Coarse-Grained Modeling of The Calcium, Sodium, Magnesium And Potassium Cations Interacting With Proteins

Abstract Metal ions play important biological roles e.g.: activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly. In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e. calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.

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Martini 3: a coarse-grained force field with an eye for atomic detail

Nature Methods ◽

10.1038/s41592-021-01111-9 ◽

2021 ◽

Author(s):

H. Jelger Risselada

Keyword(s):

Force Field ◽

Coarse Grained

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Martini Coarse-Grained Force Field: Extension to RNA

Biophysical Journal ◽

10.1016/j.bpj.2017.05.043 ◽

2017 ◽

Vol 113 (2) ◽

pp. 246-256 ◽

Cited By ~ 49

Author(s):

Jaakko J. Uusitalo ◽

Helgi I. Ingólfsson ◽

Siewert J. Marrink ◽

Ignacio Faustino

Keyword(s):

Force Field ◽

Field Extension ◽

Coarse Grained

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2P044 Comparative simulations of protein-ligand binding processes using the MARTINI coarse-grained force field(01B. Protein: Structure & Function,Poster)

Seibutsu Butsuri ◽

10.2142/biophys.53.s166_2 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S166

Author(s):

Tatsuki Negami ◽

Tohru Terada ◽

Kentaro Shimizu

Keyword(s):

Protein Structure ◽

Ligand Binding ◽

Force Field ◽

Structure Function ◽

Coarse Grained

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

Journal of Computational Chemistry ◽

10.1002/jcc.25571 ◽

2018 ◽

Vol 39 (28) ◽

pp. 2360-2370 ◽

Cited By ~ 3

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

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

Soft Matter ◽

10.1039/d1sm01194d ◽

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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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.9b06700 ◽

2019 ◽

Vol 123 (37) ◽

pp. 7829-7839

Author(s):

Karolina Ziȩba ◽

Magdalena Ślusarz ◽

Rafał Ślusarz ◽

Adam Liwo ◽

Cezary Czaplewski ◽

...

Keyword(s):

Membrane Proteins ◽

Force Field ◽

Lipid Bilayer ◽

Coarse Grained

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A forty-year journey in plant research: original contributions to flavonoid biochemistry

Canadian Journal of Botany ◽

10.1139/b05-030 ◽

2005 ◽

Vol 83 (5) ◽

pp. 433-450 ◽

Cited By ~ 18

Author(s):

Ragai K Ibrahim

Keyword(s):

Three Dimensional ◽

Biological Significance ◽

Flavonoid Biosynthesis ◽

Dimensional Structure ◽

Enzymatic Reactions ◽

Research Career ◽

Substrate Preferences ◽

Genes Encoding ◽

The Common ◽

New Compounds

This review highlights original contributions by the author to the field of flavonoid biochemistry during his research career of more than four decades. These include elucidation of novel aspects of some of the common enzymatic reactions involved in the later steps of flavonoid biosynthesis, with emphasis on methyltransferases, glucosyltransferases, sulfotransferases, and an oxoglutarate-dependent dioxygenase, as well as cloning, and inferences about phylogenetic relationships, of the genes encoding some of these enzymes. The three-dimensional structure of a flavonol O-methyltransferase was studied through homology-based modeling, using a caffeic acid O-methyltransferase as a template, to explain their strict substrate preferences. In addition, the biological significance of enzymatic prenylation of isoflavones, as well as their role as phytoanticipins and inducers of nodulation genes, are emphasized. Finally, the potential application of knowledge about the genes encoding these enzyme reactions is discussed in terms of improving plant productivity and survival, modification of flavonoid profiles, and the search for new compounds with pharmaceutical and (or) nutraceutical value.Key words: flavonoid enzymology, metabolite localization, gene cloning, 3-D structure, phylogeny.

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

The Journal of Chemical Physics ◽

10.1063/1.4974833 ◽

2017 ◽

Vol 146 (5) ◽

pp. 054501 ◽

Cited By ~ 34

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

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

Volume 4: 8th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, Parts A and B ◽

10.1115/detc2011-48376 ◽

2011 ◽

Cited By ~ 1

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.

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