scholarly journals The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5403
Author(s):  
Hangxin Liu ◽  
Shuqing Xiang ◽  
Haomiao Zhu ◽  
Li Li
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Biological Significance ◽  
Mean Square Displacement ◽  
Chemical Properties ◽  
Dynamics Simulation ◽  
Hydration Water ◽  
Total Change ◽  
Dynamical Properties ◽  
Dynamics Simulations

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.

scholarly journals Structural and Dynamic Properties of Hydrophobic Eutectic Solvents Based on Menthol and Fatty Acids: a Molecular Dynamics Simulation Study

2021 ◽  
Author(s):  
Samaneh Barani Pour ◽  
Jaber Jahanbin Sardroodi ◽  
Alireza Rastkar Ebrahimzadeh
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acids ◽  
Dynamic Properties ◽  
Mean Square Displacement ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Eutectic Mixtures ◽  
Dynamical Properties ◽  
Reorientation Dynamics ◽  
Dynamics Simulations

Abstract The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. We focused on the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions(CDFs), the radial distribution functions (RDFs), and the angular distribution functions (ADFs), and the Hydrogen bonding network between species and Spatial distribution functions (SDF). Further interaction between menthol and Caprylic acid molecules was confirmed by the results of these analyzes. Also, the transport properties of the mixtures were investigated by using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. The simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamical Properties ◽  
Dynamics Simulations

Molecular dynamics simulations were applied to an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, to gain insights into the structural and dynamical properties.

Molecular dynamics simulation of aggregation of monocrystal and polycrystal copper nanoparticles

2019 ◽  
Vol 33 (16) ◽  
pp. 1950168
Author(s):  
Linxing Zhang ◽  
Guang Hong ◽  
Shouyin Cai
Keyword(s):  
Molecular Dynamics ◽  
Lattice Structure ◽  
Displacement Vector ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Gyration Radius ◽  
Mean Square ◽  
Shrinkage Ratio ◽  
Lower Temperature ◽  
Dynamics Simulations

Molecular dynamics simulations were employed to investigate the aggregation of monocrystal and polycrystal nanoparticles. The lattice structure, displacement vector, potential energy, shrinkage ratio, relative gyration radius and mean square displacement of the two systems are compared. The results indicate that the aggregation of polycrystal nanoparticles is more drastic than that of monocrystal nanoparticles. Besides, the polycrystal nanoparticles are found contacted and melted at lower-temperature than that of monocrystal nanoparticles. The reason for all these phenomena is that there is additional surface energy in the grain boundary of polycrystal nanoparticles.

A Molecular Dynamics Simulation of the Transport Properties of Molten (La1/3, K)Cl

2005 ◽  
Vol 60 (3) ◽  
pp. 187-192 ◽  
Author(s):  
Masahiko Matsumiya ◽  
Koichi Seo
Keyword(s):  
Molecular Dynamics ◽  
Charge Asymmetry ◽  
The Self ◽  
Dynamics Simulation ◽  
Alkali Chloride ◽  
Self Diffusion ◽  
Dynamical Properties ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
Self Diffusion Coefficient

Molecular dynamics simulations of molten (La1/3, K)Cl at 1123 K have been performed in order to investigate the correlation between simulated dynamical properties such as the self-exchange velocity (ν), the self-diffusion coefficient (D) and the electrical conductivity (κ) and the corresponding experimental values. The simulated results revealed that v and D of potassium decrease with increasing mole fraction of lanthanum, as expected from the experimental internal cation mobilities, b. The decrease of bK, νK and DK is ascribed to the tranquilization effect by La3+, which strongly interacts with Cl−. In contrast, bLa, νLa, and DLa increase with increasing concentration of La3+. The distorted linkage of the network structure of [LaCl6]3− units was disconnected with increasing the concentration of the alkali chloride. This might be attributed to the stronger association of La3+ with Cl− due to the enhanced charge asymmetry of the two cations neighboring Cl−. The sequence of the calculated v’s, D’s, and κ’s is consistent with those of the referred experimental results.

scholarly journals Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Fancui Meng
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Md Simulation ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Simulation Time ◽  
Dynamics Method

The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.

scholarly journals Effects of H2A.B incorporation on nucleosome structures and dynamics

2020 ◽  
Author(s):  
Havva Kohestani ◽  
Jeff Wereszczynski
Keyword(s):  
Molecular Dynamics ◽  
Gene Transcription ◽  
Molecular Mechanisms ◽  
Chemical Properties ◽  
Dynamics Simulation ◽  
Enhanced Sampling ◽  
Entry And Exit ◽  
Nucleosome Core ◽  
Dna Accessibility ◽  
Dynamics Simulations

ABSTRACTThe H2A.B histone variant is an epigenetic regulator involved in transcriptional upregulation, DNA synthesis, and splicing that functions by replacing the canonical H2A histone in the nucleosome core particle. Introduction of H2A.B results in less compact nucleosome states with increased DNA unwinding and accessibility at the nucleosomal entry and exit sites. Despite being well characterized experimentally, the molecular mechanisms by which H2A.B incorporation alters nucleosome stability and dynamics remain poorly understood. To study the molecular mechanisms of H2A.B, we have performed a series of conventional and enhanced sampling molecular dynamics simulation of H2A.B and canonical H2A containing nucleosomes. Results of conventional simulations show that H2A.B weakens protein/protein and protein/DNA interactions at specific locations throughout the nucleosome. These weakened interactions result in significantly more DNA opening from both the entry and exit sites in enhanced sampling simulations. Furthermore, free energy profiles show that H2A.B containing nucleosomes have significantly broader free wells, and that H2A.B allows for sampling of states with increased DNA breathing, which are shown to be stable on the hundreds of nanoseconds timescale with further conventional simulations. Together, our results show the molecular mechanisms by which H2A.B creates less compacted nucleosome states as a means of increasing genetic accessibility and gene transcription.SIGNIFICANCENature has evolved a plethora of mechanisms for altering the physical and chemical properties of chromatin fibers as a means of controlling gene expression. These epigenetic processes may serve to increase or decrease DNA accessibility, manage the recruitment of remodeling factors, or tune the stability of the nucleosomes that make up chromatin. Here, we have used both conventional and enhanced sampling molecular dynamics simulations to understand how one of these epigenetic mechanisms, the substitution of canonical H2A proteins with the H2A.B variant, exerts its influence on the structures and dynamics of the nucleosome. Results show at the molecular level how this variant alters inter-molecular interactions to increase DNA accessibility as a means of increasing genetic accessibility and gene transcription.

Molecular dynamics simulation and free energy analysis of the interaction of platinum-based anti-cancer drugs with DNA

2016 ◽  
Vol 15 (06) ◽  
pp. 1650054 ◽  
Author(s):  
Seifollah Jalili ◽  
Mina Maddah ◽  
Jeremy Schofield
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Hydrogen Bonds ◽  
Binding Free Energy ◽  
Double Helix ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Cancer Drugs ◽  
Anti Cancer ◽  
Dynamics Simulations

Cisplatin and oxaliplatin are two widely-used anti-cancer drugs which covalently bind to a same location in DNA strands. Platinum agents make intrastrand and interstrand cross-links with the N7 atoms of guanine nucleotides which prevent DNA from polymerization by causing a distortion in the double helix. Molecular dynamics simulations and free energy calculations were carried out to investigate the binding of two platinum-based anti-cancer drugs with DNA. We compared the binding of these drugs which differ in their carrier ligands, and hence their potential interactions with DNA. When a platinum agent binds to nucleotides, it causes a high amount of deformation in DNA structure. To find the extent of deformation, torsion angles and base pair and groove parameters of DNA were considered. These parameters were compared with normal B-DNA which was considered as the undamaged DNA. The formation of hydrogen bonds between drugs and DNA nucleotides was examined in solution. It was shown that oxaliplatin forms more hydrogen bonds than cisplatin. Our results confirm that the structure of the platinated DNA rearranges significantly and cisplatin tries to deform DNA more than oxaliplatin. The binding free energies were also investigated to understand the affinities, types and the contributions of interactions between drugs and DNA. It was concluded that oxaliplatin tendency for binding to DNA is more than cisplatin in solvent environment. The binding free energy was calculated based on the MM/PBSA and MM/GBSA methods and the results of QM/MM calculations verified them.

scholarly journals Exploring interfacial dynamics in homodimeric S-ribosylhomocysteine lyase (LuxS) from Vibrio cholerae through molecular dynamics simulations

RSC Advances ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 1700-1714
Author(s):  
Khair Bux ◽  
Thomas S. Hofer ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Vibrio Cholerae ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Interfacial Dynamics ◽  
Dimeric Form ◽  
Dynamical Properties ◽  
Dynamics Simulations

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme.

scholarly journals Hydration and its Hydrogen Bonding State on a Protein Surface in the Crystalline State as Revealed by Molecular Dynamics Simulation

2021 ◽  
Vol 9 ◽  
Author(s):  
Hiroshi Nakagawa ◽  
Taro Tamada
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystalline State ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Protein Crystal ◽  
Hydration Water ◽  
Protein Surface ◽  
Bonding State

Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules form a hydration water network on a protein surface via hydrogen bonds. This study examined the hydration structure and hydrogen bonding state of a protein, staphylococcal nuclease, at various hydration levels in its crystalline state by all-atom molecular dynamics (MD) simulation. Hydrophilic residues were more hydrated than hydrophobic residues. As the water content increases, both types of residues were uniformly more hydrated. The number of hydrogen bonds per single water asymptotically approaches 4, the same as bulk water. The distances and angles of hydrogen bonds in hydration water in the protein crystal were almost the same as those in the tetrahedral structure of bulk water regardless of the hydration level. The hydrogen bond structure of hydration water observed by MD simulations of the protein crystalline state was compared to the Hydrogen and Hydration Database for Biomolecule from experimental protein crystals.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

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