Ion-mediated charge-charge interactions drive aggregation of surface-functionalized gold nanoparticles

Monolayer-protected metal nanoparticles (NPs) are not only promising materials with a wide range of potential industrial and biological applications, but they are also a powerful tool to investigate the behavior of matter at nanoscopic scales, including the stability of dispersions and colloidal systems. This stability is dependent on a delicate balance between electrostatic and steric interactions that occur in the solution, and it is described in quantitative terms by the classic Derjaguin-Landau-Vewey-Overbeek (DLVO) theory, that posits that aggregation between NPs is driven by hydrophobic interactions and opposed by electrostatic interactions. To investigate the limits of this theory at the nanoscale, where the continuum assumptions required by the DLVO theory break down, here we investigate NP dimerization by computing the Potential of Mean Force (PMF) of this process using fully atomistic MD simulations. Serendipitously, we find that electrostatic interactions can lead to the formation of metastable NP dimers. These dimers are stabilized by complexes formed by negatively charged ligands belonging to distinct NPs that are bridged by positively charged ions present in solution. We validate our findings by collecting tomographic EM images of NPs in solution and by quantifying their radial distribution function, that shows a marked peak at interparticle distance comparable with that of MD simulations. Taken together, our results suggest that not only hydrophobic interactions, but also electrostatic interactions, contribute to attraction between nano-sized charged objects at very short length scales.

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Adhesion, forces and the stability of interfaces

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.15.12 ◽

2019 ◽

Vol 15 ◽

pp. 106-129

Author(s):

Robin Guttmann ◽

Johannes Hoja ◽

Christoph Lechner ◽

Reinhard J Maurer ◽

Alexander F Sax

Keyword(s):

Electrostatic Interactions ◽

Hydrophobic Interactions ◽

System Stability ◽

Adhesion Forces ◽

Dispersion Interactions ◽

Time Dispersion ◽

Wide Range ◽

Long Time ◽

The Stability ◽

Adhesive Forces

Weak molecular interactions (WMI) are responsible for processes such as physisorption; they are essential for the structure and stability of interfaces, and for bulk properties of liquids and molecular crystals. The dispersion interaction is one of the four basic interactions types – electrostatics, induction, dispersion and exchange repulsion – of which all WMIs are composed. The fact that each class of basic interactions covers a wide range explains the large variety of WMIs. To some of them, special names are assigned, such as hydrogen bonding or hydrophobic interactions. In chemistry, these WMIs are frequently used as if they were basic interaction types. For a long time, dispersion was largely ignored in chemistry, attractive intermolecular interactions were nearly exclusively attributed to electrostatic interactions. We discuss the importance of dispersion interactions for the stabilization in systems that are traditionally explained in terms of the “special interactions” mentioned above. System stabilization can be explained by using interaction energies, or by attractive forces between the interacting subsystems; in the case of stabilizing WMIs, one frequently speaks of adhesion energies and adhesive forces. We show that the description of system stability using maximum adhesive forces and the description using adhesion energies are not equivalent. The systems discussed are polyaromatic molecules adsorbed to graphene and carbon nanotubes; dimers of alcohols and amines; cellulose crystals; and alcohols adsorbed onto cellulose surfaces.

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Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review

Nanomaterials ◽

10.3390/nano9020285 ◽

2019 ◽

Vol 9 (2) ◽

pp. 285 ◽

Cited By ~ 30

Author(s):

Li Wang ◽

Coucong Gong ◽

Xinzhu Yuan ◽

Gang Wei

Keyword(s):

Self Assembly ◽

Electrostatic Interactions ◽

Materials Science ◽

Hydrophobic Interactions ◽

The Self ◽

Functional Nanomaterials ◽

Light Stimulation ◽

Dna Base ◽

Wide Range ◽

Structure And Functions

Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π–π stacking, DNA base pairing, and ligand–receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

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Intermolecular Interaction of Hthyni Protein with Double Methylated DNA at 5m-Cytosine Nucleotide

Journal of Institute of Science and Technology ◽

10.3126/jist.v25i1.29444 ◽

2020 ◽

Vol 25 (1) ◽

pp. 37-44

Author(s):

Rajendra Prasad Koirala ◽

Shyam Prakash Khanal ◽

Sudip Shiwakoti ◽

Narayan Prasad Adhikari

Keyword(s):

Nuclear Protein ◽

Hydrophobic Interactions ◽

Md Simulations ◽

Van Der Waals Interactions ◽

Salt Bridges ◽

Protein Residues ◽

Methylated Dna ◽

The Stability ◽

Dna Complex ◽

Binding Mechanisms

Human thymocyte nuclear protein 1 (hTHYN1) is one of the DNA binding proteins. It is essential for the regulation of Pax5 expression and the development of B cells in humans. Its thermodynamic and biological functions have been unclear yet. The study of the binding mechanism of hTHYN1 protein with DNA is essential to understand various biochemical functions in the human body. In this work, molecular dynamics (MD) simulations have been performed to understand the binding mechanisms of double methylated DNA (dmDNA) at cytosine nucleotide with hTHYN1 protein. Hydrogen bonding and other non-bonded (electrostatics and van der Waals) interactions among the residue-nucleotide pairs have been observed during the MD simulations and are also found responsible to form protein-DNA complex and to provide the stability of the structure. No salt bridges and hydrophobic interactions have been detected. Some of the protein residues in hTHYN1 have been found to strongly cooperate in the formation of the DNA-protein complex. Arginine residue of hTHYN1 has been observed as a major contributor in binding to the DNA. Many other residues also have significant roles in binding with DNA.

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ADS-J1 Disaggregates Semen-derived Amyloid Fibrils

10.1101/292342 ◽

2018 ◽

Author(s):

J. Li ◽

Z. Yang ◽

H. Liu ◽

Y. Lan ◽

T. Zhang ◽

...

Keyword(s):

Viral Infection ◽

Conformational Changes ◽

Electrostatic Interactions ◽

Amyloid Fibrils ◽

Hydrophobic Interactions ◽

Sexual Transmission ◽

Md Simulations ◽

Potential Mode ◽

Biochemical Measurements ◽

Hiv 1

ABSTRACTSemen-derived amyloid fibrils, composing SEVI (semen-derived enhancer of viral infection) fibrils and SEM1 fibrils, could remarkably enhance HIV-1 sexual transmission and thus, are potential targets for the development of an effective microbicide. Previously, we found that ADS-J1, apart from being an HIV-1 entry inhibitor, could also potently inhibit seminal amyloid fibrillization and block fibril-mediated enhancement of viral infection. However, the remodeling effects of ADS-J1 on mature seminal fibrils were unexplored. Herein, we investigated the capacity of ADS-J1 to disassemble seminal fibrils and the potential mode of action by applying several biophysical and biochemical measurements, combined with molecular dynamic (MD) simulations. We found that ADS-J1 effectively remodeled SEVI, SEM186-107 fibrils and endogenous seminal fibrils. Unlike epi-gallocatechin gallate (EGCG), a universal amyloid fibril breaker, ADS-J1 disaggregated SEVI fibrils into monomeric peptides, which was independent of oxidation reaction. MD simulations revealed that ADS-J1 displayed strong binding potency to the full-length PAP248-286 via electrostatic interactions, hydrophobic interactions and hydrogen bonds. ADS-J1 might initially bind to the fibrillar surface and then occupy the amyloid core, which eventually lead to fibril disassembly. Furthermore, the binding of ADS-J1 with PAP248-286 might induce conformational changes of PAP248-286. Disassembled PAP248-286 might not be favor to re-aggregate into fibrils. ADS-J1 also exerts abilities to remodel a panel of amyloid fibrils, including Aβ1-42, hIAPP1-37 and EP2 fibrils. ADS-J1 displays promising potential to be a combination microbicide and an effective lead-product to treat amyloidogenic diseases.

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Protein's native structure is dynamically stabilized by electronic polarization

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633614400057 ◽

2014 ◽

Vol 13 (03) ◽

pp. 1440005 ◽

Cited By ~ 9

Author(s):

Li L. Duan ◽

Ye Mei ◽

Qing G. Zhang ◽

Bo Tang ◽

John Z. H. Zhang

Keyword(s):

Electrostatic Interactions ◽

Model Building ◽

Md Simulations ◽

Native Structure ◽

Electronic Polarization ◽

Amber Force Field ◽

Time Simulation ◽

Long Time ◽

Dynamic Structures ◽

The Stability

In this paper, molecular dynamics (MD) simulations were performed for a number of benchmark proteins using both the standard assisted model building with energy refinement (AMBER) charge and the dynamically adjusted polarized protein-specific charge (DPPC) from quantum fragment calculations to provide accurate electrostatic interactions. Our result shows that proteins' dynamic structures drifted away from the native structures in simulations under standard (nonpolarizable) AMBER force field. For comparison, proteins' native structures were dynamically stable after a long time simulation under DPPC. The free energy landscape reveals that the native structure is the lowest energy conformation under DPPC, while it is not under standard AMBER charge. To further investigate the polarization effect on the stability of native structures of proteins, we restarted from some decoy structures generated from simulations using standard AMBER charges and then carried out further MD simulation using DPPC to refine those structures. Our study shows that the native structures from these decoy structures can be mostly recovered using DPPC and that the dynamic structures with the highest population in cluster analysis are in close agreement with the corresponding native structures. The current study demonstrates the importance of electronic polarization of protein in stabilizing the native structure.

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On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure

Minerals ◽

10.3390/min11101138 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1138

Author(s):

Edgar Galicia-Andrés ◽

Chris Oostenbrink ◽

Martin H. Gerzabek ◽

Daniel Tunega

Keyword(s):

Humic Substances ◽

Electrostatic Interactions ◽

Md Simulations ◽

Dominant Factor ◽

Microscopic Structure ◽

Hierarchical Arrangement ◽

Macro Scale ◽

The Stability ◽

Clay Aggregates ◽

Mineral Aggregates

Soil organic matter (SOM) and various inorganic minerals represent key components of soils. During pedogenesis and due to biological activity these species interact, having a crucial impact on the formation of an aggregated soil structure with a hierarchical arrangement from nano to macro scale. In this process, the formation of organo–mineral microaggregates represents a dominant factor affecting soil functions and properties. This study focuses on the interactions between humic substances (HSs) and the mineral kaolinite as typical representatives of SOM and soil minerals. By performing classical molecular dynamics (MD) simulations on models of HSs and kaolinite, we demonstrate how two dominant but chemically different kaolinite surfaces affect the stability of HSs microaggregates. By analyzing volumetric, structural, and energetic properties of SOM–kaolinite models, we explain possible mechanisms of the formation of stable SOM–clay aggregates and show how a polarized environment affects the electrostatic interactions, stabilizing the microscopic structure of SOM–mineral aggregates. Our results showed that when stable aggregates of HSs are confined in kaolinite nanopores, their interactions with kaolinite surfaces disintegrate them into smaller subaggregates. These subaggregates are adsorbed more strongly on the polar aluminol surface of kaolinite compared to less the active hydrophobic siloxane surface.

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Some Remarks on Colloid Stability: Selected Examples Taken from the Milk Chain for Food Prepares

Colloids and Interfaces ◽

10.3390/colloids4040058 ◽

2020 ◽

Vol 4 (4) ◽

pp. 58

Author(s):

Camillo La Mesa ◽

Gianfranco Risuleo

Keyword(s):

Phase Separation ◽

Double Layer ◽

Van Der Waals ◽

Interparticle Distance ◽

Worked Examples ◽

Dlvo Theory ◽

Colloid Stability ◽

Stabilization Phase ◽

The Stability ◽

Repulsive Forces

Different forces play key roles in the stability of food colloid dispersions. The focus here is on those controlling attraction and/or repulsion, which concur to stabilization, phase separation, coagulation and are quite evident in water-based systems. The combination of attractive and repulsive forces favors or hinders the association of colloid entities; such processes are often met in food technology. The above processes depend on the forces at work and colloid concentration in the medium (i.e., on interparticle distance). Worked examples deal with milk manipulation procedures, ending in cheese formation. The whole milk sequence is controlled by the combination of forces leading to aggregation and phase separation of casein and other milk components. Thereafter, one gets either fresh, for prompt consumption, or aged cheeses. The combination of attractive (van der Waals, vdW, and depletion) with repulsive (double layer, DL, but also steric) forces results in the dominance of aggregation versus dispersion modes in the milk transformation chain, which depends on the distance among colloid particles, on the amplitude of the mentioned forces, and on their decay. The combined role of double layer and van der Waals (vdW) forces is at the basis of the DLVO theory on colloid stability, which is properly modified when these forces overlap with steric stabilization and, eventually, with depletion. Steric effects are dispersive, and depletion ones favor colloid nucleation in a single phase. The milk manipulation chain is a worked example of the intriguing association features controlled by the mentioned forces (and of ancillary ones, as well), and indicates which forces favor the formation of products such as parmesan or mozzarella cheese but are not alien to the preparation of many other dairy products.

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Contribution of the KCa3.1 channel–calmodulin interactions to the regulation of the KCa3.1 gating process

The Journal of General Physiology ◽

10.1085/jgp.201210933 ◽

2013 ◽

Vol 142 (1) ◽

pp. 37-60 ◽

Cited By ~ 11

Author(s):

Patricia Morales ◽

Line Garneau ◽

Hélène Klein ◽

Marie-France Lavoie ◽

Lucie Parent ◽

...

Keyword(s):

Crystal Structure ◽

Electrostatic Interactions ◽

Hydrophobic Interactions ◽

Homology Model ◽

Terminal Region ◽

Activation Process ◽

Open Probability ◽

Channel Activation ◽

C Terminus ◽

The Stability

The Ca2+-activated potassium channel of intermediate conductance, KCa3.1, is now emerging as a therapeutic target for a large variety of health disorders. The Ca2+ sensitivity of KCa3.1 is conferred by the Ca2+-binding protein calmodulin (CaM), with the CaM C-lobe constitutively bound to an intracellular domain of the channel C terminus. It was proposed on the basis of the crystal structure obtained for the C-terminal region of the rat KCa2.2 channel (rSK2) with CaM that the binding of Ca2+ to the CaM N-lobe results in CaM interlocking the C-terminal regions of two adjacent KCa3.1 subunits, leading to the formation of a dimeric structure. A study was thus undertaken to identify residues of the CaM N-lobe–KCa3.1 complex that either contribute to the channel activation process or control the channel open probability at saturating Ca2+ (Pomax). A structural homology model of the KCa3.1–CaM complex was first generated using as template the crystal structure of the C-terminal region of the rat KCa2.2 channel with CaM. This model was confirmed by cross-bridging residues R362 of KCa3.1 and K75 of CaM. Patch-clamp experiments were next performed, demonstrating that the solvation energy of the residue at position 367 in KCa3.1 is a key determinant to the channel Pomax and deactivation time toff. Mutations of residues M368 and Q364 predicted to form anchoring points for CaM binding to KCa3.1 had little impact on either toff or Pomax. Finally, our results show that channel activation depends on electrostatic interactions involving the charged residues R362 and E363, added to a nonpolar energy contribution coming from M368. We conclude that electrostatic interactions involving residues R362 and E363 and hydrophobic effects at M368 play a prominent role in KCa3.1 activation, whereas hydrophobic interactions at S367 are determinant to the stability of the CaM–KCa3.1 complex throughout gating.

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MATERIALS SELECTION FOR PRODUCTION OF MICROSPHERES PROTECTING LACTOFERRIN UNDER ACID CONDITIONS

Science Evolution ◽

10.21603/2500-1418-2016-1-1-92-102 ◽

2016 ◽

pp. 92-102 ◽

Cited By ~ 2

Author(s):

Marina Novoselova ◽

Alexander Prosekov ◽

Alexander Prosekov

Keyword(s):

Tannic Acid ◽

Electrostatic Interactions ◽

Hydrophobic Interactions ◽

Inflammatory Diseases ◽

Adsorbed Layer ◽

Multifunctional Protein ◽

Acidic Conditions ◽

Selection For ◽

The Stability ◽

Subsequent Layer

Lactoferrin is a multifunctional protein of the transferrin family, which can be found in the human and other mammals milk. On the basis of many biological functions of lactoferrin, researchers have considered various possibilities of its application in health care, in the prevention and treatment of infectious and inflammatory diseases. However, lactoferrin is exposed to pepsin degradation in the gastrointestinal tract, decreasing its bioactivity after oral administration. In this regard, appropriate delivery system of lactoferrin, which ensures its delivery intact to the receptors in the small intestine requires. In this study, the different compositions of the capsules in combination with tannic acid, formed mainly by hydrogen and hydrophobic interactions were showed. Its stability toward acidic conditions (0.1 M HCl) was investigated. Complexes with polyelectrolytes (and its pairs): PSS/PAH, Parg as the first adsorbed layer on CaCO3 particles formed by electrostatic interactions were presented. As the results, the adsorption of these polyelectrolytes led to greater stability of the obtained capsules. Bovine serum albumin and tannic acid, in particular with the use of poly-L-arginine as the first layer, increasing the stability of the obtained microspheres were selected as the most promising materials for the microcapsules synthesis. The changes in the morphology of [BSA/TA] and Parg [BSA/TA] capsules depending on the various number of bilayers (from 3 to 6) were analyzes. The thickness of capsule was increased on 1-2 nm by applying each subsequent layer. It was noted BSA/TA capsules looked thinner than Parg [BSA/TA] capsules with the same number of bilayers.

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Aggregation of Lipid A Variants: a Hybrid Particle-Field Model

10.26434/chemrxiv.11101637.v1 ◽

2019 ◽

Author(s):

Antonio De Nicola ◽

Thereza A. Soares ◽

Sigbjørn Løland Bore ◽

G. J. Agur Sevink ◽

Michele Cascella ◽

...

Keyword(s):

Self Assembly ◽

Electrostatic Interactions ◽

Lipid A ◽

Md Simulations ◽

Coarse Grained ◽

Water Mixture ◽

Particle Field ◽

Hybrid Particle ◽

Acyl Chains ◽

The Stability

Lipid A is one of three components of bacterial lipopolysaccharides (constituting the outer membrane of Gram-negative bacteria) and is recognized to have an important biological role in inflammatory response of the immune system. Its biological activity is modulated by the number of acyl-chains and from the electrostatic interactions with the different counter-ions. In this paper we report a coarse-grained model of poly-acyl Lipid A based on the hybrid particle field molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayer with two different acyl-chains, hexa- and tetra-. We find a good agreement of the particle distribution along the cross-section of bilayer by comparing the density profiles calculated from hPF-MD simulations with respect to reference all-atom. Moreover, we validate the model simulating the self-assembly of lamellar phase from an initial random distribution of Lipid A/N2+molecules in water. Finally, we test the stability of a vesicle composed of hexa-acylated Lipid A in water. The proposed model is able to maintain stable bilayer aggregates and spherical vesicle, and to correctly reproduce the phase behavior of Lipid A/Ca2+/Water mixture.

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