scholarly journals Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.

2003 ◽  
Vol 50 (3) ◽  
pp. 789-798 ◽  
Author(s):  
Tomasz Róg ◽  
Krzysztof Murzyn ◽  
Marta Pasenkiewicz-Gierula
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Md Simulations ◽  
Computational Method ◽  
Simulation Protocol ◽  
Speed Up ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations complement experimental methods in studies of the structure and dynamics of lipid bilayers. The choice of algorithms employed in this computational method represents a trade-off between the accuracy and real calculation time. The largest portion of the simulation time is devoted to calculation of long-range electrostatic interactions. To speed-up evaluation of these interactions, various approximations have been used. The most common ones are the truncation of long-range interactions with the use of cut-offs, and the particle-mesh Ewald (PME) method. In this study, several multi-nanosecond cut-off and PME simulations were performed to establish the influence of the simulation protocol on the bilayer properties. Two bilayers were used. One consisted of neutral phosphatidylcholine molecules. The other was a mixed lipid bilayer consisting of neutral phosphatidylethanolamine and negatively charged phosphatidylglycerol molecules. The study shows that the cut-off simulation of a bilayer containing charge molecules generates artefacts; in particular the mobility and order of the charged molecules are vastly different from those determined experimentally. In the PME simulation, the bilayer properties are in general agreement with experimental data. The cut-off simulation of bilayers containing only uncharged molecules does not generate artefacts, nevertheless, the PME simulation gives generally better agreement with experimental data.

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

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.

scholarly journals Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Ronak Y. Patel ◽  
Petety V. Balaji
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Membrane Structure ◽  
Lipid Membrane ◽  
Biological Membranes ◽  
Md Simulations ◽  
Atomic Level ◽  
Structure And Dynamics ◽  
Hydrogen Bonding Interactions ◽  
Dynamics Simulations

Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.

scholarly journals Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations

2021 ◽  
Author(s):  
Jingxuan Zhu ◽  
Juexin Wang ◽  
Weiwei Han ◽  
Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Md Simulation ◽  
Biological Process ◽  
Dynamic Networks ◽  
Md Simulations ◽  
Amino Acid Mutation ◽  
Long Range Interactions ◽  
Decoder Architecture ◽  
Dynamics Simulations

Abstract Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference (NRI) model based on a graph neural network (GNN), which adopts an encoder-decoder architecture to simultaneously infer latent interactions to probe protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between the two distant sites in the Pin1, SOD1, and MEK1 systems.

scholarly journals Electrostatic Interactions with Choline and Phosphate Groups Regulate Cisplatin Permeation through a Dioleoylphosphocholine Bilayer

2020 ◽  
Author(s):  
Lorena Ruano ◽  
Gustavo Cárdenas ◽  
Juan Jose Nogueira
Keyword(s):  
Free Energy ◽  
Lipid Bilayers ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Umbrella Sampling ◽  
Energy Minimum ◽  
Free Energy Minimum ◽  
Dynamics Simulations ◽  
First Moment ◽  
Phosphate Groups

The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin in the polar region of the membrane is controlled, in a first moment, by long-range electrostatic interactions with the choline groups, which trap the drug in a shallow free-energy minimum. Then, cisplatin is driven to a deeper free-energy minimum by long-range electrostatic interactions with the phosphate groups. From this minimum to the middle of the bilayer the electrostatic repulsion between cisplatin and the choline groups partially cancels out the electrostatic attraction between cisplatin and the phosphate groups, inducing a general drop of the total interaction with the polar heads. In addition, the attractive interactions with the non-polar tails, which are dominated by van der Waals contributions, gain significance. The large energy barrier found when going from the global minimum to the middle of the membrane indicates that the non-electrostatic interactions between the drug and the non-polar tails are badly reproduced by the fixed point-charge force field used here, and that the introduction of polarization effects are likely necessary.

Molecular Basis Explanation of Imatinib Resistance of Bcr-Abl Due to T315I and P-Loop Mutations from Molecular Dynamics Simulations.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2917-2917
Author(s):  
Tai-Sung Lee ◽  
Steven Potts ◽  
Hagop Kantarjian ◽  
Jorge Cortes ◽  
Francis Giles ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Electrostatic Interactions ◽  
Large Scale ◽  
Resistance Mechanism ◽  
Md Simulations ◽  
Resistance Mechanisms ◽  
Static Structure ◽  
Imatinib Resistance ◽  
Dynamics Simulations

Abstract Molecular dynamics (MD) simulations on the complex of imatinib with the wild-type, T315I, and other 10 P-loop mutants of the tyrosine kinase Bcr-Abl have been performed to study the imatinib resistance mechanism at the atomic level. MD simulations show that large scale computational simulations could offer insight information that a static structure or simple homology modeling methods cannot provide for studying the Bcr-Abl imatinib resistance problem, especially in the case of conformational changes due to remote mutations. By utilizing the Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA) techniques and analyzing the interactions between imatinib and individual residues, imatinib resistance mechanisms not previously thought have been revealed. Non-directly contacted P-loop mutations either unfavorably change the direct electrostatic interactions with imatinib, or cause the conformational changes influencing the contact energies between imatinib and other non-P-loop residues. We demonstrate that imatinib resistance of T315I mainly comes from the breakdown of the interactions between imatinib and E286 and M290, contradictory to previously suggested that the missing hydrogen bonding is the main contribution. We also demonstrate that except for the mutations of the direct contact residues, such as L248 and Y253, the unfavorable electrostatic interaction between P-loop and imatinib is the main reason for resistance for the P-loop mutations. Furthermore, in Y255H, protonation of the histidin is essential for rendering this mutation resistant to Gleevec. Our results demonstrate that MD is a powerful way to verify and predict clinical response or resistance to imatinib and other potential drugs.

scholarly journals Investigating an Efficient and Accurate Protocol for Sampling Structures from Molecular Dynamics Simulations: A Close Look by Different Wavelet Families

2021 ◽  
Author(s):  
Mateus Gonçalves ◽  
Arismar Junior ◽  
Elaine da Cunha ◽  
Teodorico Ramalho
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Md Simulations ◽  
Quantum Calculations ◽  
Sampling Protocol ◽  
Molecular Systems ◽  
Electronic Parameters ◽  
Dynamics Simulations ◽  
Over Time ◽  
Wavelet Family

Molecular Dynamics (MD) simulations are widely used to predict the behavior of molecular systems over time. However, one of the great challenges of MD simulations is how to treat the thousands of configurations obtained from calculations, since the number of the quantum calculations (QM) required for evaluating electronic parameters is too high and, sometimes, computationally impracticable. Thus, an efficient and accurate sampling protocol is essential for combining classical MD and QM calculations. In this article, based on the OWSCA methodology, 93 wavelet signals were analyzed in order to further refine the methodology and identify the best wavelet family for [Fe(H2O)6]2+ and [Mn(H2O)6]2+ complexes in solution. Our results point out that the bior1.3 was the best wavelet, values closest to the experimental data were obtained for both studied systems.

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