Many-body effect determines the selectivity for Ca2+and Mg2+in proteins

Ion channels and ion selectivity

(2017) Benoît Roux   Essays in Biochemistry

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field

(2017) Zhifeng Jing et al.   JOURNAL OF CHEMICAL PHYSICS

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability

(2017) Robert M. Parrish et al.   Journal of Chemical Theory and Computation

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

(2017) Matthew Harger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions

(2017) Halil I. Okur et al.   JOURNAL OF PHYSICAL CHEMISTRY B

General Principles and Strategies for Salting-Out Informed by the Hofmeister Series

(2017) Alan M. Hyde et al.   ORGANIC PROCESS RESEARCH & DEVELOPMENT

Anion Binding in Solution: Beyond the Electrostatic Regime

(2017) Yun Liu et al.   Chem

Thermodynamic Study on the Protonation and Complexation of GLDA with Ca2+ and Mg2+ at Different Ionic Strengths and Ionic Media at 298.15 K

(2016) Clemente Bretti et al.   JOURNAL OF CHEMICAL AND ENGINEERING DATA

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

(2016) Karl T. Debiec et al.   Journal of Chemical Theory and Computation

Ion-Specific Effects in Carboxylate Binding Sites

(2016) Mark J. Stevens et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory

(2016) Amir N. Kucharski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins

(2015) Van Ngo et al.   Journal of Chemical Theory and Computation

Magnesium in Man: Implications for Health and Disease

(2015) Jeroen H. F. de Baaij et al.   PHYSIOLOGICAL REVIEWS

Aiming for Benchmark Accuracy with the Many-Body Expansion

(2014) Ryan M. Richard et al.   ACCOUNTS OF CHEMICAL RESEARCH

Quantitation of the Calcium and Membrane Binding Properties of the C2 Domains of Dysferlin

(2014) Nazish Abdullah et al.   BIOPHYSICAL JOURNAL

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization

(2014) Miriam Kohagen et al.   Journal of Physical Chemistry Letters

Competition among Metal Ions for Protein Binding Sites: Determinants of Metal Ion Selectivity in Proteins

(2013) Todor Dudev et al.   CHEMICAL REVIEWS

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Differential Role of the Protein Matrix on the Binding of a Catalytic Aspartate to Mg2+ vs Ca2+: Application to Ribonuclease H

(2013) C. Satheesan Babu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Role of Carboxylate Side Chains in the Cation Hofmeister Series

(2012) Jaibir Kherb et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Second Ca2+-Binding Domain of NCX1 Binds Mg2+with High Affinity

(2011) Vincent Breukels et al.   BIOCHEMISTRY

Accounting for electronic polarization in non-polarizable force fields

(2011) Igor Leontyev et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase

(2010) Yunpeng Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Computational Studies on Polarization Effects and Selectivity in K+Channels

(2010) Christopher J. R. Illingworth et al.   Journal of Chemical Theory and Computation

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electronic Properties and Desolvation Penalties of Metal Ions Plus Protein Electrostatics Dictate the Metal Binding Affinity and Selectivity in the Copper Efflux Regulator

(2010) Li Rao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Two mechanisms of ion selectivity in protein binding sites

(2010) H. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrated metal ions in aqueous solution: How regular are their structures?

(2010) Ingmar Persson   PURE AND APPLIED CHEMISTRY

Cytosolic Ca2+ Buffers

(2010) B. Schwaller   Cold Spring Harbor Perspectives in Biology

Many-body effects and simulations of potassium channels

(2009) C. J. Illingworth et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Metal Binding Affinity and Selectivity in Metalloproteins: Insights from Computational Studies

(2008) Todor Dudev et al.   Annual Review of Biophysics

IMPROVED SCALES FOR METAL ION SOFTNESS AND TOXICITY

(2008) Thomas B. Kinraide   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY