scholarly journals Studies of Trans- and Cis-Xylomollin Molecular Structures Using Molecular Dynamics Simulations

2013 ◽  
Vol 5 ◽  
pp. 46-58
Author(s):  
Radia Mahboub
Keyword(s):  
Comparative Study ◽  
Md Simulation ◽  
Md Simulations ◽  
Molecular Structures ◽  
Stable Configuration ◽  
Gas Phases ◽  
Configuration Energy ◽  
Dynamics Simulations ◽  
Efficient Program ◽  
The Comparative Study

The present work describes the comparative study of the trans- and the cis-xylomollin structures. We have determined the two bridgehead H5 and H9 configurations using simulation calculations for both trans- and cis- distereoisomers. Molecular Dynamic (MD) simulations of the trans- and cis- xylomollin were performed with an efficient program. The geometries, interaction energies, bonds, angles, and the Van der Waals (VDW) interactions were carried out in solution and gas phases. This comparative study shows that the trans-xylomollin acquires the high configuration energy under the AMBER field using MD method. This molecule reaches its high stable configuration state in solution environment. Our MD simulation results are goods and in agreement with those of literature.

scholarly journals Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations

2021 ◽  
Author(s):  
Jingxuan Zhu ◽  
Juexin Wang ◽  
Weiwei Han ◽  
Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Md Simulation ◽  
Biological Process ◽  
Dynamic Networks ◽  
Md Simulations ◽  
Amino Acid Mutation ◽  
Long Range Interactions ◽  
Decoder Architecture ◽  
Dynamics Simulations

Abstract Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference (NRI) model based on a graph neural network (GNN), which adopts an encoder-decoder architecture to simultaneously infer latent interactions to probe protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between the two distant sites in the Pin1, SOD1, and MEK1 systems.

scholarly journals A New Algorithm for Contact Angle Estimation in Molecular Dynamics Simulations

2015 ◽  
Author(s):  
Sumith Yd ◽  
Shalabh C. Maroo
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Md Simulation ◽  
Spline Interpolation ◽  
Vertical Axis ◽  
Md Simulations ◽  
Computationally Efficient ◽  
B Spline ◽  
Wetting Properties ◽  
Dynamics Simulations

It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating the time evolution of contact angle. This is a tedious effort to do manually or with image processing algorithms. In this work we propose a new algorithm to estimate contact angle from MD simulations directly and in a computationally efficient way. This algorithm segregates the droplet molecules from the vapor molecules using Mahalanobis distance (MND) technique. Then the density is smeared onto a 2D grid using 4th order B-spline interpolation function. The vapor liquid interface data is estimated from the grid using density filtering. With the interface data a circle is fitted using Landau method. The equation of this circle is solved for obtaining the contact angle. This procedure is repeated by rotating the droplet about the vertical axis. We have applied this algorithm to a number of studies (different potentials and thermostat methods) which involves the MD simulation of water.

scholarly journals Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism in Escherichia coli: Insights from Molecular Dynamics Simulations

Biomolecules ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 133 ◽  
Author(s):  
Faiza Durrani ◽  
Roquyya Gul ◽  
Muhammad Mirza ◽  
Naheed Kaderbhai ◽  
Matheus Froeyen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Md Simulation ◽  
Simulation Analysis ◽  
Signal Sequence ◽  
Binding Free Energy ◽  
Signal Recognition Particle ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Dynamics Simulations

The disulfide bond signal sequence (DsbAss) protein is characterized as an important virulence factor in gram-negative bacteria. This study aimed to analyze the “alanine” alteration in the hydrophobic (H) region of DsbAss and to understand the conformational DsbAss alteration(s) inside the fifty-four homolog (Ffh)-binding groove which were revealed to be crucial for translocation of ovine growth hormone (OGH) to the periplasmic space in Escherichia coli via the secretory (Sec) pathway. An experimental design was used to explore the hydrophobicity and alteration of alanine (Ala) to isoleucine (Ile) in the tripartite structure of DsbAss. As a result, two DsbAss mutants (Ala at positions -11 and -13) with same hydrophobicity of 1.539 led to the conflicting translocation of the active OGH gene. We performed molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GBSA) binding free energy calculations to examine the interaction energetic and dynamic aspects of DsbAss/signal repetition particle 54 (SRP54) binding, which has a principle role in Escherichia coli Sec pathways. Although both DsbAss mutants retained helicity, the MD simulation analysis evidenced that altering Ala-13 changed the orientation of the signal peptide in the Ffh M binding domain groove, favored more stable interaction energies (MM-GBSA ΔGtotal = −140.62 kcal mol−1), and hampered the process of OGH translocation, while Ala-11 pointed outward due to unstable conformation and less binding energy (ΔGtotal = −124.24 kcal mol−1). Here we report the dynamic behavior of change of “alanine” in the H-domain of DsbAss which affects the process of translocation of OGH, where MD simulation and MM-GBSA can be useful initial tools to investigate the virulence of bacteria.

scholarly journals Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography

2020 ◽  
Vol 117 (44) ◽  
pp. 27132-27140
Author(s):  
Mateusz Sikora ◽  
Utz H. Ermel ◽  
Anna Seybold ◽  
Michael Kunz ◽  
Giulia Calloni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Electron Tomography ◽  
Md Simulations ◽  
Cell Junctions ◽  
Biophysical Properties ◽  
In Silico Screening ◽  
Desmosomal Cadherins ◽  
Cryo Electron Tomography ◽  
Dynamics Simulations

Desmosomes are cell–cell junctions that link tissue cells experiencing intense mechanical stress. Although the structure of the desmosomal cadherins is known, the desmosome architecture—which is essential for mediating numerous functions—remains elusive. Here, we recorded cryo-electron tomograms (cryo-ET) in which individual cadherins can be discerned; they appear variable in shape, spacing, and tilt with respect to the membrane. The resulting sub-tomogram average reaches a resolution of ∼26 Å, limited by the inherent flexibility of desmosomes. To address this challenge typical of dynamic biological assemblies, we combine sub-tomogram averaging with atomistic molecular dynamics (MD) simulations. We generate models of possible cadherin arrangements and perform an in silico screening according to biophysical and structural properties extracted from MD simulation trajectories. We find a truss-like arrangement of cadherins that resembles the characteristic footprint seen in the electron micrograph. The resulting model of the desmosomal architecture explains their unique biophysical properties and strength.

scholarly journals Spontaneous self-assembly and structure of perfluoroalkylalkane surfactant hemimicelles by molecular dynamics simulations

2019 ◽  
Vol 116 (30) ◽  
pp. 14868-14873 ◽  
Author(s):  
Gonçalo M. C. Silva ◽  
Pedro Morgado ◽  
Pedro Lourenço ◽  
Michel Goldmann ◽  
Eduardo J. M. Filipe
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Md Simulation ◽  
Grazing Incidence ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Spontaneous Formation ◽  
Rational Explanation ◽  
Dynamics Simulations

Fully atomistic molecular-dynamics (MD) simulations of perfluoroalkylalkane molecules at the surface of water show the spontaneous formation of aggregates whose size and topography closely resemble the experimentally observed hemimicelles for this system. Furthermore, the grazing incidence X-ray diffraction (GIXD) pattern calculated from the simulation trajectories reproduces the experimental GIXD spectra previously obtained, fully validating the MD simulation results. The detailed analysis of the internal structure of the aggregates obtained by the MD simulations supports a definite rational explanation for the spontaneous formation, stability, size, and shape of perfluoroalkylalkane hemimicelles at the surface of water.

scholarly journals Dynamics Simulation Studies of Solvation Effect on the Trans-Xylomollin Conformation

2013 ◽  
Vol 13 ◽  
pp. 132-146
Author(s):  
Radia Mahboub
Keyword(s):  
Md Simulations ◽  
Dynamics Simulation ◽  
Solvation Effect ◽  
Distance Restraint ◽  
Stable Conformation ◽  
Langevin Dynamic ◽  
Gas Phases ◽  
Distance Restraints ◽  
Efficient Program ◽  
Conformation State

The present work describes the solvation effect on the trans-xylomollin conformation. We have studied the trans-xylomollin conformations with the distance restraints using simulation calculations. Distance Restraint Molecular Dynamic (DR-MD) and Distance Restraint Langevin Dynamic (DR-LD) simulations of the trans-xylomollin were performed with an efficient program. The geometries, interaction energies, bonds, angles, and the Van der Waals (VDW) interactions were carried out in solution and gas phases. This comparative study shows that the trans-xylomollin acquires low total energy in solution using DR-MD method and stable conformation under the AMBER field. This molecule reaches its high stable conformation state in solution environment. The solvation effect is more important with DR-MD simulations. Our results are goods and in agreement with the used force field.

scholarly journals Exploring the Cold-Adaptation Mechanism of Serine Hydroxymethyltransferase by Comparative Molecular Dynamics Simulations

2021 ◽  
Vol 22 (4) ◽  
pp. 1781
Author(s):  
Zhi-Bi Zhang ◽  
Yuan-Ling Xia ◽  
Guang-Heng Dong ◽  
Yun-Xin Fu ◽  
Shu-Qun Liu
Keyword(s):  
Molecular Dynamics ◽  
Cold Adaptation ◽  
Active Sites ◽  
Structural Parameters ◽  
Md Simulations ◽  
Molecular Structures ◽  
Serine Hydroxymethyltransferase ◽  
Adaptation Mechanism ◽  
Thermo Stability ◽  
Dynamics Simulations

Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from Psychromonas ingrahamii and its mesophilic counterpart, mSHMT from Escherichia coli, were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.

Molecular Dynamics Simulations on Sliding Friction between Amorphous Si-DLC Films

2011 ◽  
Vol 675-677 ◽  
pp. 953-956
Author(s):  
Yang Wang ◽  
Hui Qing Lan ◽  
Can Liu
Keyword(s):  
Friction Force ◽  
Md Simulation ◽  
Sliding Friction ◽  
Md Simulations ◽  
Carbon Films ◽  
Wear Performance ◽  
The Past ◽  
Significant Interest ◽  
Amorphous Si ◽  
Dynamics Simulations

Diamond-like carbon films have been extensively studied over the past decades due to their unique combination of properties, in particular, Si-DLC films are of significant interest for tribological effects. They possess the potential to improve wear performance in humid atmospheres and at higher temperatures. MD simulations were carried out to generate Si-DLC films at different silicon contents from 0 to 50%, in order to theoretically investigate the influence of silicon contents on microstructures and tribological properties between Si-DLC films. The results show that the sp3/sp2 ratio in Si-DLC films increases with the increasing silicon content. The MD simulation results suggest that the friction force increases with addition of silicon to DLC films. The bond numbers of interfilms have showed that the silicon addition promotes the bonding of interfilms forming, which results in the friction force increased.

Molecular Dynamics Simulations and the Landauer’s Principle

2018 ◽  
Vol 25 (02) ◽  
pp. 1850006
Author(s):  
Ihab H. Naeim ◽  
J. Batle ◽  
S. Kadry ◽  
O. Tarawneh
Keyword(s):  
Molecular Dynamics ◽  
Information Theory ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Canonical Ensemble ◽  
Md Simulations ◽  
Present Contribution ◽  
Bistable Potential ◽  
Landauer’S Principle ◽  
Dynamics Simulations

Landauer’s principle is a fundamental link between thermodynamics and information theory, which implies that the erasure of information comes at an energetic price. In the present contribution we analyze to what extend the usual molecular dynamics (MD) simulation formalism can handle the Landauer’s bound kBT ln 2 in the simplest case of one particle treated classically. The erasure of one bit of information is performed by adiabatically varying the shape of a bistable potential in a full cycle. We will highlight the inadequacy of either the microcanonical or canonical ensemble treatments currently employed in MD simulations and propose potential solutions.

scholarly journals Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations

2021 ◽  
Author(s):  
Jingxuan Zhu ◽  
Juexin Wang ◽  
Weiwei Han ◽  
Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Binding Sites ◽  
Md Simulation ◽  
Dynamic Networks ◽  
Md Simulations ◽  
Amino Acid Mutation ◽  
Long Range Interactions ◽  
Decoder Architecture ◽  
Dynamics Simulations

AbstractProtein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allostery effect. However, current MD simulations cannot reach the time scales of whole allostery processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference (NRI) model based on a graph neural network (GNN), which adopts an encoder-decoder architecture to simultaneously infer latent interactions to probe protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between the two distant binding sites in the Pin1, SOD1, and MEK1 systems.

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