Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

2015 ◽  
Vol 119 (11) ◽  
pp. 4220-4229 ◽  
Author(s):  
Vojtěch Mlýnský ◽  
Petra Kührová ◽  
Marie Zgarbová ◽  
Petr Jurečka ◽  
Nils G. Walter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Hairpin Ribozyme ◽  
Dynamics Simulations

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

Ab initio based force field and molecular dynamics simulations of crystalline TATB

2004 ◽  
Vol 120 (15) ◽  
pp. 7059-7066 ◽  
Author(s):  
Richard H. Gee ◽  
Szczepan Roszak ◽  
Krishnan Balasubramanian ◽  
Laurence E. Fried
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

A Reactive Force Field (ReaxFF) for Molecular Dynamics Simulations of NiO Reduction in H2Environments

2017 ◽  
Vol 78 (1) ◽  
pp. 2765-2771
Author(s):  
Simon Oberhoffer ◽  
Albert M Iskandarov ◽  
Yoshitaka Umeno
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Dynamics Simulations

scholarly journals First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity

2011 ◽  
Author(s):  
Keivan Esfarjani ◽  
Gang Chen ◽  
Asegun Henry
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Properties ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Density Functional ◽  
Interatomic Potential ◽  
Force Constants ◽  
Dynamics Simulations

Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

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