scholarly journals A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers

2022 ◽  
Author(s):  
Chanadan Douykhumklaw ◽  
Thana Sutthibutpong
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Template Molecule ◽  
Aniline Oligomers ◽  
The Mean ◽  
The Stability ◽  
Further Development ◽  
Aniline Oligomer

Abstract Molecularly imprinted polymers (MIP) are the polymers created by molecular imprinting techniques that leave cavities for the specific interactions with a template molecule, and have been applied in molecular selectivity tasks. In this study, the molecular dynamics (MD) simulation technique was used to demonstrate that aniline oligomer could be developed as a potential MIP for detection and separation of the spectinomycin drug molecule for gonorrhoea treatment. MD simulations were performed for the systems of a spectinomycin within aniline oligomers of different sizes. The mean square displacement (MSD) and the diffusivity calculated from MD simulations showed that the diffusion coefficient was significantly dropped when the length of aniline oligomer was greater than two. The diffusion coefficient of spectinomycin became the lowest within aniline trimers, corresponded to the highest atomic distribution of MIP around the template. Then, the specific cavity in MIP systems with and without spectinomycin were calculated to assess the stability of the cavity created by the template. The volume of a cavity created within the trimer system was closest to the spectinomycin volume, and therefore became the optimal oligomer size for further development of MIP.

New View of Low-Temperature Sintering Phenomenon of Nanometer-Size Particles Based on Molecular Dynamics Study

MRS Advances ◽  
2016 ◽  
Vol 1 (30) ◽  
pp. 2167-2172
Author(s):  
Norie Matsubara ◽  
Shinji Munetoh ◽  
Osamu Furukimi
Keyword(s):  
Molecular Dynamics ◽  
Surface Layer ◽  
Diffusion Coefficient ◽  
Heating Temperature ◽  
Md Simulations ◽  
Atomic Scale ◽  
Self Diffusion ◽  
The Mean ◽  
The Relationship ◽  
Self Diffusion Coefficient

ABSTRACTIn this study, we have investigated a behavior of particle with diameter several ten nanometers size at the time of heating on an atomic scale by numerical analysis using the molecular dynamics (MD) simulation. On solving the equation of motion, the Langevin equation was adopted. The Finnis-Sinclair potential, which can well reproduce the mechanical properties of a BCC-metal, was used as the interatomic force. We determined the relationship between the melting point (Tm) of the nano-sized particles and its diameter by MD simulations. We have also investigated the self-diffusion coefficient of each atom-forming at a temperature larger or less than Tm of the submicron-size metal particles . As a result, even in case of heating at a temperature larger than Tm, the mean self-diffusion coefficient at the center of a particle was 10-7–10-6 cm2/sec. On the other hand, at the surface layer of the particle was two to three orders of magnitude larger than that at the center. Those particles were in a quasi-molten state. It is conceivable that the thickness of the surface layer can explain a phenomenon that sintering progresses as the heating temperature increases.

The Influence of Graphene Sheet on the Dynamics of Cholesterol Molecules in the Lodgment Located near a Transmembrane Protein – MD Study

2008 ◽  
Vol 140 ◽  
pp. 141-146
Author(s):  
P. Raczynski ◽  
A. Dawid ◽  
Z. Gburski
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Graphene Sheet ◽  
Transmembrane Protein ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Mean Square ◽  
Velocity Autocorrelation ◽  
The Mean ◽  
Velocity Autocorrelation Functions

Molecular dynamics (MD) simulations have been made for a cluster of cholesterols localized near the transmembrane protein at the physiological temperature of 310 K. It was observed that the cholesterol molecules form a lodgment on the surface of protein. Additional studies were made of the influence of graphene sheet on several physical observables of cholesterol molecules including: the radial distribution function, the mean square displacement, diffusion coefficient and the linear and angular velocity autocorrelation functions.

Molecular Dynamics Study of Microscopic Mechanism of Diffusion in Li2SiO3 System

1991 ◽  
Vol 46 (7) ◽  
pp. 616-620 ◽  
Author(s):  
Junko Habasaki
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Md Simulation ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Lithium Ions ◽  
Microscopic Mechanism ◽  
Trapping Model ◽  
The Mean

MD simulation has been performed to learn the microscopic mechanism of diffusion of ions in the Li2SiO3 system. The motion of lithium ions can be explained by the trapping model, where lithium is trapped in the polyhedron and moves with fluctuation of the coordination number. The mean square displacement of lithium was found to correlate well with the net changes in coordination number.

scholarly journals Structural Properties of G,T-Parallel Duplexes

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Anna Aviñó ◽  
Elena Cubero ◽  
Raimundo Gargallo ◽  
Carlos González ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Theoretical Calculations ◽  
Md Simulations ◽  
Theoretical Studies ◽  
Duplex Structure ◽  
Strong Stabilization ◽  
The Stability ◽  
The Impact

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

scholarly journals Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism

2018 ◽  
Vol 19 (11) ◽  
pp. 3524 ◽  
Author(s):  
Guodong Hu ◽  
Xiu Yu ◽  
Yunqiang Bian ◽  
Zanxia Cao ◽  
Shicai Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Noncoding Rna ◽  
Md Simulations ◽  
Normal Function ◽  
Toxin Complex ◽  
Potentials Of Mean Force ◽  
Protein Toxins ◽  
Function Relationship ◽  
The Stability ◽  
Smd Simulations

ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.

Cooperative Premelting Effects on a (110) FCC Surface: A Molecular Dynamics Study

1985 ◽  
Vol 63 ◽  
Author(s):  
V. Rosato ◽  
V. Pontikis ◽  
G. Ciccotti
Keyword(s):  
Molecular Dynamics ◽  
Order Parameter ◽  
Mean Square Displacement ◽  
Excess Energy ◽  
Surface Layers ◽  
Defect Production ◽  
Free Surfaces ◽  
Lennard Jones ◽  
Coexistence Line ◽  
The Mean

ABSTRACTThe thermodynamicaL and structural behavior of a (110) face of a (12–6) Lennard-Jones fcc solid has been investigated by MoLecuLar Dynamics computer simulation on the solid-gas coexistence Line up to a temperature T= 0.94 TM (TM: melting point). We have found evidence for cooperative defect production on free surfaces which Leads to a structural transitiDn above T≈0.7 TM. This transition is studied using as an order parameter the excess energy for surface Layers due to missing bonds parallel to the surface with respect to the bulk. Furthermore we report the vaLues of the mean square displacement for surface and bulk atoms as a function of temperature. Despite their high values at the surface, surface Layers are not molten but only highly disordered above the transition temperature.

scholarly journals Stability of Two-quartet G-quadruplexes and Their Dimers in Atomistic Simulations

2019 ◽  
Author(s):  
Barira Islam ◽  
Petr Stadlbauer ◽  
Michaela Vorlíčková ◽  
Jean-Louis Mergny ◽  
Michal Otyepka ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
The Other ◽  
Atomistic Simulations ◽  
Structural Element ◽  
Dna And Rna ◽  
Open Issue ◽  
Water Models ◽  
Weakly Stable ◽  
The Stability

ABSTRACTG-quadruplexes (GQs) are four-stranded non-canonical DNA and RNA architectures that can be formed by guanine-rich sequences. The stability of GQs increases with the number of G-quartets and three G-quartets generally form stable GQs. However, the stability of two-quartet GQs is an open issue. To understand the intrinsic stability of two-quartet GQ stems, we have carried out a series of unbiased molecular dynamics (MD) simulations (∼505 µs in total) of two- and four-quartet DNA and RNA GQs, with attention paid mainly to parallel-stranded arrangements. We used AMBER DNA parmOL15 and RNA parmOL3 force fields and tested different ion and water models. DNA two-quartet parallel-stranded GQs unfolded in all the simulations while the equivalent RNA GQ was stable in most of the simulations. GQs composed of two stacked units of two-quartet GQs were stable for both DNA and RNA. The simulations suggest that a minimum of three quartets are needed to form an intrinsically stable all-anti parallel-stranded DNA GQ. Parallel two-quartet DNA GQ may exist if substantially stabilized by another molecule or structural element, including multimerisation. On the other hand, we predict that isolated RNA two-quartet parallel GQs may form, albeit being weakly stable. We also show that ionic parameters and water models should be chosen with caution because some parameter combinations can cause spurious instability of GQ stems. Some in-so-far unnoticed limitations of force-field description of multiple ions inside the GQs are discussed, which compromise capability of simulations to fully capture the effect of increase of the number of quartets on the GQ stability.

scholarly journals Forever Young: Structural Stability of Telomeric Guanine-Quadruplexes in Presence of Oxidative DNA Lesions

2020 ◽  
Author(s):  
Tom Miclot ◽  
Camille Corbier ◽  
Alessio Terenzi ◽  
Cécilia Hognon ◽  
Stéphanie Grandemange ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Molecular Dynamics ◽  
Structural Stability ◽  
Md Simulations ◽  
Dna Lesions ◽  
Computational Investigation ◽  
Telomeric Dna ◽  
G Quadruplex ◽  
The Stability

AbstractHuman telomeric DNA (h-Telo), in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics (MD) simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.

scholarly journals Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Entropy ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 405
Author(s):  
Piotr Weber ◽  
Piotr Bełdowski ◽  
Krzysztof Domino ◽  
Damian Ledziński ◽  
Adam Gadomski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
Mean Square Displacement ◽  
Conformational Space ◽  
Global Dynamics ◽  
Mean Square ◽  
Conformational Entropy ◽  
The Mean ◽  
Dynamics Simulations

This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes type exponent of 0 . 4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher’s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal–Wallis test, we also analyze differences between the mean root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306 K – 309 K are different than in another temperature. Using the Kullback–Leibler theory, we investigate differences between the distribution of the mean root mean square displacement for each temperature and time window.

scholarly journals A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

2017 ◽  
Author(s):  
Wei Chen ◽  
Zhiye Tang ◽  
Tim Cholko ◽  
Chia-en A. Chang
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Ligand Binding ◽  
Md Simulations ◽  
Electrostatic Energy ◽  
Major Protein ◽  
Type I ◽  
Type Ii ◽  
Protein Motions ◽  
The Stability

AbstractThe activities of CDK8 with partner Cyclin C (CycC) are a common feature of many diseases, especially cancers. Here we report the study of dynamic behaviors and energy profiles of 13 CDK8/CycC systems, including the DMG-in and DMG-out conformations as well as 5 type I ligands and 5 type II ligands, with all-atom unbiased molecular dynamics (MD) simulations. We observed numerous regional motions within CDK8, which move in concert to form five major protein motions. The motion of the activation loop doesn’t appear to influence the binding of both types of ligands. Type I ligands remarkably reduce the motion of the C-terminal tail through the strong cation-π interaction between the ligands and ARG356, and type II ligands stabilize the αC helix by forming stable hydrogen bonds with GLU66. The MD calculations also confirmed the importance of CycC to the stability of the CDK8 system as well as the ligand binding. The MMPB/SA results show that van der Waals interaction is the main driving force for the binding of both types of ligands, but electrostatic energy and entropy penalty plays important roles in the binding of type II ligands. The volume analysis results indicate that the induced fitting theory applies in the binding of type I ligands. These results would help to improve the affinities of the existing ligands. Our MD work is complementary to crystal structures and may have implications in the development of new CDK8 inhibitors as well as in the field of drug discovery.

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