scholarly journals How a Hemicarcerand Incarcerates Guests at Room Temperature Decoded with Modular Simulations

2020 ◽  
Author(s):  
Katherine G. McFerrin ◽  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Model Building ◽  
Three Dimensional ◽  
Building Blocks ◽  
Water Soluble ◽  
Modular Approach ◽  
Molecular Complexation ◽  
Three Dimensional Models ◽  
Dynamics Simulations

AbstractHemicarcerands are host molecules created to study constrictive binding with guest molecules for insights into the rules of molecular complexation. However, the molecular dynamics simulations that facilitate such studies have been limited because three-dimensional models of hemicarcerands are tedious to build and their atomic charges are complicated to derive. There have been no molecular dynamics simulations of the reported water-soluble hemicarcerand (Octacid4) that explain how it uniquely encapsulates its guests at 298 K and keeps them encapsulated at 298 K in NMR experiments. Herein we report a modular approach to hemicarcerand simulations that simplifies the model building and charge derivation in a manner reminiscent of the approach to protein simulations with truncated amino acids as building blocks. We also report that apo Octacid4 in water adopts two clusters of conformations, one of which has an equatorial portal open thus allowing guests to enter the cavity of Octacid4, in microsecond molecular dynamics simulations performed using the modular approach at 298 K. Under the same simulation conditions, the guest-bound Octacid4 adopts one cluster of conformations with all equatorial portals closed thus keeping the guests incarcerated. These results explain the unique constrictive binding of Octacid4 and suggest that the guest-induced host conformational change that impedes decomplexation is a previously unrecognized conformational characteristic that promotes strong molecular complexation.

scholarly journals How the water-soluble hemicarcerand incarcerates guests at room temperature decoded with modular simulations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Katherine G. McFerrin ◽  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Room Temperature ◽  
Model Building ◽  
Three Dimensional ◽  
Building Blocks ◽  
Water Soluble ◽  
Molecular Complexation ◽  
Three Dimensional Models ◽  
Dynamics Simulations

AbstractMolecular dynamics simulations of hemicarcerands and related variants allow the study of constrictive binding and offer insight into the rules of molecular complexation, but are limited because three-dimensional models of hemicarcerands are tedious to build and their atomic charges are complicated to derive. There have been no molecular dynamics simulations of the reported water-soluble hemicarcerand (Octacid4) that explain how Octacid4 encapsulates guests at 298 K and keeps them encapsulated at 298 K in NMR experiments. Herein we report a modular approach to hemicarcerand simulations that simplifies the model building and charge derivation in a manner reminiscent of the approach to protein simulations with truncated amino acids as building blocks. We also report that in aqueous molecular dynamics simulations at 298 K apo Octacid4 adopts two clusters of conformations one of which has an equatorial portal open but the guest-bound Octacid4 adopts one cluster of conformations with all portals closed. These results explain how Octacid4 incarcerates guests at room temperature and suggest that the guest-induced host conformational change that impedes decomplexation is a previously unrecognized conformational characteristic that promotes strong molecular complexation.

scholarly journals Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

2018 ◽  
Vol 115 (45) ◽  
pp. 11519-11524 ◽  
Author(s):  
Caitlin M. Quinn ◽  
Mingzhang Wang ◽  
Matthew P. Fritz ◽  
Brent Runge ◽  
Jinwoo Ahn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Building Blocks ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Capsid Assembly ◽  
Dynamic Regulation ◽  
Angle Spinning ◽  
Dynamics Simulations ◽  
Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

Molecular-Dynamics Simulations of Granular Axial Segregation in a Rotating Cylinder

1998 ◽  
Vol 12 (04) ◽  
pp. 115-122 ◽  
Author(s):  
Sakamoto Shoichi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Process ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Rotating Cylinder ◽  
Axial Segregation ◽  
Cohesive Forces ◽  
Dynamics Simulations ◽  
Different Diameters ◽  
Narrow Bands

In order to investigate segregation of granular binary-mixtures in a horizontally rotating cylinder, three-dimensional molecular dynamics simulations are carried out. Two kinds of particles, which have different diameters and/or different roughness of surfaces, are segregated into three bands. It is found that particles receive averaged force cohesively at the boundaries of segregated bands. The present analysis shows that segregated narrow bands are formed by diffusion process and that the cohesive forces operating at the boundaries stabilize them.

Molecular Dynamics Simulations of Coupling between Flow and Heat Transfer in a Nanochannel

2012 ◽  
Vol 455-456 ◽  
pp. 155-160
Author(s):  
Zhi Hai Kou ◽  
Min Li Bai
Keyword(s):  
Heat Transfer ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wall Temperature ◽  
Solid Wall ◽  
Slip Length ◽  
Three Dimensional ◽  
Flow And Heat Transfer ◽  
Kapitza Length ◽  
Dynamics Simulations

Simulation of microscale thermo-fluidic transport has attracted considerable attention in recent years owing to rapid advances in nanoscience and nanotechnology. The three-dimensional molecular dynamics simulations are performed for coupling between flow and heat transfer in a nanochannel. Effects of interface wettability, shear rate and wall temperature are discussed. It is found that there exist the relatively immobile solid-like layers adjacent to each solid wall with higher number density. Both slip length and Kapitza length at the solid-liquid interface increase linearly with the increasing wall temperature. The Kapitza length decreases monotonously with the increasing shear rates. The slip length is found to be overestimated by 5.10% to 10.27%, while Kapitza length is overestimated by 8.92% to 19.09% for the solid-solid interaction modeled by the Lennard-Jones potential.

Catalyzed β scission of a carbenium ion III — Scission observed in ab initio molecular dynamics simulations

2009 ◽  
Vol 87 (10) ◽  
pp. 1512-1520 ◽  
Author(s):  
Greg M. Berner ◽  
Allan L. L. East
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Time Windows ◽  
Three Dimensional ◽  
Ab Initio Molecular Dynamics ◽  
Catalytic Systems ◽  
Carbenium Ions ◽  
Carbenium Ion ◽  
Dynamics Simulations

The β scission (cracking) of branched carbenium ions have been observed in molecular dynamics simulations, possibly for the first time. Simulations were performed with molecular dynamics based on PW91 density functional theory, and which included three-dimensional periodic boundary replication of the unit cell to mimic long-range bulk effects. A rising-temperature algorithm was used to encourage reaction within the narrow time windows (∼10 ps) of the simulations. Twenty-eight simulations were performed, featuring alkyl ions in three different catalytic systems: the ionic liquid, [(C5H5NH+)5(Al2Cl7−)6]−, the chabazite zeolite, [AlSi23O48]−, and the chabazite zeolite, [Al4Si20O45(OH)3]−. Twenty-four runs began with unbranched sec-n-alkyl ions, but only one exhibited β scission, and only after branching to a tertiary ion and under extreme heating. In contrast, the four simulations that began with branched alkyl ions were all successful in demonstrating β scission at lower temperatures: 2,4,4-trimethyl-2-pentyl ion and 2,4-dimethyl-2-hexyl ion in each of the first two catalysts. The lifetimes of desorbed alkyl ions in the chabazite models were < 5 ps at 1000–1500 K. The β scission results support the classical Weitkamp et al. ( Appl. Catal. 1983, 8, 123 ) mechanism over the nonclassical Sie ( Ind. Eng. Chem. Res. 1992, 31, 1881 ) and the chemisorping Kazansky et al. ( J. Catal. 1989, 119, 108 ) mechanisms.

scholarly journals QM/MM description of periodic systems

2015 ◽  
Vol 14 (07) ◽  
pp. 1550054 ◽  
Author(s):  
K. Doll ◽  
T. Jacob
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Liquid Water ◽  
Three Dimensional ◽  
Water Dimer ◽  
Periodic Systems ◽  
Quantum Mechanical ◽  
Dynamics Simulations

A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.

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