scholarly journals The impact of mutation L138F/L210F on the Orai channel: a molecular dynamics simulation study

2021 ◽  
Author(s):  
Xiaoqian Zhang ◽  
Hua Yu ◽  
Xiangdong Liu ◽  
Chen Song
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Calcium Release ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Hydrophobic Region ◽  
Crac Channel ◽  
Dynamics Simulations ◽  
The Impact ◽  
Basic Region

The calcium release-activated calcium (CRAC) channel, composed of the Orai channel and the STIM protein, plays a crucial role in maintaining the Ca2+ concentration in cells. Previous studies showed that the L138F mutation in the human Orai1 creates a constitutively open channel independent of STIM, causing severe myopathy, but how the L138F mutation activates Orai1 is still unclear. Here, based on the crystal structure of Drosophila melanogaster Orai (dOrai), molecular dynamics simulations for the wild-type (WT) and the L210F (corresponding to L138F in the human Orai1) mutant were conducted to investigate their structural and dynamical properties. The results showed that the L210F dOrai mutant tends to have a more hydrated hydrophobic region (V174 to F171), as well as more dilated basic region (K163 to R155) and selectivity filter (E178). Sodium ions were located deeper in the mutant than in the WT. Further analysis revealed two local but essential conformational changes that may be the key to the activation. A rotation of F210, a previously undescribed feature, was found to result in the opening of the K163 gate through hydrophobic interactions. At the same time, a counter-clockwise rotation of F171 occurred more frequently in the mutant, resulting in a wider hydrophobic gate with more hydration. Ultimately, the opening of the two gates may facilitate the opening of the Orai channel independent of STIM.

scholarly journals The Impact of Mutation L138F/L210F on the Orai Channel: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaoqian Zhang ◽  
Hua Yu ◽  
Xiangdong Liu ◽  
Chen Song
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Calcium Release ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Hydrophobic Region ◽  
In The Wild ◽  
Dynamics Simulations ◽  
The Impact

The calcium release-activated calcium channel, composed of the Orai channel and the STIM protein, plays a crucial role in maintaining the Ca2+ concentration in cells. Previous studies showed that the L138F mutation in the human Orai1 creates a constitutively open channel independent of STIM, causing severe myopathy, but how the L138F mutation activates Orai1 is still unclear. Here, based on the crystal structure of Drosophila melanogaster Orai (dOrai), molecular dynamics simulations for the wild-type (WT) and the L210F (corresponding to L138F in the human Orai1) mutant were conducted to investigate their structural and dynamical properties. The results showed that the L210F dOrai mutant tends to have a more hydrated hydrophobic region (V174 to F171), as well as more dilated basic region (K163 to R155) and selectivity filter (E178). Sodium ions were located deeper in the mutant than in the wild-type. Further analysis revealed two local but essential conformational changes that may be the key to the activation. A rotation of F210, a previously unobserved feature, was found to result in the opening of the K163 gate through hydrophobic interactions. At the same time, a counter-clockwise rotation of F171 occurred more frequently in the mutant, resulting in a wider hydrophobic gate with more hydration. Ultimately, the opening of the two gates may facilitate the opening of the Orai channel independent of STIM.

Molecular Dynamics Simulations of Structures of Amorphous Carbon Films via Deposition

2011 ◽  
Vol 194-196 ◽  
pp. 2220-2224
Author(s):  
Hui Qing Lan ◽  
Zheng Ling Kang
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Growth Dynamics ◽  
Carbon Films ◽  
Film Structure ◽  
Dynamics Simulation ◽  
Carbon Ions ◽  
Amorphous Carbon Films ◽  
Dynamics Simulations ◽  
The Impact

The growth of amorphous carbon films via deposition is investigated using molecular dynamics simulation with a modified Tersoff potential. The impact energy of carbon atoms ranges from 1 to 50 eV and the temperature of the diamond substrate is 300 K. The effects of the incident energy on the growth dynamics and film structure are studied in a detail. Simulation results show that the mobility of surface atoms in the cascade region is enhanced by impacting energetic carbon ions, especially at moderate energy, which favors the growth of denser and smoother films with better adhesion to the substrate. Our results agree qualitatively with the experimental observation.

MOLECULAR MODELING OF THE INTERACTIONS BETWEEN HISTONE DEACETYLASE 8 AND INHIBITORS

2012 ◽  
Vol 11 (04) ◽  
pp. 907-924 ◽  
Author(s):  
DAWEI HUANG ◽  
XIAOHUI LI ◽  
ZHILONG XIU
Keyword(s):  
Molecular Dynamics ◽  
Histone Deacetylases ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Zinc Ion ◽  
Dynamics Simulation ◽  
Amino Acid Residues ◽  
Domain Docking ◽  
Dynamics Simulations ◽  
Linker Domain

Inhibitors of histone deacetylases (HDACs) have become an attractive class of anticancer agent. To understand the interaction between HDAC8 and inhibitors, including "pan-" inhibitors that inhibit many HDACs isoforms and selective inhibitors with no linker domain, docking and molecular dynamics simulation were conducted. Docking results showed the presence of π-π interactions between "linkerless" inhibitors and the aromatic amino acid residues of HDAC8 in the active site. Binding between HDAC8 and inhibitors was also stabilized by hydrogen bond and hydrophobic interaction. In molecular dynamics simulations, the zinc ion was shown to coordinate one more atom of HDAC8-"linkerless" inhibitor complexes than HDAC8-"pan-" inhibitor complexes. Persistent hydrogen bonds also existed between Tyr306 of HDAC8 and some inhibitors. When inhibitors with large cap groups bound to the active pocket of HDAC8, Phe152 and Met274 shifted from their initial positions and the entrance of the active pocket became more open, resulting in the formation of sub-pocket. Hydrophobic interactions contributed most favorably to the binding free energy between HDAC8 and inhibitors. Lys33, Asp178, Asp267, Tyr306 and Leu308 of HDAC8 were favorable for binding with all inhibitors.

Comparison of the effect of poly(N-vinyl caprolactam) and poly(N-isopropyl acrylamide) trimers on the stability of hydrated Na-montmorillonite: A molecular dynamics study

2020 ◽  
pp. 096739112093524
Author(s):  
Jiafang Xu ◽  
Moussa Camara ◽  
Hualin Liao ◽  
Hong Guo ◽  
Kouassi Louis Kra ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Stable State ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Radius Of Gyration ◽  
Molecular Arrangement ◽  
Isopropyl Acrylamide ◽  
The Stability ◽  
The Impact

In the present study, we performed a molecular dynamics simulation of the intercalation of poly( N-isopropyl acrylamide) (NIPAM)3 and poly( N-vinyl caprolactam) (NVCL)3 trimers into Na-montmorillonite (Na-Mt) to evaluate their effects on the interlayer structure and the stability of hydrated Na-Mt. The impact of both trimers on the interlayer species and their dynamics properties at different temperatures in a canonical ensemble (NVT) were investigated. The results showed that the electrostatic forces exerted by Na cations on H2O molecules and the interlayer H2O molecular arrangement are not affected by the rise in temperature after adding both trimers. Trimer addition reinforced the structure of interlayer H2O molecules so that the effect of temperature increase on them became negligible. The structural dynamics evolution of the radius of gyration of both trimers showed the existence of conformation changes when temperature increased. These conformational changes are more complex in the case of (NVCL)3 than (NIPAM)3 due to its large monomers. Both trimers reduced the mobility of interlayer particles with a better inhibition effect obtained for (NVCL)3 compared to (NIPAM)3. The concentration profile of interlayers’ species showed the affinity of Na cations for clay mineral surfaces while H2O molecules moved away. Compared these two trimers, the most stable state of Na-Mt is achieved with (NVCL)3. These results could help highlight the inhibition properties of (NIPAM)3 and (NVCL)3 on hydrated Na-Mt and to predict its stability against changes in environmental conditions.

scholarly journals Molecular Dynamics Simulations on Influence of Defect on Thermal Conductivity of Silicon Nanowires

2021 ◽  
Vol 9 ◽  
Author(s):  
Hao Li ◽  
Qiancheng Rui ◽  
Xiwen Wang ◽  
Wei Yu
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Silicon Nanowires ◽  
Surface Defects ◽  
Low Frequency ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
The Impact

A non-equilibrium molecular dynamics simulation method is conducted to study the thermal conductivity (TC) of silicon nanowires (SiNWs) with different types of defects. The impacts of defect position, porosity, temperature, and length on the TC of SiNWs are analyzed. The numerical results indicate that SiNWs with surface defects have higher TC than SiNWs with inner defects, the TC of SiNWs gradually decreases with the increase of porosity and temperature, and the impact of temperature on the TC of SiNWs with defects is weaker than the impact on the TC of SiNWs with no defects. The TC of SiNWs increases as their length increases. SiNWs with no defects have the highest corresponding frequency of low-frequency peaks of phonon density of states; however, when SiNWs have inner defects, the lowest frequency is observed. Under the same porosity, the average phonon participation of SiNWs with surface defects is higher than that of SiNWs with inner defects.

scholarly journals Molecular Dynamics Simulations to Investigate How PZM21 Affects the Conformational State of the μ-Opioid Receptor Upon Activation

2020 ◽  
Vol 21 (13) ◽  
pp. 4699 ◽  
Author(s):  
Zhennan Zhao ◽  
Tingting Huang ◽  
Jiazhong Li
Keyword(s):  
Molecular Dynamics ◽  
Side Effects ◽  
G Protein ◽  
Opioid Receptor ◽  
Conformational Changes ◽  
Opioid Analgesics ◽  
Dynamics Simulation ◽  
Analgesic Effects ◽  
Μ Opioid Receptor ◽  
Dynamics Simulations

Opioid analgesics such as morphine have indispensable roles in analgesia. However, morphine use can elicit side effects such as respiratory depression and constipation. It has been reported that G protein-biased agonists as substitutes for classic opioid agonists can alleviate (or even eliminate) these side effects. The compounds PZM21 and TRV130 could be such alternatives. Nevertheless, there are controversies regarding the efficacy and G protein-biased ability of PZM21. To demonstrate a rationale for the reduced biasing agonism of PZM21 compared with that of TRV130 at the molecular level, we undertook a long-term molecular dynamics simulation of the μ-opioid receptor (MOR) upon the binding of three ligands: morphine, TRV130, and PZM21. We found that the delayed movement of the W2936.48 (Ballesteros–Weinstein numbering) side chain was a factor determining the dose-dependent agonism of PZM21. Differences in conformational changes of W3187.35, Y3267.43, and Y3367.53 in PZM21 and TRV130 explained the observed differences in bias between these ligands. The extent of water movements across the receptor channel was correlated with analgesic effects. Taken together, these data suggest that the observed differences in conformational changes of the studied MOR–ligand complexes point to the low-potency and lower bias effects of PZM21 compared with the other two ligands, and they lay the foundation for the development of G protein-biased agonists.

Understanding the impact of Fc glycosylation on its conformational changes by molecular dynamics simulations and bioinformatics

2015 ◽  
Vol 11 (12) ◽  
pp. 3415-3424 ◽  
Author(s):  
Yubo Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Effector Function ◽  
Disease Pathogenesis ◽  
Dynamics Simulations ◽  
The Impact

N-linked glycosylation of Fc at N297 plays an important role in its effector function, aberrance of which would cause disease pathogenesis.

scholarly journals The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11590
Author(s):  
Aweke Mulu ◽  
Mulugeta Gajaa ◽  
Haregewoin Bezu Woldekidan ◽  
Jerusalem Fekadu W/mariam
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
World Health ◽  
Main Protease ◽  
Health Organization ◽  
Dynamics Simulations ◽  
Simulation Parameters ◽  
The Impact

The newly occurred SARS-CoV-2 caused a leading pandemic of coronavirus disease (COVID-19). Up to now it has infected more than one hundred sixty million and killed more than three million people according to 14 May 2021 World Health Organization report. So far, different types of studies have been conducted to develop an anti-viral drug for COVID-19 with no success yet. As part of this, silico were studied to discover and introduce COVID-19 antiviral drugs and results showed that protease inhibitors could be very effective in controlling. This study aims to investigate the binding affinity of three curcumin derived polyphenols against COVID-19 the main protease (Mpro), binding pocket, and identification of important residues for interaction. In this study, molecular modeling, auto-dock coupled with molecular dynamics simulations were performed to analyze the conformational, and stability of COVID-19 binding pocket with diferuloylmethane, demethoxycurcumin, and bisdemethoxycurcumin. All three compounds have shown binding affinity −39, −89 and −169.7, respectively. Demethoxycurcumin and bisdemethoxycurcumin showed an optimum binding affinity with target molecule and these could be one of potential ligands for COVID-19 therapy. And also, COVID-19 main protease binding pocket binds with the interface region by one hydrogen bond. Moreover, the MD simulation parameters indicated that demethoxycurcumin and bisdemethoxycurcumin were stable during the simulation run. These findings can be used as a baseline to develop therapeutics with curcumin derived polyphenols against COVID-19.

scholarly journals Ligand-induced DNA conformational changes in proflavine minor groove-bound complexes studied by molecular dynamics simulation

2019 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Dna Intercalation ◽  
Time Range ◽  
Dna Minor Groove ◽  
Dna Conformational Changes

Background: Minor groove binding is a rate-limiting step in proflavine-DNA intercalation reaction. This step is believed also to be responsible for the sequence-dependent kinetics of proflavine binding to DNA. At the same time, most studies are focused on the final stage of the reaction – the intercalation complex, and there is a lack of data concerning the structure and stability of proflavine-DNA minor groove-bound complexes. Objectives: The objective of this study was to investigate the stability of proflavine minor groove-bound complexes with DNA oligonucleotides of different sequence by molecular dynamics simulation and to analyze the DNA conformational changes caused by the proflavine binding. Materials and methods: The molecular dynamics simulations of proflavine minor groove-bound complexes with poly(dA)·poly(dT) and poly(dCG)·poly(dCG) oligonucleotides of 30 bp length were done in program package AMBER12 with explicit water (SPC/E) and ions (NaCl 0.15 M) using force fields FF14SB for DNA and GAFF for ligand. The starting configurations of complexes were obtained by docking method in AutoDock 3.05. After multi-stage equilibration protocol, each system was simulated at T=300 K and p=1 bar for a 50 ns production phase. Then trajectories were post-processed in AMBERTools17 and VMD-1.9.3 packages. Results: Our simulations confirm that proflavine-DNA minor groove-bound complexes are stable in the 50 ns time range but there are some structural rearrangements in them with respect to the initial structures. The narrowing of the DNA minor groove is observed in the proflavine binding site. In proflavine-poly(dCG)·poly(dCG) complex it is more pronounced and is accompanied by the BI/BII transitions in DNA and the reorientation of ligand. In proflavine-poly(dA)·poly(dT) complex the specific intermolecular hydrogen bonds are formed, which are optimized by the changes in opening and propeller twisting of involved AT-base pairs. Complexes are stabilized by the van der Waals and hydrophobic interactions, which are more favorable in the proflavine-poly(dA)·poly(dT) complex. Conclusions: Our results show that the binding of proflavine to a minor groove of DNA induces the conformational changes in the DNA that are important for the resulting complex stability.

scholarly journals The crystal structure of the tetrameric human vasohibin-1–SVBP complex reveals a variable arm region within the structural core

2020 ◽  
Vol 76 (10) ◽  
pp. 993-1000
Author(s):  
Akihito Ikeda ◽  
Seia Urata ◽  
Tadashi Ando ◽  
Yasuhiro Suzuki ◽  
Yasufumi Sato ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Basis ◽  
Regulatory Mechanism ◽  
Hydrophobic Interactions ◽  
Terminal Region ◽  
Dynamics Simulation ◽  
Mutual Exchange ◽  
Structure Determinations ◽  
Dynamics Simulations

Vasohibins regulate angiogenesis, tumor growth, metastasis and neuronal differentiation. They form a complex with small vasohibin-binding protein (SVBP) and show tubulin tyrosine carboxypeptidase activity. Recent crystal structure determinations of vasohibin–SVBP complexes have provided a molecular basis for complex formation, substrate binding and catalytic activity. However, the regulatory mechanism and dynamics of the complex remain elusive. Here, the crystal structure of the VASH1–SVBP complex and a molecular-dynamics simulation study are reported. The overall structure of the complex was similar to previously reported structures. Importantly, however, the structure revealed a domain-swapped heterotetramer that was formed between twofold symmetry-related molecules. This heterotetramerization was stabilized by the mutual exchange of ten conserved N-terminal residues from the VASH1 structural core, which was intramolecular in other structures. Interestingly, a comparison of this region with previously reported structures revealed that the patterns of hydrogen bonding and hydrophobic interactions vary. In the molecular-dynamics simulations, differences were found between the heterotetramer and heterodimer, where the fluctuation of the N-terminal region in the heterotetramer was suppressed. Thus, heterotetramer formation and flexibility of the N-terminal region may be important for enzyme activity and regulation.

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