scholarly journals Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens’ Minisatellite 33.15-Tagged Transcript pAKT-45 Variants

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Mohd Shahbaaz ◽  
Awad Saeed Al-Samghan ◽  
Arshi Malik ◽  
Sarah Afaq ◽  
Afaf S. Alwabli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homo Sapiens ◽  
Md Simulations ◽  
Early Embryogenesis ◽  
Cellular Proteins ◽  
Conformational Behavior ◽  
Gene Functions ◽  
Mrna Transcripts ◽  
Water Conditions ◽  
Explicit Water

The spermatozoa are transcriptionally dormant entities which have been recognized to be an archive of mRNA, coding for a variety of functionally crucial cellular proteins. This significant repository of mRNA is predicted to be associated with early embryogenesis and postfertilization. The mRNA transcripts which are tagged with minisatellites have been involved in the regulation of the gene functions as well as their organization. However, very little information is available regarding the expression of the transcripts tagged with minisatellites in spermatozoa. Therefore, in order to understand the functions and the conformational behavior of the proteins expressed from these minisatellite-tagged transcripts, we have performed a detailed in silico analysis using the sequences of the transcripts. The protein predicted from KF274549 showed the functionalities similar to uncharacterized C4orf26 proteins, while that obtained from KF274557 predicted to be a metallophosphoesterase. Furthermore, the structural folds in the structure of these predicted proteins were analyzed by using the homology modeling and their conformational behaviors in the explicit water conditions were analyzed by using the techniques of Molecular Dynamics (MD) simulations. This detailed analysis will facilitate the understanding of these proteins in the spermatozoon region and can be used for uncovering other attributes of the metabolic network.

scholarly journals Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number

Polymers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 552
Author(s):  
Andrey O. Kurbatov ◽  
Nikolay K. Balabaev ◽  
Mikhail A. Mazo ◽  
Elena Yu. Kramarenko
Keyword(s):  
Molecular Dynamics ◽  
Functional Materials ◽  
Md Simulations ◽  
Conformational Behavior ◽  
Carbosilane Dendrimers ◽  
Density Profiles ◽  
The Core ◽  
Adsorbed Atoms ◽  
Composition Structure ◽  
Surface Spreading

We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for the design of functional materials on the basis of silicon-containing dendrimers.

scholarly journals Studying Equilibria of Polymers in Solution by Direct Molecular Dynamics Simulations: Poly(N-isopropylacrylamide) in Water as a Test Case

2021 ◽  
Author(s):  
Edder García ◽  
Hans Hasse
Keyword(s):  
Molecular Dynamics ◽  
Coarse Graining ◽  
Md Simulations ◽  
Solvent System ◽  
Test Case ◽  
Equilibration Time ◽  
Production Run ◽  
Large Phase ◽  
Dynamics Simulations ◽  
Explicit Water

It is well known that studying equilibria of polymers in solution by atomistic simulations is computationally demanding as a large phase space has to be adequately sampled. Nevertheless, direct molecular dynamics (MD) simulations are often used for this purpose in the literature. To assess whether such approach is adequate, we have conducted a case study for a polymer+solvent system that has been commonly studied with direct MD simulations by many authors: poly(N-isopropylacrylamide) (PNIPAM) in water. The total simulation time of the present study is much longer than that typically used in MD simulations of that system. A NIPAM chain of 30 monomers was studied in explicit water at 295K. Three initial configurations were used. For each configuration, five replicas were run for 1000ns. The statistical analysis of our data shows that the equilibration time is of the order of 600-700ns and that the remaining time for the production run is not sufficient to sample the equilibrium state adequately. These results underpin the well-known difficulty of sampling equilibrium states of polymers in solution with direct MD simulations and the need for a careful interpretation of results of such studies. The problem with the unsatisfactory sampling persists despite the increasing available computing power. Therefore, enhanced sampling techniques and workarounds, such as simplified scenarios or coarse-graining, remain important.

scholarly journals Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

2017 ◽  
Vol 13 ◽  
pp. 714-719 ◽  
Author(s):  
Franca Castiglione ◽  
Fabio Ganazzoli ◽  
Luciana Malpezzi ◽  
Andrea Mele ◽  
Walter Panzeri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Inclusion Complexes ◽  
Water Solution ◽  
Md Simulations ◽  
Conformational Transitions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fused Ring ◽  
Explicit Water

Tricyclic fused-ring cyclobenzaprine (1) and amitriptyline (2) form 1:1 inclusion complexes with β-cyclodextrin (β-CD) in the solid state and in water solution. Rotating frame NOE experiments (ROESY) showed the same geometry of inclusion for both 1/β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD) simulations in solution and in the solid state from single-crystal X-ray diffraction of 1/β-CD and 2/β-CD complexes. The latter complex was found in a single conformation in the solid state, whilst the MD simulations in explicit water reproduced the conformational transitions observed experimentally for the free molecule.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Andrey Sarikov ◽  
Anna Marzegalli ◽  
Luca Barbisan ◽  
Massimo Zimbone ◽  
Corrado Bongiorno ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stacking Faults ◽  
Md Simulations ◽  
Stacking Fault ◽  
Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

scholarly journals Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2621
Author(s):  
Seunghwa Yang
Keyword(s):  
Molecular Dynamics ◽  
Load Transfer ◽  
Cell Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Covalent Grafting ◽  
Modelling Strategies ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

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