Protein's native structure is dynamically stabilized by electronic polarization

2014 ◽  
Vol 13 (03) ◽  
pp. 1440005 ◽  
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.

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

Minerals ◽  
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.

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

2021 ◽  
Author(s):  
Emanuele Petretto ◽  
Quy K. Ong ◽  
Francesca Olgiati ◽  
Mao Ting ◽  
Pablo Campomanes ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Hydrophobic Interactions ◽  
Interparticle Distance ◽  
Md Simulations ◽  
Dlvo Theory ◽  
Potential Of Mean Force ◽  
Colloidal Systems ◽  
Wide Range ◽  
The Stability ◽  
Charged Ions

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.

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

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

<p>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/N<sup>2+</sup>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/Ca<sup>2+</sup>/Water mixture.</p>

scholarly journals Adhesion, forces and the stability of interfaces

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.

scholarly journals A theoretical approach on the ability of functionalized gold nanoparticles for detection of Cd2+

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammad Khavani ◽  
Aliyeh Mehranfar ◽  
Mohammad Izadyar
Keyword(s):  
Gold Nanoparticles ◽  
Metal Ions ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Md Simulations ◽  
Orbital Interactions ◽  
Donor Acceptor ◽  
The Stability ◽  
Functionalized Aunps

AbstractCadmium (Cd) as a toxic element that is widely present in water, soil, and air has important effects on human health, therefore proposing an accurate and selective method for detection of this element is of importance. In this article, by employing full atomistic molecular dynamics (MD) simulations and density functional theory dispersion corrected (DFT-D3) calculations, the effects of 6-mercaptonicotinic acid (MNA) and l-cysteine (CYS) on the stability of gold nanoparticles (AuNPs) and their sensitivity against Cd2+ were investigated. The obtained results indicate that pure AuNPs are not stable in water, while functionalized AuNPs with CYS and MNA groups have considerable stability without aggregation. In other words, the functional groups on the surface of AuNPs elevate their resistance against aggregation by an increase in the repulsive interactions between the gold nanoparticles. Moreover, functionalized AuNPs have considerable ability for selective detection of Cd2+ in the presence of different metal ions. Based on the MD simulation results, MNA-CYS-AuNPs (functionalized AuNPs with both functional groups) have the maximum sensitivity against Cd2+ in comparison with MNA-AuNPs and CYS-AuNPs due to the strong electrostatic interactions. DFT-D3 calculations reveal that the most probable interactions between the metal ions and functional groups are electrostatic, and Cd2+ can aggregate functionalized AuNPs due to strong electrostatic interactions with MNA and CYS groups. Moreover, charge transfer and donor–acceptor analyses show that molecular orbital interactions between the functional groups and Cd2+ can be considered as the driving force for AuNPs aggregation. A good agreement between the theoretical results and experimental data confirms the importance of the molecular modeling methods as a fast scientific protocol for designing new functionalized nanoparticles for application in different fields.

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

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

<p>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/N<sup>2+</sup>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/Ca<sup>2+</sup>/Water mixture.</p>

Sustainability and adaptability of regional development in the conditions of digitalization

2020 ◽  
Vol 19 (9) ◽  
pp. 1550-1613
Author(s):  
O.E. Akimova ◽  
S.K. Volkov ◽  
E.A. Gladkaya ◽  
I.M. Kuzlaeva
Keyword(s):  
Sustainable Development ◽  
Regional Development ◽  
Economic Behavior ◽  
Regional Inequality ◽  
Environmental Damage ◽  
Economic Potential ◽  
Human Welfare ◽  
Long Time ◽  
The Stability ◽  
Smart Technologies

Subject. The article discusses the sustainability of regional economy development, its definition, and the substance of sustainable development. Objectives. We aim at performing a comprehensive analysis of indicators of sustainability and adaptability of regional development in the context of digitalization, formulating a strategy for economic behavior that takes into account the multidimensional nature of regional inequality and is focused on boosting the economic potential of regions. Methods. The study draws on dialectic and systems approaches, general scientific methods of retrospective, situational, economic and statistical, and comparative analysis. Results. The sustainability of the region focuses on improving the human welfare over long time horizon. This happens in three areas, i.e. maximizing the efficiency of resource use; ensuring justice and democracy; minimizing resource consumption and environmental damage. The stability of the region can be assessed by using one parameter, or by combining the parameters in accordance with the type of region and expected results. Conclusions. The adaptation of a region to changing conditions depends on its type (‘adapted’, ‘adaptive’, and ‘non-adapted’). Regional inequality has two main components: difference in economic potential and social satisfaction of residents. Another component, affecting the stability and adaptability of regions, is the level of their digitalization. However, some regions have only formally embarked on the path of digitalization. Moreover, a focus on smart technologies, solutions and digitalization often leads to ignoring the goals of sustainable development. Smart technologies should be aimed at ensuring sustainability within the framework of the smart sustainable city concept.

Polysaccharide Structures in the Outer Mucilage of Arabidopsis Seeds Visualized by AFM

2020 ◽  
Author(s):  
MAK Williams ◽  
V Cornuault ◽  
AH Irani ◽  
VV Symonds ◽  
J Malmström ◽  
...  
Keyword(s):  
Average Length ◽  
American Chemical Society ◽  
Md Simulations ◽  
Chemical Society ◽  
Side Chains ◽  
Rhamnogalacturonan I ◽  
Afm Imaging ◽  
Minor Population ◽  
The Stability ◽  
A Minor

© 2020 American Chemical Society. Evidence is presented that the polysaccharide rhamnogalacturonan I (RGI) can be biosynthesized in remarkably organized branched configurations and surprisingly long versions and can self-assemble into a plethora of structures. AFM imaging has been applied to study the outer mucilage obtained from wild-type (WT) and mutant (bxl1-3 and cesa5-1) Arabidopsis thaliana seeds. For WT mucilage, ordered, multichain structures of the polysaccharide RGI were observed, with a helical twist visible in favorable circumstances. Molecular dynamics (MD) simulations demonstrated the stability of several possible multichain complexes and the possibility of twisted fibril formation. For bxl1-3 seeds, the imaged polymers clearly showed the presence of side chains. These were surprisingly regular and well organized with an average length of ∼100 nm and a spacing of ∼50 nm. The heights of the side chains imaged were suggestive of single polysaccharide chains, while the backbone was on average 4 times this height and showed regular height variations along its length consistent with models of multichain fibrils examined in MD. Finally, in mucilage extracts from cesa5-1 seeds, a minor population of chains in excess of 30 μm long was observed.

In Silico and in Vitro Evaluation of Deamidation Effects on the Stability of the Fusion Toxin DAB389IL-2

2019 ◽  
Vol 16 (4) ◽  
pp. 307-313 ◽  
Author(s):  
Nasrin Zarkar ◽  
Mohammad Ali Nasiri Khalili ◽  
Fathollah Ahmadpour ◽  
Sirus Khodadadi ◽  
Mehdi Zeinoddini
Keyword(s):  
In Silico ◽  
Catalytic Domain ◽  
Md Simulations ◽  
Special Importance ◽  
Native Form ◽  
Vitro Experiment ◽  
In Vitro Experiment ◽  
Pharmaceutical Protein ◽  
The Stability

Background: DAB389IL-2 (Denileukin diftitox) as an immunotoxin is a targeted pharmaceutical protein and is the first immunotoxin approved by FDA. It is used for the treatment of various kinds of cancer such as CTCL lymphoma, melanoma, and Leukemia but among all of these, treatment of CTCL has special importance. DAB389IL-2 consists of two distinct parts; the catalytic domain of Diphtheria Toxin (DT) that genetically fused to the whole IL-2. Deamidation is the most important reaction for chemical instability of proteins occurs during manufacture and storage. Deamidation of asparagine residues occurs at a higher rate than glutamine residues. The structure of proteins, temperature and pH are the most important factors that influence the rate of deamidation. Methods: Since there is not any information about deamidation of DAB389IL-2, we studied in silico deamidation by Molecular Dynamic (MD) simulations using GROMACS software. The 3D model of fusion protein DAB389IL-2 was used as a template for deamidation. Then, the stability of deamidated and native form of the drug was calculated. Results: The results of MD simulations were showed that the deamidated form of DAB389IL-2 is more unstable than the normal form. Also, deamidation was carried by incubating DAB389IL-2, 0.3 mg/ml in ammonium hydrogen carbonate for 24 h at 37o C in order to in vitro experiment. Conclusion: The results of in vitro experiment were confirmed outcomes of in silico study. In silico and in vitro experiments were demonstrated that DAB389IL-2 is unstable in deamidated form.

scholarly journals Climate Change and Internet of Things Technologies—Sustainable Premises of Extending the Culture of the Amurg Cultivar in Transylvania—A Use Case for Târnave Vineyard

2021 ◽  
Vol 13 (15) ◽  
pp. 8170
Author(s):  
Veronica Sanda Chedea ◽  
Ana-Maria Drăgulinescu  ◽  
Liliana Lucia Tomoiagă  ◽  
Cristina Bălăceanu ◽  
Maria Lucia Iliescu 
Keyword(s):  
Climate Change ◽  
Weather Conditions ◽  
White Wine ◽  
Time Investment ◽  
Protected Designation Of Origin ◽  
Average Annual Temperature ◽  
Insect Infestations ◽  
Long Time ◽  
The Stability ◽  
Red Grape

Known for its dry and semi-dry white wine, the Târnave vineyard located in central Transylvania is challenged by the current climate change, which has resulted in an increase of the period of active vegetation by approximately 15–20 days, the average annual temperature by 1–1.5 °C and also the amount of useful temperatures (useful thermal balance for the grapevine). Furthermore, the frost periods have been reduced. Transylvania is an important Romanian region for grapevine cultivation. In this context, one can use the climatic changes to expand their wine assortment by cultivating an autochthonous grapevine variety called Amurg. Amurg is a red grape cultivar homologated at SCDVV Blaj, which also homologated 7 cultivars and 11 clones. Because viticulture depends on the stability of meteorological and hydrological parameters of the growing area, its foundations are challenged by climate change. Grapevine production is a long time investment, taking at least five years before the freshly planted vines produce the desired quality berries. We propose the implementation of a climate change-based precision viticulture turn-key solution for environmental monitoring in the Târnave vineyard. This solution aims to evaluate the grapevine’s micro-climate to extend the sustainable cultivation of the Amurg red grapes cultivar in Transylvania with the final goal of obtaining Protected Designation of Origin (PDO) rosé and red wines from this region. Worldwide, the changing conditions from the existing climate (a 30-year average), used in the past hundred years to dictate local standards, such as new and erratic trends of temperature and humidity regimes, late spring freezes, early fall frosts, storms, heatwaves, droughts, area wildfires, and insect infestations, would create dynamic problems for all farmers to thrive. These conditions will make it challenging to predict shifts in each of the components of seasonal weather conditions. Our proposed system also aims to give a solution that can be adapted to other vineyards as well.

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