Martini Coarse-Grained Model of Hyaluronic Acid for the Structural Change of Its Gel in the Presence of Monovalent and Divalent Salts

Hyaluronic acid (HA) has a wide range of biomedical applications including the formation of hydrogels, microspheres, sponges, and films. The modeling of HA to understand its behavior and interaction with other biomolecules at the atomic level is of considerable interest. The atomistic representation of long HA polymers for the study of the macroscopic structural formation and its interactions with other polyelectrolytes is computationally demanding. To overcome this limitation, we developed a coarse grained (CG) model for HA adapting the Martini scheme. A very good agreement was observed between the CG model and all-atom simulations for both local (bonded interactions) and global properties (end-to-end distance, a radius of gyration, RMSD). Our CG model successfully demonstrated the formation of HA gel and its structural changes at high salt concentrations. We found that the main role of CaCl2 is screening the electrostatic repulsion between chains. HA gel did not collapse even at high CaCl2 concentrations, and the osmotic pressure decreased, which agrees well with the experimental results. This is a distinct property of HA from other proteins or polynucleic acids which ensures the validity of our CG model. Our HA CG model is compatible with other CG biomolecular models developed under the Martini scheme, which allows for large-scale simulations of various HA-based complex systems.

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Modelling structural rearrangements in proteins using Euclidean distance matrices

F1000Research ◽

10.12688/f1000research.25235.1 ◽

2020 ◽

Vol 9 ◽

pp. 728

Author(s):

Aleix Lafita ◽

Alex Bateman

Keyword(s):

Euclidean Distance ◽

Large Scale ◽

Structural Changes ◽

Homology Modelling ◽

Distance Matrix ◽

Coarse Grained ◽

Matrix Transformations ◽

Structural Rearrangements ◽

Circular Permutations ◽

Modelling Approach

Proteins undergo large structural rearrangements such as circular permutations, dimerisation via domain swapping, and loss of core secondary structure elements in domain atrophy, among others. These structural changes can be naturally represented as distance matrix transformations, exploiting their conserved native residue contacts at the protein core. Here we present an homology modelling approach to formulate structural rearrangements as a Euclidean distance matrix (EDM) problem and use it to build their 3D structures. This modelling approach aims to be lightweight, flexible and fast, suitable for large-scale analyses. Models are typically coarse-grained and solely based on protein geometry. We demonstrate various applications of EDM-based modelling for protein structure analysis and release an open repository with the source code at: https://github.com/lafita/protein-edm-demo.

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Classification of protein–protein association rates based on biophysical informatics

BMC Bioinformatics ◽

10.1186/s12859-021-04323-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Kalyani Dhusia ◽

Yinghao Wu

Keyword(s):

Large Scale ◽

Cross Validation ◽

Protein Complexes ◽

Dynamic Properties ◽

Conformational Dynamics ◽

Classification Model ◽

Coarse Grained ◽

Modeling Framework ◽

Validation Data ◽

Wide Range

Abstract Background Proteins form various complexes to carry out their versatile functions in cells. The dynamic properties of protein complex formation are mainly characterized by the association rates which measures how fast these complexes can be formed. It was experimentally observed that the association rates span an extremely wide range with over ten orders of magnitudes. Identification of association rates within this spectrum for specific protein complexes is therefore essential for us to understand their functional roles. Results To tackle this problem, we integrate physics-based coarse-grained simulations into a neural-network-based classification model to estimate the range of association rates for protein complexes in a large-scale benchmark set. The cross-validation results show that, when an optimal threshold was selected, we can reach the best performance with specificity, precision, sensitivity and overall accuracy all higher than 70%. The quality of our cross-validation data has also been testified by further statistical analysis. Additionally, given an independent testing set, we can successfully predict the group of association rates for eight protein complexes out of ten. Finally, the analysis of failed cases suggests the future implementation of conformational dynamics into simulation can further improve model. Conclusions In summary, this study demonstrated that a new modeling framework that combines biophysical simulations with bioinformatics approaches is able to identify protein–protein interactions with low association rates from those with higher association rates. This method thereby can serve as a useful addition to a collection of existing experimental approaches that measure biomolecular recognition.

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Laboratory Study of Hydraulic Conductivity for Coarse Aggregate Bases

Transportation Research Record Journal of the Transportation Research Board ◽

10.1177/0361198196151900103 ◽

1996 ◽

Vol 1519 (1) ◽

pp. 19-27 ◽

Cited By ~ 2

Author(s):

Brian W. Randolph ◽

Jiangeng Cai ◽

Andrew G. Heydinger ◽

Jiwan D. Gupta

Keyword(s):

Hydraulic Conductivity ◽

Large Scale ◽

Base Material ◽

Testing Procedure ◽

Test Methods ◽

Standard Test ◽

Coarse Grained ◽

Test Results ◽

Wide Range ◽

Pavement Structures

Inadequate drainage of pavement structures has been identified as a primary cause of pavement distress. Hydraulic conductivity is the most important factor controlling drainage capability. Coarse grained materials have high values of hydraulic conductivity. ASTM and AASHTO standard test methods are limited for coarse materials used in pavement bases and subbases because of their high permeability and large particle sizes and the horizontal flow in the field conditions. A large scale horizontal permeameter and a testing procedure were developed and the range of hydraulic conductivities of six base and subbase specifications made up of three material types provided by the Ohio Department of Transportation were evaluated. A horizontal permeameter (305 × 305 × 457 mm) and a testing procedure were developed to reduce errors produced by sidewall leakage, partial saturation, measurement of small head differences, and interpretation of turbulent flow as laminar flow. Fifty-four samples were tested, including various gradations of nonstabilized, portland cement stabilized, and asphalt stabilized bases made of limestone, gravel, or slag materials. The results obtained were analyzed and compared with previous research, empirical relations, and field test results of similar base and subbase materials. The comparisons and analyses indicate that the permeameter and the procedure produce representative results. Test results indicate a wide range of hydraulic conductivities for gradations at each extreme of a specification. Effective porosities were also found to be as low as 6 percent for the fine gradation of a common limestone base material.

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Large-scale field phenotyping using backpack LiDAR and GUI-based CropQuant-3D to measure structural responses to different nitrogen treatments in wheat

10.1101/2021.05.19.444842 ◽

2021 ◽

Author(s):

Yulei Zhu ◽

Gang Sun ◽

Guohui Ding ◽

Jie Zhou ◽

Mingxing Wen ◽

...

Keyword(s):

Large Scale ◽

Structural Changes ◽

Field Experiments ◽

Computing Time ◽

Point Clouds ◽

Combined System ◽

Wheat Varieties ◽

Wide Range ◽

Field Phenotyping ◽

Nitrogen Treatments

Plant phenomics is widely recognised as a key area to bridge the gap between traits of agricultural importance and genomic information. A wide range of field-based phenotyping solutions have been developed. Nevertheless, disadvantages of these current systems have been identified concerning mobility, affordability, accuracy, scalability, and the ability to analyse big data collected. Here, we present a novel solution that combines a commercial backpack LiDAR device and graphical user interface (GUI) based software called CropQuant-3D, which has been applied to analyse 3D morphological traits in wheat. To our knowledge, this is the first use of backpack LiDAR in field-based plant research, acquiring millions of 3D points to represent spatial features of crops. A key part of the innovation is the GUI-based software that can extract plot-based traits from large and complex point clouds with limited computing time. We describe how we developed and used the combined system to quantify canopy structural changes, impossible to measure previously. Also, we demonstrate the biological relevance of our work through a case study that examined wheat varieties to three different levels of nitrogen fertilisation in field experiments. The results indicate that the solution can differentiate significant genotype and treatment effects on key traits, with strong correlations with manual measurements. Hence, we believe that the solution presented here could consistently and speedily quantify traits at a larger scale, indicating the system could be used as a reliable research tool in large-scale and multi-location field phenotyping to contribute to the resolution of the phenotyping bottleneck.

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ECHINOCOCCOSIS OF LUNGS COMPLICATED BY PECILOMYCOSIS

10.31435/rsglobal/023 ◽

2020 ◽

Author(s):

Adolat Vakhidova ◽

◽

Gavkhar Khudoyarova ◽

Komil Boltaev ◽

◽

...

Keyword(s):

Medical Care ◽

Large Scale ◽

Biological Significance ◽

Healthcare Sector ◽

Main Role ◽

Central Asian ◽

Number Of Patients ◽

Wide Range ◽

The Republic

To date, large-scale targeted measures have been taken in the domestic healthcare sector to radically improve the quality and significantly expand the range of medical care provided to the population. In this direction, especially in improving the quality of treatment of echinococcosis, positive results have been achieved. Along with this, to improve the system of medical care, scientific-based results are required to assess the effectiveness of new methods of prevention and treatment of hydatids liver diseases. Among the most relevant aspects of the problem of echinococcosis are the identification of factors that affect the development of the disease, the causes of complications and relapses. It, along with numerous States, is also quite often found on the territory of Central Asian countries, which includes Uzbekistan. It is safe to say that echinococcosis today is one of the most important world problems of medical, veterinary and biological significance. Echinococcosis is a serious human disease that affects various organs, especially the liver and lungs, and more than 1.5 thousand operations are performed for it per year; only in terms of referrals to surgical clinics, the incidence rate ranges from 4 to 9 per 100 thousand people; the number of patients with complicated forms reaches 25-45% the number of postoperative complications – 20-30 %; lethality – 2-5 %. In some regions of the Republic, the incidence of echinococcosis in people as a result of indirect hemagglutination is 8-9%, according to autopsy data-2-3 %. The main role in the complex of anti-helminth measures continues to play a specific deworming of animals and humans. The success of deworming depends on highly effective and low-toxic anthelmintic agents, many of which, despite a wide range, do not meet modern requirements.

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Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1910044117 ◽

2020 ◽

Vol 117 (13) ◽

pp. 7216-7224 ◽

Cited By ~ 5

Author(s):

Akshay Sridhar ◽

Stephen E. Farr ◽

Guillem Portella ◽

Tamar Schlick ◽

Modesto Orozco ◽

...

Keyword(s):

Large Scale ◽

Coarse Grained ◽

Multiscale Approach ◽

Protein Disorder ◽

Wide Range ◽

Chromatin Structural ◽

Degree Of Condensation ◽

Dynamics Simulations ◽

Nucleosome Binding

Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1—a ubiquitous nucleosome-binding protein—remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.

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Formation and Investigation of Physicochemical, Biological and Bacteriostatic Properties of Nanocomposite Foils Containing Silver Nanoparticles and Graphene Oxide in Hyaluronic Acid Matrix

Materials ◽

10.3390/ma14123377 ◽

2021 ◽

Vol 14 (12) ◽

pp. 3377

Author(s):

Karen Khachatryan ◽

Lusine Khachatryan ◽

Marcel Krzan ◽

Magdalena Krystyjan ◽

Lidia Krzemińska-Fiedorowicz ◽

...

Keyword(s):

Silver Nanoparticles ◽

Graphene Oxide ◽

Hyaluronic Acid ◽

Structural Changes ◽

Fourier Transforms ◽

Sodium Hyaluronate ◽

Size Exclusion ◽

Biomedical Sciences ◽

Vis Spectroscopy ◽

Wide Range

Natural polysaccharides, including hyaluronic acid, find a wide range of applications in biomedical sciences. There is a growing interest in nanocomposites containing hyaluronic acid and nanoparticles such as nanometals or graphene. In this study, we prepared foils of pure sodium hyaluronate and sodium hyaluronate containing nanosilver, graphene oxide, nanosilver/graphene oxide and characterized their properties. UV-vis spectroscopy and scanning electron microscopy (SEM) confirmed the formation of 10–20 nm silver nanoparticles. The structural changes were investigated using Fourier transforms infrared (FTIR) spectra and size exclusion chromatography. The obtained results suggest changes in molecular weights in the samples containing nanoparticles, which was highest in a sample containing nanosilver/graphene oxide. We also assessed the mechanical properties of the foils (thickness, tensile strength and elongation at break) and their wettability. The foils containing nanosilver and nanosilver/graphene oxide presented bacteriostatic activity against E. coli, Staphylococcus spp. and Bacillus spp., which was not observed in the control and sample containing graphene oxide. The composites containing graphene oxide and nanosilver/graphene oxide exhibited a cytotoxic effect on human melanoma WM266-4 cell lines (ATCC, Manassas, VA, USA).

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Electron microscopy study of reactively sputter-deposited Ti/N films on silicon

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100131449 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1362-1363

Author(s):

V. C. Kannan ◽

A. K. Singh ◽

R. B. Irwin ◽

S. Chittipeddi ◽

F. D. Nkansah ◽

...

Keyword(s):

Integrated Circuits ◽

Large Scale ◽

Hexagonal Phase ◽

Microscopy Study ◽

Electron Microscopy Study ◽

Process Conditions ◽

Tin Films ◽

Wide Range ◽

Fcc Phase ◽

Circuits Vlsi

Titanium nitride (TiN) films have historically been used as diffusion barrier between silicon and aluminum, as an adhesion layer for tungsten deposition and as an interconnect material etc. Recently, the role of TiN films as contact barriers in very large scale silicon integrated circuits (VLSI) has been extensively studied. TiN films have resistivities on the order of 20μ Ω-cm which is much lower than that of titanium (nearly 66μ Ω-cm). Deposited TiN films show resistivities which vary from 20 to 100μ Ω-cm depending upon the type of deposition and process conditions. TiNx is known to have a NaCl type crystal structure for a wide range of compositions. Change in color from metallic luster to gold reflects the stabilization of the TiNx (FCC) phase over the close packed Ti(N) hexagonal phase. It was found that TiN (1:1) ideal composition with the FCC (NaCl-type) structure gives the best electrical property.

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Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

Marine Ecology Progress Series ◽

10.3354/meps13419 ◽

2020 ◽

Vol 648 ◽

pp. 19-38

Author(s):

AI Azovsky ◽

YA Mazei ◽

MA Saburova ◽

PV Sapozhnikov

Keyword(s):

Species Abundance ◽

Abundance Ratio ◽

Wave Action ◽

Coarse Grained ◽

Sediment Properties ◽

Β Diversity ◽

Α Diversity ◽

Wide Range ◽

Similar Mode ◽

Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

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THE SOME QUESTIONS OF AUTONOMOUS MOTION AND MANAGEMENT OF LAND-MOBILE ROBOTIC COMPLEXES FOR UKRAINIAN GROUND FORCESE

Collection of scientific works of Odesa Military Academy ◽

10.37129/2313-7509.2019.11.53-58 ◽

2019 ◽

pp. 53-58

Author(s):

О. Кravchuk ◽

V. Symonenkov ◽

I. Symonenkova ◽

O. Hryhorev

Keyword(s):

Large Scale ◽

Armed Forces ◽

Distributed Information ◽

Wide Range ◽

Highly Effective ◽

Information Management Systems ◽

Robotic Devices ◽

Principles And Standards ◽

And Control ◽

The Eu

Today, more than forty countries of the world are engaged in the development of military-purpose robots. A number of unique mobile robots with a wide range of capabilities are already being used by combat and intelligence units of the Armed forces of the developed world countries to conduct battlefield intelligence and support tactical groups. At present, the issue of using the latest information technology in the field of military robotics is thoroughly investigated, and the creation of highly effective information management systems in the land-mobile robotic complexes has acquired a new phase associated with the use of distributed information and sensory systems and consists in the transition from application of separate sensors and devices to the construction of modular information subsystems, which provide the availability of various data sources and complex methods of information processing. The purpose of the article is to investigate the ways to increase the autonomy of the land-mobile robotic complexes using in a non-deterministic conditions of modern combat. Relevance of researches is connected with the necessity of creation of highly effective information and control systems in the perspective robotic means for the needs of Land Forces of Ukraine. The development of the Armed Forces of Ukraine management system based on the criteria adopted by the EU and NATO member states is one of the main directions of increasing the effectiveness of the use of forces (forces), which involves achieving the principles and standards necessary for Ukraine to become a member of the EU and NATO. The inherent features of achieving these criteria will be the transition to a reduction of tasks of the combined-arms units and the large-scale use of high-precision weapons and land remote-controlled robotic devices. According to the views of the leading specialists in the field of robotics, the automation of information subsystems and components of the land-mobile robotic complexes can increase safety, reliability, error-tolerance and the effectiveness of the use of robotic means by standardizing the necessary actions with minimal human intervention, that is, a significant increase in the autonomy of the land-mobile robotic complexes for the needs of Land Forces of Ukraine.

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