scholarly journals Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

2017 ◽  
Vol 114 (51) ◽  
pp. 13345-13350 ◽  
Author(s):  
Erte Xi ◽  
Vasudevan Venkateshwaran ◽  
Lijuan Li ◽  
Nicholas Rego ◽  
Amish J. Patel ◽  
...  
Keyword(s):  
Self Assembly ◽  
Driving Forces ◽  
Hydrophobic Interactions ◽  
Density Fluctuations ◽  
Hydroxyl Groups ◽  
Water Density ◽  
Hydration Shells ◽  
Protein Mutants ◽  
Assembled Monolayers ◽  
Water Adhesion

Hydrophobic interactions drive many important biomolecular self-assembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute–water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.

scholarly journals Understanding Hydrophobic Effects: Insights from Water Density Fluctuations

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Nicholas B. Rego ◽  
Amish J. Patel
Keyword(s):  
Materials Science ◽  
Hydrophobic Interactions ◽  
Hydrophobic Hydration ◽  
Surface Hydrophobicity ◽  
Bulk Water ◽  
Density Fluctuations ◽  
Annual Review ◽  
Publication Date ◽  
Water Density ◽  
Hydrophobic Effects

The aversion of hydrophobic solutes for water drives diverse interactions and assemblies across materials science, biology, and beyond. Here, we review the theoretical, computational, and experimental developments that underpin a contemporary understanding of hydrophobic effects. We discuss how an understanding of density fluctuations in bulk water can shed light on the fundamental differences in the hydration of molecular and macroscopic solutes; these differences, in turn, explain why hydrophobic interactions become stronger upon increasing temperature. We also illustrate the sensitive dependence of surface hydrophobicity on the chemical and topographical patterns the surface displays, which makes the use of approximate approaches for estimating hydrophobicity particularly challenging. Importantly, the hydrophobicity of complex surfaces, such as those of proteins, which display nanoscale heterogeneity, can nevertheless be characterized using interfacial water density fluctuations; such a characterization also informs protein regions that mediate their interactions. Finally, we build upon an understanding of hydrophobic hydration and the ability to characterize hydrophobicity to inform the context-dependent thermodynamic forces that drive hydrophobic interactions and the desolvation barriers that impede them. Expected final online publication date for the Annual Review of Condensed Matter Physics, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Investigation of Au SAMs Photoclick Derivatization by PM-IRRAS

2019 ◽  
Author(s):  
Mark Workentin ◽  
François Lagugné-Labarthet ◽  
Sidney Legge
Keyword(s):  
Cell Adhesion ◽  
Self Assembly ◽  
Materials Science ◽  
Fibroblast Cell ◽  
Fine Tuning ◽  
Chemical System ◽  
Infrared Reflection ◽  
Assembled Monolayers ◽  
One Step ◽  
High Degree

In this work we present a clean one-step process for modifying headgroups of self-assembled monolayers (SAMs) on gold using photo-enabled click chemistry. A thiolated, cyclopropenone-caged strained alkyne precursor was first functionalized onto a flat gold substrate through self-assembly. Exposure of the cyclopropenone SAM to UV-A light initiated the efficient photochemical decarbonylation of the cyclopropenone moiety, revealing the strained alkyne capable of undergoing the interfacial strain-promoted alkyne-azide cycloaddition (SPAAC). Irradiated SAMs were derivatized with a series of model azides with varied hydrophobicity to demonstrate the generality of this chemical system for the modification and fine-tuning of the surface chemistry on gold substrates. SAMs were characterized at each step with polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) to confirm successful functionalization and reactivity. Furthermore, to showcase the compatibility of this approach with biochemical applications, cyclopropenone SAMs were irradiated and modified with azide-bearing cell adhesion peptides to promote human fibroblast cell adhesion, then imaged by live cell fluorescence microscopy. Thus, the “photoclick” methodology reported here represents an improved, versatile, catalyst-free protocol that allows for a high degree of control over the modification of material surfaces, with applicability in materials science as well as biochemistry.<br>

Stochastic Computing via In Operando Modulation of Rectification in Molecular Tunneling Junctions

2020 ◽  
Author(s):  
Xinkai Qiu ◽  
Sylvia Rousseva ◽  
Gang Ye ◽  
Jan C. Hummelen ◽  
Ryan Chiechi
Keyword(s):  
Self Assembly ◽  
Variable Temperature ◽  
Self Assembled Monolayers ◽  
Microfluidic Channels ◽  
Proof Of Concept ◽  
Glycol Ethers ◽  
Stochastic Computing ◽  
Assembled Monolayers ◽  
In Operando ◽  
Tunneling Junctions

This paper describes the reconfiguration of molecular tunneling junctions during operation via the self-assembly of bilayers of glycol ethers. We use well-established functional groups to modulate the magnitude and direction of rectification in assembled tunneling junctions by exposing them to solutions containing different glycol ethers. Variable-temperature measurements establish that rectification occurs by a bias-dependent tunneling-hopping mechanism and that glycol ethers, beside being an unusually efficient tunneling medium, behave identically to alkanes. We fabricated memory bits from crossbar junctions prepared by injecting eutectic Ga-In into microfluidic channels. Two 8-bit registers were able to perform logical AND operations on bit strings encoded into chemical packets as microfluidic droplets that alter the composition of the crossbar junctions through self-assembly to effect memristor-like properties. This proof of concept work demonstrates the potential for fieldable molecular-electronic devices based on tunneling junctions of self-assembled monolayers and bilayers.

Surface modification of ZnO on the Zn-polar 0001 face by self-assembled triptycene-based polar molecules along with an increase of electric conductance

2022 ◽  
Author(s):  
Hiroki Shioya ◽  
Naoko Inoue ◽  
Masaro Yoshida ◽  
Yoshihiro IWASA
Keyword(s):  
Surface Modification ◽  
Critical Role ◽  
Polar Molecules ◽  
Hydroxyl Groups ◽  
Oxide Semiconductors ◽  
Assembled Monolayers ◽  
Temperature Dependences ◽  
Order Of Magnitude ◽  
Sheet Conductance ◽  
Self Assembled

Abstract Application of self-assembled monolayers (SAMs) is a representative method of surface modification for tuning material properties. In this study we examine the influence of the surface modification by coating the Zn-polar 0001 surface of ZnO single crystal with a SAM of triptycene-based polar molecules in our own technique and investigated temperature dependences of the sheet conductance of the surface with and without the SAM. The sheet conductance at 70 K with the SAM is increased by an order of magnitude, compared to the case without the SAM. We infer that the additional electrons are introduced at the surface by the polar triptycene molecules, whose electropositive hydroxyl groups are supposed to face toward the Zn-polar surface of ZnO. The present result implies that the molecular orientation of the triptycene SAM plays a critical role on the surface properties of oxide semiconductors.

Driving Forces for Layer-by-Layer Self-Assembly of Films of SiO2Nanoparticles and Heme Proteins

Langmuir ◽  
2004 ◽  
Vol 20 (3) ◽  
pp. 722-729 ◽  
Author(s):  
Pingli He ◽  
Naifei Hu ◽  
James F. Rusling
Keyword(s):  
Self Assembly ◽  
Heme Proteins ◽  
Driving Forces ◽  
Layer By Layer

scholarly journals Rules for the self-assembly of ESCRT-III on endosomes

2021 ◽  
Author(s):  
Simon Sprenger ◽  
Simona M. Migliano ◽  
Florian Oleschko ◽  
Marvin Kobald ◽  
Michael Hess ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrophobic Interactions ◽  
The Self ◽  
Amino Acid Residues ◽  
Lateral Expansion ◽  
Endosomal Sorting ◽  
Aaa Atpase ◽  
Charged Amino Acids ◽  
Membrane Budding ◽  
Positively Charged

ABSTRACTThe endosomal sorting complexes required for transport (ESCRT) mediate various membrane remodeling processes in cells by mechanism that are incompletely understood. Here we combined genetic experiments in budding yeast with site-specific cross-linking to identify rules that govern the self-assembly of individual ESCRT-III proteins into functional ESCRT-III complexes on endosomes. Together with current structural models of ESCRT-III, our findings suggest that, once nucleated, the growing Snf7 protofilament seeds the lateral co-assembly of a Vps24 - Vps2 heterofilament. Both Vps24 and Vps2 use positively charged amino acid residues in their helices α1 to interact with negatively charged amino acids in helix α4 of Snf7 subunits of the protofilament. In the Vps24 - Vps2 heterofilament, the two subunits alternate and interact with each other using hydrophobic interactions between helices α2/α3. The co-assembly of the Vps24 - Vps2 heterofilament restricts the lateral expansion of Snf7 protofilaments and leads the immediate recruitment of the AAA-ATPase Vps4. This self-assembly process of three ESCRT-III subunits results in the formation of a Snf7 protofilament and the co-assembly of a Vps24 - Vps2 heterofilament. This sets the stage for Vps4 recruitment and the subsequent ATP-driven dynamic self-organization of ESCRT-III / Vps4 assemblies and the ensuing membrane budding and scission events.

Self-assembly of gold nanoparticles in a block copolymer aggregate template driven by hydrophobic interactions

2019 ◽  
Vol 10 (46) ◽  
pp. 6269-6277
Author(s):  
Jong Dae Jang ◽  
Sang-Woo Jeon ◽  
Young-Jin Yoon ◽  
Joona Bang ◽  
Young Soo Han ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Block Copolymer ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Self Assembled

We report various self-assembled structures of gold nanoparticles in a block copolymer aggregate template, which are easily driven by hydrophobic interactions.

scholarly journals The potential of magnetisation transfer NMR to monitor the dissolution process of cellulose in cold alkali

Cellulose ◽  
2019 ◽  
Vol 26 (18) ◽  
pp. 9403-9412 ◽  
Author(s):  
Maria Gunnarsson ◽  
Merima Hasani ◽  
Diana Bernin
Keyword(s):  
Hydrophobic Interactions ◽  
Dissolution Process ◽  
Mechanistic Study ◽  
Dissolution Mechanism ◽  
Hydroxyl Groups ◽  
Similar Amount ◽  
Magnetisation Transfer ◽  
Promising Alternative ◽  
Nmr Methods ◽  
Increasing Temperature

Abstract Cellulose is the most important biopolymer on earth and, when derived from e.g. wood, a promising alternative to for example cotton, which exhibits a large environmental burden. The replacement depends, however, on an efficient dissolution process of cellulose. Cold aqueous alkali systems are attractive but these solvents have peculiarities, which might be overcome by understanding the acting mechanisms. Proposed dissolution mechanisms are for example the breakage of hydrophobic interactions and partly deprotonation of the cellulose hydroxyl groups. Here, we performed a mechanistic study using equimolar aqueous solutions of LiOH, NaOH and KOH to elucidate the dissolution process of microcrystalline cellulose (MCC). The pH was the highest for KOH(aq) followed by NaOH(aq) and LiOH(aq). We used a combination of conventional and advanced solution-state NMR methods to monitor the dissolution process of MCC by solely increasing the temperature from − 10 to 5 °C. KOH(aq) dissolved roughly 25% of the maximum amount of MCC while NaOH(aq) and LiOH(aq) dissolved up to 70%. Water motions on nanoscale timescales present in non-frozen water, remained unaffected on the addition of MCC. Magnetisation transfer (MT) NMR experiments monitored the semi-rigid MCC as a function of temperature. Interestingly, although NaOH(aq) and LiOH(aq) were able to dissolve a similar amount at 5 °C, MT spectra revealed differences with increasing temperature, suggesting a difference in the swollen state of MCC in LiOH(aq) already at − 10 °C. Furthermore, MT NMR shows a great potential to study the water exchange dynamics with the swollen and semi-rigid MCC fraction in these systems, which might give valuable insights into the dissolution mechanism in cold alkali.

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