Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations

2018 ◽  
Vol 148 (23) ◽  
pp. 234105 ◽  
Author(s):  
Dominik Sidler ◽  
Simon Frasch ◽  
Michael Cristòfol-Clough ◽  
Sereina Riniker
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Reaction Field ◽  
Dynamics Simulations

Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions

2009 ◽  
Vol 113 (10) ◽  
pp. 3112-3128 ◽  
Author(s):  
Maria M. Reif ◽  
Vincent Kräutler ◽  
Mika A. Kastenholz ◽  
Xavier Daura ◽  
Philippe H. Hünenberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Dynamics Simulations

Handling Electrostatic Interactions in Molecular Simulations: A Systematic Study

2008 ◽  
Vol 73 (4) ◽  
pp. 481-506 ◽  
Author(s):  
Jiří Kolafa ◽  
Filip Moučka ◽  
Ivo Nezbeda
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Short Range ◽  
Ewald Summation ◽  
Field Methods ◽  
Reaction Field ◽  
Lennard Jones ◽  
Dynamics Simulations

Two qualitatively different models with strong long-range electrostatic interactions, Lennard-Jones diatomics with an embedded dipole moment and TIP4P/2005 water, are considered in extensive Monte Carlo and molecular dynamics simulations to systematically study the differences in results caused by different treatments of the long-range electrostatic interactions. In addition to the standard Ewald summation and reaction field methods, we consider also two variants of short-range approximations. Both thermodynamic and structural properties, and both homogeneous and inhomogeneous phases are considered. It is shown that the accuracy of the short-range approximations with carefully selected parameters may be sufficient for a number of applications; however, in some cases one can encounter accuracy limits or structural or other artifacts.

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

Sign in / Sign up

Export Citation Format

Share Document