SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics

2015 ◽  
Vol 11 (2) ◽  
pp. 723-739 ◽  
Author(s):  
Leonardo Darré ◽  
Matías Rodrigo Machado ◽  
Astrid Febe Brandner ◽  
Humberto Carlos González ◽  
Sebastián Ferreira ◽  
...  
Keyword(s):  
Force Field ◽  
Long Range ◽  
Coarse Grained ◽  
Aqueous Solvation

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers

2011 ◽  
Author(s):  
Mohammad Poursina ◽  
Jeremy Laflin ◽  
Kurt S. Anderson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Force ◽  
Center Of Mass ◽  
Computational Cost ◽  
Field Approximation ◽  
The Body ◽  
Divide And Conquer ◽  
Coarse Grained ◽  
Coarse Grain

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

2021 ◽  
Vol 17 (3) ◽  
pp. 1562-1580 ◽  
Author(s):  
Yalun Yu ◽  
Andreas Krämer ◽  
Richard M. Venable ◽  
Andrew C. Simmonett ◽  
Alexander D. MacKerell ◽  
...  
Keyword(s):  
Force Field ◽  
Long Range ◽  
Automated Optimization

Quantifying the Predictive Skill in Long-Range Forecasting. Part II: Model Error in Coarse-Grained Markov Models with Application to Ocean-Circulation Regimes

2012 ◽  
Vol 25 (6) ◽  
pp. 1814-1826 ◽  
Author(s):  
Dimitrios Giannakis ◽  
Andrew J. Majda
Keyword(s):  
Long Range ◽  
Ocean Circulation ◽  
Climate Models ◽  
Markov Models ◽  
Low Frequency ◽  
Model Error ◽  
Ocean Model ◽  
Coarse Grained ◽  
Predictive Skill ◽  
Relaxation To Equilibrium

Abstract An information-theoretic framework is developed to assess the predictive skill and model error in imperfect climate models for long-range forecasting. Here, of key importance is a climate equilibrium consistency test for detecting false predictive skill, as well as an analogous criterion describing model error during relaxation to equilibrium. Climate equilibrium consistency enforces the requirement that long-range forecasting models should reproduce the climatology of prediction observables with high fidelity. If a model meets both climate consistency and the analogous criterion describing model error during relaxation to equilibrium, then relative entropy can be used as an unbiased superensemble measure of the model’s skill in long-range coarse-grained forecasts. As an application, the authors investigate the error in modeling regime transitions in a 1.5-layer ocean model as a Markov process and identify models that are strongly persistent but their predictive skill is false. The general techniques developed here are also useful for estimating predictive skill with model error for Markov models of low-frequency atmospheric regimes.

scholarly journals Martini Coarse-Grained Force Field: Extension to RNA

2017 ◽  
Vol 113 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Jaakko J. Uusitalo ◽  
Helgi I. Ingólfsson ◽  
Siewert J. Marrink ◽  
Ignacio Faustino
Keyword(s):  
Force Field ◽  
Field Extension ◽  
Coarse Grained

scholarly journals A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

2018 ◽  
Vol 39 (28) ◽  
pp. 2360-2370 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Artur Giełdoń ◽  
Yanping Yin ◽  
Yi He ◽  
Harold A. Scheraga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Force Fields ◽  
Coarse Grained ◽  
Protein Nucleic Acid ◽  
New Protein

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...

scholarly journals FcαRI binding at the IgA1 CH2–CH3 interface induces long-range conformational changes that are transmitted to the hinge region

2018 ◽  
Vol 115 (38) ◽  
pp. E8882-E8891 ◽  
Author(s):  
Monica T. Posgai ◽  
Sam Tonddast-Navaei ◽  
Manori Jayasinghe ◽  
George M. Ibrahim ◽  
George Stan ◽  
...  
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Conformational Changes ◽  
Lectin Binding ◽  
Coarse Grained ◽  
Alanine Scanning Mutagenesis ◽  
Long Distance ◽  
Receptor Binding Site ◽  
Binding Interface ◽  
Functional Dynamics

IgA effector functions include proinflammatory immune responses triggered upon clustering of the IgA-specific receptor, FcαRI, by IgA immune complexes. FcαRI binds to the IgA1–Fc domain (Fcα) at the CH2–CH3 junction and, except for CH2 L257 and L258, all side-chain contacts are contributed by the CH3 domain. In this study, we used experimental and computational approaches to elucidate energetic and conformational aspects of FcαRI binding to IgA. The energetic contribution of each IgA residue in the binding interface was assessed by alanine-scanning mutagenesis and equilibrium surface plasmon resonance (SPR). As expected, hydrophobic residues central to the binding site have strong energetic contributions to the FcαRI:Fcα interaction. Surprisingly, individual mutation of CH2 residues L257 and L258, found at the periphery of the FcαRI binding site, dramatically reduced binding affinity. Comparison of antibody:receptor complexes involving IgA or its precursor IgY revealed a conserved receptor binding site at the CH2–CH3 junction (or its equivalent). Given the importance of residues near the CH2–CH3 junction, we used coarse-grained Langevin dynamics simulations to understand the functional dynamics in Fcα. Our simulations indicate that FcαRI binding, either in an asymmetric (1:1) or symmetric (2:1) complex with Fcα, propagated long-range conformational changes across the Fc domains, potentially impacting the hinge and Fab regions. Subsequent SPR experiments confirmed that FcαRI binding to the Fcα CH2–CH3 junction altered the kinetics of HAA lectin binding at the IgA1 hinge. Receptor-induced long-distance conformational transitions have important implications for the interaction of aberrantly glycosylated IgA1 with anti-glycan autoantibodies in IgA nephropathy.

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