteins on a time range of nanoseconds to picoseconds (Martini et al 2013;Hoffmann et al 2019;Bouazizi and Guillot 2019).…”

“…This work considers NMR approaches and basic techniques which were used quite frequently in studying watermacromolecule interactions, discovering the details of hydration and macromolecule dynamics with the factors responsible for biological functions in complex biomaterials (Rodin 1997;Mittermaier et al 2006;Belton 2011;Foster et al 2016;Rodin 2018c;Tarannum et al 2018). The review highlights those tools that enable the studies of functional properties of materials in drug delivery (Rodin and Izmailova 1995;Huang and Melacini 2006;Baldwin and Kay 2009;Zhang et al 2013Zhang et al , 2015Bernini et al 2011). Previously published reviews on protein hydration in solutions of biomacromolecules and systems with low hydration level could be recommended as well (Kuntz 1971;Wider 1998;Otting 1997;Krishman 1996;Halle 2004;Belton 2011;Huang and Melacini 2006;Martini et al 2013;Rodin 2018bRodin , 2018c.…”