scholarly journals Adiabatic Approximation in Explicit Solvent Models of RedOx Chemistry

2016 ◽  
Vol 12 (10) ◽  
pp. 5111-5116 ◽  
Author(s):  
Valérie Vaissier ◽  
Troy Van Voorhis
Keyword(s):  
Adiabatic Approximation ◽  
Redox Chemistry ◽  
Solvent Models ◽  
Explicit Solvent

scholarly journals Making Soup: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm

2019 ◽  
Author(s):  
Leandro Oliveira Bortot ◽  
Zahedeh Bashardanesh ◽  
David van der Spoel
Keyword(s):  
Large Scale ◽  
Biological Properties ◽  
Computational Power ◽  
E Coli ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Computational Modeling And Simulation ◽  
Dynamics Simulations ◽  
The Individual ◽  
Bacterial Cytoplasm

Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to the dilute environment present in experiments made with isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. As computational power increased, modeling and simulating large scale all-atom explicit solvent models of the prokaryote cytoplasm become possible. In this work, we build an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submit it to a total of 3 μs of molecular dynamics simulations. The properties of biomolecules under crowding conditions are compared to those from simulations of the individual compounds under dilute conditions. The simulation model is found to be consistent with experimental data about the diffusion coefficient and stability of macromolecules under crowded conditions. In order to stimulate further work we provide a Python script and a set of files that enables other researchers to build their own E. coli cytoplasm models to address questions related to crowding.<br>

Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

2019 ◽  
Vol 18 (03) ◽  
pp. 1950015
Author(s):  
Zhaoxi Sun ◽  
Xiaohui Wang
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Hydrogen Bonds ◽  
Force Fields ◽  
Implicit Solvent ◽  
Conformational Ensemble ◽  
Helix Formation ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Amber Force Fields

Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.

Modeling Solvent Broadening on the Vibronic Spectra of a Series of Coumarin Dyes. From Implicit to Explicit Solvent Models

2015 ◽  
Vol 11 (12) ◽  
pp. 5810-5825 ◽  
Author(s):  
Javier Cerezo ◽  
Francisco J. Avila Ferrer ◽  
Giacomo Prampolini ◽  
Fabrizio Santoro
Keyword(s):  
Vibronic Spectra ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Coumarin Dyes

scholarly journals Explicit solvent models in protein pKa calculations

1996 ◽  
Vol 71 (1) ◽  
pp. 138-147 ◽  
Author(s):  
C.J. Gibas ◽  
S. Subramaniam
Keyword(s):  
Pka Calculations ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Protein Pka

scholarly journals The Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin

2019 ◽  
Author(s):  
Peng He ◽  
Sheila Sarkar ◽  
Emilio Gallicchio ◽  
Tom Kurtzman ◽  
Lauren Wickstrom
Keyword(s):  
Conformational Equilibrium ◽  
Implicit Solvent ◽  
Theory Analysis ◽  
State Behavior ◽  
Generalized Born ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Opening And Closing

<p>This study investigates the role of hydration and its relationship to the conformational equilibrium of the host molecule β-cyclodextrin. Molecular dynamics simulations indicate that the unbound β-cyclodextrin exhibits two state behavior in explicit solvent due to the opening and closing of its cavity. In implicit solvent, these transitions are not observed and there is one dominant conformation of β-cyclodextrin with an open cavity. Based on these observations, we investigate the hypothesis that the expulsion of thermodynamically unfavorable water molecules into the bulk plays an important role in controlling the accessibility of the closed macrostate at room temperature. We compare the results of the molecular mechanics analytical generalized Born plus non-polar solvation approach to those obtained through Grid Inhomogeneous Solvation Theory analysis with explicit solvation to elucidate the thermodynamic forces at play. The calculations help to illustrate the deficiencies of continuum solvent models and demonstrate the key role of the thermodynamics of enclosed hydration in driving the conformational equilibrium of molecules in solution. </p>

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