Protein stability and dynamics influenced by ligands in extremophilic complexes – a molecular dynamics investigation

2017 ◽  
Vol 13 (9) ◽  
pp. 1874-1887
Author(s):  
Sara Khan ◽  
Umar Farooq ◽  
Maria Kurnikova
Keyword(s):  
Molecular Dynamics ◽  
Protein Stability ◽  
Md Simulations ◽  
Bound State ◽  
Tryptophan Synthase ◽  
Α Subunit ◽  
Different Temperatures ◽  
Hyperthermophilic Organisms

In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations.

scholarly journals The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

2013 ◽  
Vol 9 ◽  
pp. 118-134 ◽  
Author(s):  
Jutta Erika Helga Köhler ◽  
Nicole Grczelschak-Mick
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Benzene Molecule ◽  
Glucose Unit ◽  
Hand Orientation ◽  
Different Temperatures ◽  
Dynamics Simulations ◽  
The Right

Four highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode. This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

scholarly journals Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4413
Author(s):  
Giovanny Aguilera-Durán ◽  
Antonio Romo-Mancillas
Keyword(s):  
Molecular Dynamics ◽  
Computational Study ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Coarse Grained ◽  
Dimensional Structure ◽  
Cytotoxic Lymphocytes ◽  
Ligand Interaction ◽  
Α Subunit

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

A Study of Nanoparticle-Enhanced Heat Transfer

2010 ◽  
Author(s):  
Lawrence M. Jones ◽  
Timothy Sirk ◽  
Eugene Brown
Keyword(s):  
Heat Transfer ◽  
Experimental Data ◽  
Molecular Dynamics ◽  
Heat Flux ◽  
Nuclear Power ◽  
Power Plants ◽  
Md Simulations ◽  
Theoretical Description ◽  
Different Temperatures ◽  
Dynamics Simulations

The study of the heat transfer characteristics of nanofluids, i.e. fluids that are suspensions of nanometer size particles, has gained significant attention in the search for new coolants that can effectively service a variety of needs ranging from the increasing heat transfer demands of ever smaller microelectronic devices to mitigating the effects of loss of coolant accidents in nuclear power plants. Experimental data has shown large increases in thermal conductivity and associated increases in the level of critical heat flux in nuclear reactors; however, in some cases the range of the applicability of the experimental results is uncertain and there is a lack of a theory by which this can be resolved. Complicating the theoretical description of heat transfer in nanofluids is the fact that fluids in the vicinity of the nanoparticles are a complex combination of phase transition, interfacial, and transport phenomena. This paper describes a study in which molecular dynamics simulations were used to enhance the understanding of the effect of nanoparticles on heat transfer. The molecular dynamics (MD) simulations presented here model a Lennard-Jones fluid in a channel where the walls are maintained at different temperatures. The heat flux is calculated for a variety of nanoparticle sizes and concentrations. The results are compared to experimental data in order to provide information that will more confidently bound the data and provide information that will guide the development of more comprehensive theories. We also anticipate that this work could contribute to the design of biosensors where suspended molecules are transported through micro- and nano-channels in the presence of heat transfer.

Multiscale modeling of thermal properties of silicene using molecular dynamics

2018 ◽  
Vol 32 (27) ◽  
pp. 1850331 ◽  
Author(s):  
D. K. Das ◽  
Jit Sarkar
Keyword(s):  
Molecular Dynamics ◽  
Thermal Properties ◽  
Multiscale Modeling ◽  
Experimental Studies ◽  
Md Simulations ◽  
Heat Of Fusion ◽  
Sample Sizes ◽  
Different Temperatures ◽  
Pressure Melting ◽  
Non Equilibrium Molecular Dynamics

Silicene sheet is prepared by atomistic multiscale modeling using molecular dynamics (MD) simulations to evaluate thermal properties of silicene at different temperatures and variable sample sizes. In this paper, by MD simulation study, we have estimated coefficient of linear and surface expansion between a temperature range from 318 K to 398 K, specific heat at constant volume and pressure, melting point, heat of fusion and thermal conductivity of silicene at different sample sizes by both equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD) approaches. The presented multiscale modeling approaches could guide experimental studies to design silicene sheet with required thermal properties for operation under specific conditions.

scholarly journals Dissecting C−H∙∙∙π and N−H∙∙∙π Interactions in Two Proteins Using a Combined Experimental and Computational Approach

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jia Wang ◽  
Lishan Yao
Keyword(s):  
Molecular Dynamics ◽  
Protein Stability ◽  
Local Environment ◽  
Md Simulations ◽  
Computational Approach ◽  
Residue Pair ◽  
Negative Cooperativity ◽  
Triple Mutant ◽  
Π Interactions ◽  
Direct Measurements

AbstractC−H∙∙∙π and N−H∙∙∙π interactions can have an important contribution for protein stability. However, direct measurements of these interactions in proteins are rarely reported. In this work, we combined the mutant cycle experiments and molecular dynamics (MD) simulations to characterize C−H∙∙∙π and N−H∙∙∙π interactions and their cooperativity in two model proteins. It is shown that the average C−H∙∙∙π interaction per residue pair is ~ −0.5 kcal/mol while the N−H∙∙∙π interaction is slightly stronger. The triple mutant box measurement indicates that N−H∙∙∙π∙∙∙C−H∙∙∙π and C−H∙∙∙π∙∙∙C−H∙∙∙π can have a positive or negative cooperativity. MD simulations suggest that the cooperativity, depending on the local environment of the interactions, mainly arises from the geometric rearrangement when the nearby interaction is perturbed.

scholarly journals MOLECULAR DYNAMICS STUDY OF OLEIC ACID-BASED SURFACTANTS FOR ENHANCED OIL RECOVERY

2020 ◽  
Vol 41 (3) ◽  
pp. 125-135
Author(s):  
Aang Suhendar ◽  
Rukman Hertadi ◽  
Yani F Alli
Keyword(s):  
Molecular Dynamics ◽  
Oleic Acid ◽  
Polyethylene Glycol ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Md Simulation ◽  
Md Simulations ◽  
Water Model ◽  
Water Layers ◽  
Different Temperatures

Surfactants have been intensively used for Enhanced Oil Recovery (EOR). Nevertheless, environmental issues cause some surfactants to become unfavored in EOR application. Biodegradable surfactants are the suitable choice to make the environment safer. However, screening surfactants that have a good performance for EOR are time-consuming and costly. Molecular Dynamics (MD) simulation is an alternative solution to reduce cost and time. In the present study, oleic acid-based surfactants that combined with the various length of polyethylene glycol were studied. The potential surfactants were screened by MD simulation to evaluate their ability to reduce the Interfacial Tension (IFT) between oil and water layers, which is the by GROMACS software with Gromos force field and SPC water model. Carboxyl-terminal of the oleic acid was substituted by a different length of polyethylene glycol. All MD simulations were prepared in octadecanewater mixture with temperature ranges of 303-363 K. Our simulations found that the increasing number of polyethylene glycol was not always followed by the decreasing of IFT value between octadecane and water layers. These results were validated with the experimental data and found the similar IFT profile. The simulation of oil emulsification showed that all surfactant samples have good performance and stability as exhibited by their emulsification rate and emulsion stability in different temperatures. The last test to get the best surfactant was the wetability test. The simulation gave the result that both PEG100-oleic and PEG400-oleic were able to change wetability of rocks from oil-wet to water-wet. Accordingly, PEG400-oleic is the best nonionic surfactant candidate due to its performance in each simulation test.

New Derivation of a Particle Wall Boundary Condition in Molecular Dynamics

2007 ◽  
Author(s):  
Peter Spijker ◽  
Albert J. Markvoort ◽  
Huub M. M. ten Eikelder ◽  
Silvia V. Nedea ◽  
Peter A. J. Hilbers
Keyword(s):  
Molecular Dynamics ◽  
Boundary Condition ◽  
Md Simulations ◽  
Pair Interaction ◽  
Parallel Plates ◽  
Crystal Lattices ◽  
Wall Boundary Condition ◽  
Wall Potential ◽  
Wall Boundary ◽  
Different Temperatures

In this paper a new particle wall boundary condition to replace explicit solid walls in molecular dynamics (MD) simulations is proposed. This new wall potential reduces the computational complexity considerably and allows the investigation of larger channels without compromising macroscopic quantities, such as density, temperature, pressure and heat flux. Since it is common practice in MD to truncate pair interaction potentials, an alternative and explicit derivation of the wall potential is possible, which is in contrast to previous work. Moreover, different types of crystal lattices can be included in the new potential. To demonstrate the applicablity of the method, MD simulations of a gas between two parallel plates at different temperatures and densities have been performed. The results of these simulations are compared to explicit wall simulations and previously proposed wall potentials. Although differences with other wall potentials are minor, some superior aspects of the new potential are addressed.

Implicit particle wall boundary condition in molecular dynamics

2008 ◽  
Vol 222 (5) ◽  
pp. 855-864 ◽  
Author(s):  
P Spijker ◽  
H M M ten Eikelder ◽  
A J Markvoort ◽  
S V Nedea ◽  
P A J Hilbers
Keyword(s):  
Molecular Dynamics ◽  
Boundary Condition ◽  
Boundary Conditions ◽  
Solid Wall ◽  
Computational Cost ◽  
Md Simulations ◽  
Parallel Plates ◽  
Wall Boundary Condition ◽  
Wall Boundary ◽  
Different Temperatures

Thin film and nano-tube manufacturing, micro-channel cooling, and many other similar interesting techniques demand the prediction of heat transfer characteristics at the nanometre scale. In this respect, the transport properties at gas—solid and liquid—solid interfaces are very important. The processes at these interfaces can be studied in detail with molecular dynamics (MD) simulations. However, the computational cost involved in simulating the solid wall currently restrains the size of channels, which can be simulated. Therefore, the solid wall is sometimes replaced by boundary conditions, which often compromise on macroscopic quantities, such as density, temperature, pressure, and heat flux. In the current paper, a new particle wall boundary condition is presented, which is in good agreement with existing boundary conditions, but allows for the pressure calculation. This new boundary condition is based on averaging the contributions of an explicit solid wall and is derived using knowledge on common practices in MD algorithms, such as truncation and shifting. Moreover, it allows for different crystal lattices to be included in the new potential. The applicability of the new method is demonstrated by MD simulations of a gas between two parallel plates at different temperatures and densities. Furthermore, these simulations are compared with explicit wall simulations and existing boundary conditions.

scholarly journals Molecular Dynamics Calculations of Grain Boundary Mobility in CdTe

Nanomaterials ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 552 ◽  
Author(s):  
Rodolfo Aguirre ◽  
Sharmin Abdullah ◽  
Xiaowang Zhou ◽  
David Zubia
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Grain Boundaries ◽  
Driving Forces ◽  
Md Simulations ◽  
Face Centered Cubic ◽  
Boundary Mobility ◽  
Grain Boundary Mobility ◽  
Different Temperatures ◽  
Lower Mobility

Molecular dynamics (MD) simulations have been applied to study mobilities of Σ3, Σ7 and Σ11 grain boundaries in CdTe. First, an existing MD approach to drive the motion of grain boundaries in face-centered-cubic and body-centered-cubic crystals was generalized for arbitrary crystals. MD simulations were next performed to calculate grain boundary velocities in CdTe crystals at different temperatures, driving forces, and grain boundary terminations. Here a grain boundary is said to be Te-terminated if its migration encounters sequentially C d · T e − C d · T e … planes, where “·” and “−” represent short and long spacing respectively. Likewise, a grain boundary is said to be Cd-terminated if its migration encounters sequentially T e · C d − T e · C d … planes. Grain boundary mobility laws, suitable for engineering time and length scales, were then obtained by fitting the MD results to Arrhenius equation. These studies indicated that the Σ3 grain boundary has significantly lower mobility than the Σ7 and Σ11 grain boundaries. The Σ7 Te-terminated grain boundary has lower mobility than the Σ7 Cd-terminated grain boundary, and that the Σ11 Cd-terminated grain boundary has lower mobility than the Σ11 Te-terminated grain boundary.

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