Hydrophobicity and geometry: Water at curved graphitic-like surfaces and within model pores in self-assembled monolayers

Alarcón, L. M.; de, Joan Manuel Montes; Accordino, Sebastián R.; Fris, J. A. Rodríguez; Appignanesi, Gustavo A.

doi:10.1016/j.fluid.2013.09.008

Cited by 14 publications

(17 citation statements)

References 35 publications

(62 reference statements)

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“…Finally, by means of the study of water density fluctuations, we shall estimate the local hydrophobicity properties both for model surfaces and for the different groups of the lipid bilayer. These studies might be relevant for the comprehension of the behavior of binding sites in different contexts which, as already indicated, are expected to present easily removable hydration water which might be replaced by the ligand upon binding (Fernández and Scheraga 2003;Fernández and Scott 2003;Fernández 2010;Qvist et al 2008;Berne et al 2009;Young et al 2007;Wang et al 2011;Kulp III et al 2011;Accordino et al 2012aAccordino et al , b, c, 2013Sierra et al 2013;Alarcón et al 2014;Bogan and Thorn 1998;Li and Liu 2009). We thus conclude with a few words of further emphasis on the relevance of this kind of knowledge to biology and to the design of new materials by highlighting the context-dependent and non-additive nature of different con-covalent interactions in an aqueous nanoenvironment, an issue that is usually greatly overlooked.…”

Section: Introductionmentioning

confidence: 88%

“…Larger holes (up to roughly L D 25 Å), where the water molecules can enter retaining their coordination, are nonetheless more hydrophobic than the perfect monolayer, which means that hydrophobicity is clearly curvature-dependent for concave surfaces. Such result of a geometrically-induced dehydration is interesting, for example, for the context of protein binding, since protein binding pockets are expected to be dry or to contain easily removable water which should be displaced by a ligand upon association (Fernández and Scheraga 2003;Fernández and Scott 2003;Fernández 2010;Qvist et al 2008;Berne et al 2009;Young et al 2007;Wang et al 2011;Kulp III et al 2011;Accordino et al 2012aAccordino et al , b, c, 2013Sierra et al 2013;Alarcón et al 2014;Bogan and Thorn 1998;Li and Liu 2009). …”

Section: Water At Self-assembled Monolayers Filling Of Cavities and mentioning

confidence: 99%

“…Such structural packing defects characterized by regions of the protein backbone exposed to the solvent has been shown to promote their local dehydration and to signal binding sites (Fernández and Scheraga 2003;Fernández and Scott 2003;Fernández 2010;Accordino et al 2012aAccordino et al , b, c, 2013Sierra et al 2013). Different approaches have indicated that the hydration properties of protein binding sites play a main role in the binding of ligands or in protein-protein association (Fernández and Scheraga 2003;Fernández and Scott 2003;Fernández 2010;Qvist et al 2008;Berne et al 2009;Young et al 2007;Wang et al 2011;Kulp III et al 2011;Accordino et al 2012aAccordino et al , b, c, 2013Sierra et al 2013;Alarcón et al 2014;Bogan and Thorn 1998;Li and Liu 2009). Ligands are expected to displace hydration water molecules from their binding site and the replacement of so-called "unfavorable" waters by groups of the ligand complementary to the protein surface has been established as a principal driving force for binding (Fernández and Scheraga 2003;Fernández and Scott 2003;Fernández 2010;Qvist et al 2008;Berne et al 2009;Young et al 2007;Wang et al 2011;Kulp III et al 2011;Accordino et al 2012aAccordino et al , b, c, 2013Sierra et al 2013;Alarcón et al 2014;Bogan and Thorn 1998;Li and Liu 2009).…”

Section: Quantifying Local Hydrophobicity: Calculations Of Water Densmentioning

confidence: 99%

“…However, the picture of (nano) confined water is still far from being complete (Giovambattista et al 2012;Rasaiah et al 2008;Berne et al 2009;Schulz et al 2011;Alarcón et al 2014). This issue is not only crucial from an intrinsic, fundamental level, but also from its far reaching implications (Fernández 2010;Qvist et al 2008;Berne et al 2009;Young et al 2007;Wang et al 2011;Kulp III et al 2011;Accordino et al 2011aAccordino et al , 2012aAccordino et al , b, c, 2013Schulz et al 2011;Sierra et al 2013;Alarcón et al 2014;Bogan and Thorn 1998;Li and Liu 2009). For example, being water the matrix of life, a full understanding of its behavior in the nano and mesoscales would be essential to understand biology at the molecular level.…”

Section: Introductionmentioning

confidence: 99%

“…One such example is the nanoconfinement produced upon association of hydrophobic surfaces, which affects the thermodynamic properties of the hydration water in order to produce the "drying" process promoter of hydrophobic collapse. Another example is the binding of a ligand to a protein, which is expected to displace easily removable hydration water (Fernández and Scheraga 2003;Fernández and Scott 2003;Fernández 2010;Qvist et al 2008;Berne et al 2009;Young et al 2007;Wang et al 2011;Kulp III et al 2011;Accordino et al 2012aAccordino et al , b, c, 2013Sierra et al 2013;Alarcón et al 2014;Bogan and Thorn 1998;Li and Liu 2009). Thus, the knowledge of how different nanoconfinement conditions (both of chemical and geometrical nature) affect hydrophobicity is therefore not only of great significance to understand and to predict the behavior of these systems, but also to guide the efforts to emulate them in bioengineering.…”

Section: Introductionmentioning

confidence: 99%

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Hydration and Nanoconfined Water: Insights from Computer Simulations

Alarcón

Fris

Morini

et al. 2015

Subcellular Biochemistry

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The comprehension of the structure and behavior of water at interfaces and under nanoconfinement represents an issue of major concern in several central research areas like hydration, reaction dynamics and biology. From one side, water is known to play a dominant role in the structuring, the dynamics and the functionality of biological molecules, governing main processes like protein folding, protein binding and biological function. In turn, the same principles that rule biological organization at the molecular level are also operative for materials science processes that take place within a water environment, being responsible for the self-assembly of molecular structures to create synthetic supramolecular nanometrically-sized materials. Thus, the understanding of the principles of water hydration, including the development of a theory of hydrophobicity at the nanoscale, is imperative both from a fundamental and an applied standpoint. In this work we present some molecular dynamics studies of the structure and dynamics of water at different interfaces or confinement conditions, ranging from simple model hydrophobic interfaces with different geometrical constraints (in order to single out curvature effects), to self-assembled monolayers, proteins and phospholipid membranes. The tendency of the water molecules to sacrifice the lowest hydrogen bond (HB) coordination as possible at extended interfaces is revealed. This fact makes the first hydration layers to be highly oriented, in some situations even resembling the structure of hexagonal ice. A similar trend to maximize the number of HBs is shown to hold in cavity filling, with small subnanometric hydrophobic cavities remaining empty while larger cavities display an alternation of filled and dry states with a significant inner HB network. We also study interfaces with complex chemical and geometrical nature in order to determine how different conditions affect the local hydration properties. Thus, we show some results for protein hydration and, particularly, some preliminary studies on membrane hydration. Finally, calculations of a local hydrophobicity measure of relevance for binding and self-assembly are also presented. We then conclude with a few words of further emphasis on the relevance of this kind of knowledge to biology and to the design of new materials by highlighting the context-dependent and non-additive nature of different non-covalent interactions in an aqueous nanoenvironment, an issue that is usually greatly overlooked.

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Section: Introductionmentioning

confidence: 88%

Section: Water At Self-assembled Monolayers Filling Of Cavities and mentioning

confidence: 99%

Section: Quantifying Local Hydrophobicity: Calculations Of Water Densmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Hydration and Nanoconfined Water: Insights from Computer Simulations

Alarcón

Fris

Morini

et al. 2015

Subcellular Biochemistry

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Membrane Hydration

2015

Subcellular Biochemistry

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The book series SUBCELLULAR BIOCHEMISTRY is a renowned and well recognized forum for disseminating advances of emerging topics in Cell Biology and related subjects. All volumes are edited by established scientists and the individual chapters are written by experts on the relevant topic. The individual chapters of each volume are fully citable and indexed in Medline/Pubmed to ensure maximum visibility of the work.

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