scholarly journals Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5855
Author(s):  
Ramón Rial ◽  
Michael González-Durruthy ◽  
Manuel Somoza ◽  
Zhen Liu ◽  
Juan M. Ruso
Keyword(s):  
Conformational Dynamics ◽  
Experimental Studies ◽  
Network Models ◽  
Van Der Waals Interactions ◽  
Machine Learning Techniques ◽  
Titration Calorimetry ◽  
Molecular Features ◽  
Plot Analysis ◽  
Aromatic Amino Acid Residue ◽  
The Stability

In this work we present a computational analysis together with experimental studies, focusing on the interaction between a benzothiazole (BTS) and lysozyme. Results obtained from isothermal titration calorimetry, UV-vis, and fluorescence were contrasted and complemented with molecular docking and machine learning techniques. The free energy values obtained both experimentally and theoretically showed excellent similarity. Calorimetry, UV-vis, and 3D/2D-lig-plot analysis revealed that the most relevant interactions between BTS and lysozyme are based on a predominance of aromatic, hydrophobic Van der Waals interactions, mainly aromatic edge-to-face (T-shaped) π-π stacking interactions between the benzene ring belonging to the 2-(methylthio)-benzothiazole moiety of BTS and the aromatic amino acid residue TRP108 of the lysozyme receptor. Next, conventional hydrogen bonding interactions contribute to the stability of the BTS-lysozyme coupling complex. In addition, mechanistic approaches performed using elastic network models revealed that the BTS ligand theoretically induces propagation of allosteric signals, suggesting non-physiological conformational flexing in large blocks of lysozyme affecting α-helices. Likewise, the BTS ligand interacts directly with allosteric residues, inducing perturbations in the conformational dynamics expressed as a moderate conformational softening in the α-helices H1, H2, and their corresponding β-loop in the lysozyme receptor, in contrast to the unbound state of lysozyme.

scholarly journals Energetics of carbohydrate binding by a 14 kDa S-type mammalian lectin

1995 ◽  
Vol 308 (1) ◽  
pp. 237-241 ◽  
Author(s):  
R Ramkumar ◽  
A Surolia ◽  
S K Podder
Keyword(s):  
Binding Constants ◽  
Van Der Waals Interactions ◽  
Titration Calorimetry ◽  
Carbohydrate Binding ◽  
Glucose Binding ◽  
The Stability ◽  
L 14 ◽  
Derivatives Of ◽  
Binding Lectin ◽  
Site Binding

The thermodynamics of the binding of derivatives of galactose and lactose to a 14 kDa beta-galactoside-binding lectin (L-14) from sheep spleen has been studied in 10 nM phosphate/150 mM NaCl/10 mM beta-mercaptoethanol buffer, pH 7.4, and in the temperature range 285-300 K using titration calorimetry. The single-site binding constants of various sugars for the lectin were in the following order: N-acetyl-lactosamine thiodigalactoside > 4-methylumbelliferyl lactoside > lactose > 4-methylumbelliferyl alpha-D-galactoside > methyl-alpha-galactose > methyl-beta-galactose. Reactions were essentially enthalpically driven with the binding enthalpies ranging from -53.8 kJ/mol for thiodigalactoside at 301 K to -2.2 kJ/mol for galactose at 300 K, indicating that hydrogen-bonding and van der Waals interactions provide the major stabilization for these reactions. However, the binding of 4-methylumbelliferyl-alpha-D-galactose displays relatively favourable entropic contributions, indicating the existence of a non-polar site adjacent to the galactose-binding subsite. From the increments in the enthalpies for the binding of lactose, N-acetyl-lactosamine and thiodigalactoside relative to methyl-beta-galactose, the contribution of glucose binding in the subsite adjacent to that for galactose shows that glucose makes a major contribution to the stability of L-14 disaccharide complexes. Observation of enthalpy-entropy compensation for the recognition of saccharides such as lactose by L-14 and the absence of it for monosaccharides such as galactose, together with the lack of appreciable changes in the heat capacity (delta Cp), indicate that reorganization of water plays an important role in these reactions.

scholarly journals STUDY OF THE ALGORITHM OF PSEUDONORMAL OPTIMIZATION ON THE STABILITY OF THE SOLUTION OF THE EQUATION PROBLEM AND THE ESTIMATION OF THE ACCURACY

2021 ◽  
Vol 1 ◽  
pp. 40-48
Author(s):  
Amridon G. Barliani ◽  
Galina A. Nefedova ◽  
Irina V. Karnetova
Keyword(s):  
Least Squares ◽  
Least Squares Method ◽  
Experimental Studies ◽  
Network Models ◽  
Optimization Method ◽  
Equation Problem ◽  
Estimated Parameters ◽  
The Matrix ◽  
The Stability ◽  
Stability Of The Solution

In geodesic practice, when designing and adjusting geodetic networks for various purposes on a computer, it is necessary to solve poorly conditioned systems of linear normal equations. In such systems, the determinant of the matrix of equations tends to zero, so the application of the least squares method leads to large distortions of the estimated parameters. Moreover, in such situations, for the least squares algorithm, a slight distortion of the input data leads to unacceptably large distortions of the final results of the equalization and accuracy estimation. In this regard, the application of the pseudonormal optimization method is proposed. The presented work is devoted to the study of the stability of the solution of the adjustment task and the estimation of accuracy obtained on the basis of the pseudonormal optimization method. The novelty is the obtained algorithm for estimating the relative error of the pseudonormal optimization method. A comparative analysis of two competing processing methods was performed for different network models. The results of experimental studies and their analysis have shown the advantage of the pseudonormal optimization method over the least squares method.

scholarly journals Performance Evaluation of Heading-and-Winning Machines in the Conditions of Potash Mines

2021 ◽  
Vol 11 (8) ◽  
pp. 3444
Author(s):  
Sergey A. Lavrenko ◽  
Dmitriy I. Shishlyannikov
Keyword(s):  
Energy Efficiency ◽  
Experimental Studies ◽  
Efficiency Coefficient ◽  
Mechanized Method ◽  
Methodological Approaches ◽  
The Stability ◽  
Technical Solutions ◽  
Potash Mine ◽  
Complex Indicators ◽  
Potassium Magnesium

The authors focus on the process of potash ore production by a mechanized method. They show that currently there are no approved procedures for assessing the performance of heading-and-winning machines operating in the conditions of potash mines. This causes difficulties in determining the field of application of heading-and-winning machines, complicates the search for implicit technical solutions for the modernisation of existing models of mining units, prohibits real-time monitoring of the stability of stope-based technological processes and makes it difficult to assess the performance of the services concerning mining enterprises. The work represents an aggregate assessment of the performance of heading-and-winning machines for potash mines by determining complex indicators describing the technological and technical levels of organising the work in stopes. Such indicators are the coefficients of productivity and energy efficiency, respectively. Experimental studies have been carried out in the conditions of the potash mine of the Verkhnekamskoye potassium-magnesium salt deposit to assess the performance of the latest and most productive Ural-20R heading-and-winning machines manufactured in Russia. Using the above methodological approaches, this paper shows that the unsatisfactory technological performance of the studied machine is due to the low productivity of the mine district transport. The average productivity coefficient was 0.29. At the same time, high values of the energy efficiency coefficient show that the productivity of the machine is on par with design conditions.

Conformational dynamics and thermodynamics of protein–ligand binding studied by NMR relaxation

2012 ◽  
Vol 40 (2) ◽  
pp. 419-423 ◽  
Author(s):  
Mikael Akke
Keyword(s):  
Ligand Binding ◽  
Bound States ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Titration Calorimetry ◽  
Conformational Entropy ◽  
Chain Order ◽  
Ligand Interactions ◽  
Galectin 3 ◽  
Relaxation Experiments

Protein conformational dynamics can be critical for ligand binding in two ways that relate to kinetics and thermodynamics respectively. First, conformational transitions between different substates can control access to the binding site (kinetics). Secondly, differences between free and ligand-bound states in their conformational fluctuations contribute to the entropy of ligand binding (thermodynamics). In the present paper, I focus on the second topic, summarizing our recent results on the role of conformational entropy in ligand binding to Gal3C (the carbohydrate-recognition domain of galectin-3). NMR relaxation experiments provide a unique probe of conformational entropy by characterizing bond-vector fluctuations at atomic resolution. By monitoring differences between the free and ligand-bound states in their backbone and side chain order parameters, we have estimated the contributions from conformational entropy to the free energy of binding. Overall, the conformational entropy of Gal3C increases upon ligand binding, thereby contributing favourably to the binding affinity. Comparisons with the results from isothermal titration calorimetry indicate that the conformational entropy is comparable in magnitude to the enthalpy of binding. Furthermore, there are significant differences in the dynamic response to binding of different ligands, despite the fact that the protein structure is virtually identical in the different protein–ligand complexes. Thus both affinity and specificity of ligand binding to Gal3C appear to depend in part on subtle differences in the conformational fluctuations that reflect the complex interplay between structure, dynamics and ligand interactions.

scholarly journals Extended-State-Observer-Based Super Twisting Control for Pneumatic Muscle Actuators

Actuators ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 35
Author(s):  
Yu Cao ◽  
Zhongzheng Fu ◽  
Mengshi Zhang ◽  
Jian Huang
Keyword(s):  
Control Method ◽  
Experimental Studies ◽  
State Observer ◽  
Extended State Observer ◽  
Extended State ◽  
Pneumatic Muscle ◽  
System States ◽  
The Stability ◽  
Twisting Control ◽  
Muscle Actuators

This paper presents a tracking control method for pneumatic muscle actuators (PMAs). Considering that the PMA platform only feedbacks position, and the velocity and disturbances cannot be observed directly, we use the extended-state-observer (ESO) for simultaneously estimating the system states and disturbances by using measurable variables. Integrated with the ESO, a super twisting controller (STC) is design based on estimated states to realize the high-precision tracking. According to the Lyapunov theorem, the stability of the closed-loop system is ensured. Simulation and experimental studies are conducted, and the results show the convergence of the ESO and the effectiveness of the proposed method.

scholarly journals Mutualistic strategies minimize coextinction in plant–disperser networks

2017 ◽  
Vol 284 (1854) ◽  
pp. 20162302 ◽  
Author(s):  
Evan C. Fricke ◽  
Joshua J. Tewksbury ◽  
Elizabeth M. Wandrag ◽  
Haldre S. Rogers
Keyword(s):  
Network Structure ◽  
Field Experiments ◽  
Empirical Relationship ◽  
Network Models ◽  
Mutualistic Interactions ◽  
Simulated Network ◽  
Direct And Indirect Impacts ◽  
Indirect Impacts ◽  
The Stability ◽  
Seed Dispersal Mutualism

The global decline of mutualists such as pollinators and seed dispersers may cause negative direct and indirect impacts on biodiversity. Mutualistic network models used to understand the stability of mutualistic systems indicate that species with low partner diversity are most vulnerable to coextinction following mutualism disruption. However, existing models have not considered how species vary in their dependence on mutualistic interactions for reproduction or survival, overlooking the potential influence of this variation on species' coextinction vulnerability and on network stability. Using global databases and field experiments focused on the seed dispersal mutualism, we found that plants and animals that depend heavily on mutualistic interactions have higher partner diversity. Under simulated network disruption, this empirical relationship strongly reduced coextinction because the species most likely to lose mutualists depend least on their mutualists. The pattern also reduced the importance of network structure for stability; nested network structure had little effect on coextinction after simulations incorporated the empirically derived relationship between partner diversity and mutualistic dependence. Our results highlight a previously unknown source of stability in mutualistic networks and suggest that differences among species in their mutualistic strategy, rather than network structure, primarily accounts for stability in mutualistic communities.

Adhesion of Partially and Fully Collapsed Nanotubes

2018 ◽  
Vol 86 (1) ◽  
Author(s):  
Ming Li ◽  
Hao Li ◽  
Fengwei Li ◽  
Zhan Kang
Keyword(s):  
Finite Deformation ◽  
Adhesion Energy ◽  
Van Der Waals Interactions ◽  
Critical Conditions ◽  
Nano Composites ◽  
Deformation Model ◽  
Analysis And Design ◽  
Structural Rigidity ◽  
Multiwall Nanotubes ◽  
The Stability

The competition between the structural rigidity and the van der Waals interactions may lead to collapsing of aligned nanotubes, and the resulting changes of both configurations and properties promise the applications of nanotubes in nano-composites and nano-electronics. In this paper, a finite-deformation model is applied to study the adhesion of parallel multiwall nanotubes with both partial and full collapsing, in which the noncontact adhesion energy is analytically determined. The analytical solutions of both configurations and energies of collapsed nanotubes are consistent with the molecular dynamics (MD) results, demonstrating the effectiveness of the finite-deformation model. To study the critical conditions of generating the partially and fully collapsed multiwall nanotubes, our analytical model gives the predictions for both the geometry- and energy-related critical diameters, which are helpful for the stability analysis and design of nanotube-based nano-devices.

Coupled Stability of Multiport Systems—Theory and Experiments

1994 ◽  
Vol 116 (3) ◽  
pp. 419-428 ◽  
Author(s):  
J. E. Colgate
Keyword(s):  
Stability Property ◽  
Force Feedback ◽  
Linear Time ◽  
Experimental Studies ◽  
Sufficient Conditions ◽  
Direct Drive ◽  
Property A ◽  
Linear Time Invariant ◽  
The Stability ◽  
Necessary And Sufficient

This paper presents both theoretical and experimental studies of the stability of dynamic interaction between a feedback controlled manipulator and a passive environment. Necessary and sufficient conditions for “coupled stability”—the stability of a linear, time-invariant n-port (e.g., a robot, linearized about an operating point) coupled to a passive, but otherwise arbitrary, environment—are presented. The problem of assessing coupled stability for a physical system (continuous time) with a discrete time controller is then addressed. It is demonstrated that such a system may exhibit the coupled stability property; however, analytical, or even inexpensive numerical conditions are difficult to obtain. Therefore, an approximate condition, based on easily computed multivariable Nyquist plots, is developed. This condition is used to analyze two controllers implemented on a two-link, direct drive robot. An impedance controller demonstrates that a feedback controlled manipulator may satisfy the coupled stability property. A LQG/LTR controller illustrates specific consequences of failure to meet the coupled stability criterion; it also illustrates how coupled instability may arise in the absence of force feedback. Two experimental procedures—measurement of endpoint admittance and interaction with springs and masses—are introduced and used to evaluate the above controllers. Theoretical and experimental results are compared.

scholarly journals Experimental Study of the Chaotic Jerk Circuit Application for Chaos Shift Keying

2021 ◽  
Vol 58 (4) ◽  
pp. 55-68
Author(s):  
F. Capligins ◽  
A. Litvinenko ◽  
A. Aboltins ◽  
E. Austrums ◽  
A. Rusins ◽  
...  
Keyword(s):  
Experimental Study ◽  
Voltage Drop ◽  
Experimental Studies ◽  
Chaotic Synchronization ◽  
Channel Noise ◽  
Error Feedback ◽  
Shift Keying ◽  
The Stability ◽  
Chaos Shift Keying ◽  
The Impact

Abstract The paper presents a study of the chaotic jerk circuit (CJC) employment capabilities for digital communications. The concept of coherent chaos shift keying (CSK) communication system with controlled error feedback chaotic synchronization is proposed for a specific CJC in two modifications. The stability of chaotic synchronization between the two CJCs was evaluated in terms of voltage drop at the input of the slave circuit and the impact of channel noise using simulations and experimental studies.

scholarly journals Structural, elastic, electronic and thermal properties of InAs: A study of functional density

2017 ◽  
Vol 26 (46) ◽  
Author(s):  
Víctor Mendoza-Estrada ◽  
Melissa Romero-Baños ◽  
Viviana Dovale-Farelo ◽  
William López-Pérez ◽  
Álvaro González-García ◽  
...  
Keyword(s):  
Thermal Properties ◽  
Density Functional ◽  
Experimental Studies ◽  
Debye Model ◽  
Band Gap Energy ◽  
Functional Theory ◽  
Zinc Blende ◽  
The Density Functional Theory ◽  
The Stability ◽  
Experimental Values

In this research, first-principles calculations were carried out within the density functional theory (DFT) framework, using LDA and GGA, in order to study the structural, elastic, electronic and thermal properties of InAs in the zinc-blende structure. The results of the structural properties (a, B0, ) agree with the theoretical and experimental results reported by other authors. Additionally, the elastic properties, the elastic constants (C11, C12 and C44), the anisotropy coefficient (A) and the predicted speeds of the sound ( , , and ) are in agreement with the results reported by other authors. In contrast, the shear modulus (G), the Young's modulus (Y) and the Poisson's ratio (v) show some discrepancy with respect to the experimental values, although, the values obtained are reasonable. On the other hand, it is evident the tendency of the LDA and GGA approaches to underestimate the value of the band-gap energy in semiconductors. The thermal properties (V, , θD yCV) of InAs, calculated using the quasi-harmonic Debye model, are slightly sensitive as the temperature increases. According to the stability criteria and the negative value of the enthalpy of formation, InAs is mechanically and thermodynamically stable. Therefore, this work can be used as a future reference for theoretical and experimental studies based on InAs.

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