Recent development and application of constant pH molecular dynamics

Chen, Wei; Shi, Chuanyin; Shen, Jana

doi:10.1080/08927022.2014.907492

Cited by 114 publications

(134 citation statements)

References 64 publications

(137 reference statements)

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“…It takes ca. 500 ps to achieve pK a convergence (Chen et al 2014). Characteristics AADs are found around 0.6-1.0 pK a units.…”

Section: Other Common Constant Ph Simulation Methodsmentioning

confidence: 88%

“…This was the beginning of a new era of CpH simulation methods still under intense development for biological systems (Baptista et al 1997;Wallace and Shen 2012;Dashti et al 2012;Goh et al 2013a;Chen et al 2013Chen et al , 2014Chen and Roux 2015;Socher and Stich 2016;Donnini et al 2016). Several new simulation schemes that allow pH-coupled MD have emerged following either the Baptista's hybrid MD/PB approach (Baptista et al 1997) or are rooted in the "λ"'s dynamics method (Kong and Brooks 1996).…”

Section: Other Common Constant Ph Simulation Methodsmentioning

confidence: 99%

“…With the increase of computer power, it became doable to replace the implicit solvent model by full atomistic representations (Wallace and Shen 2012;Dashti et al 2012;Chen et al 2013Chen et al , 2014Goh et al 2013a, b;Lee et al 2015Lee et al , 2016Donnini et al 2016). Brooks's lab was the first to extend the CpH MD to nucleic acids in explicit TIP3P water molecules (Goh et al 2013a, b).…”

Section: Other Common Constant Ph Simulation Methodsmentioning

confidence: 99%

“…This might offer to the reader some updated practical guide to choose among the options based on the present discussions. An old and less detailed comparison was published before (Chen et al 2014). Note that a special chapter for pK a calculations is related with membrane proteins (not covered in this review).…”

Section: Comparison Between the Different Theoretical Methodsmentioning

confidence: 99%

“…Different aspects of available computational methods to study acid-base processes in biomolecules have been reviewed in the literature (Mongan and Case 2005;Chen et al 2008Chen et al , 2014Wallace and Shen 2009;Alexov et al 2011;Kim and McCammon 2016), evidencing their increasingly important role in biophysics, biochemistry, and biotechnological processes. Most of the reviews concentrated their discussions on atomistic level constant-pH (CpH) molecular dynamics (MD) techniques.…”

Section: Introductionmentioning

confidence: 99%

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Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

daSilva

Dias

2017

Biophys Rev

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pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-ofthe-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.

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“…It takes ca. 500 ps to achieve pK a convergence (Chen et al 2014). Characteristics AADs are found around 0.6-1.0 pK a units.…”

Section: Other Common Constant Ph Simulation Methodsmentioning

confidence: 88%

Section: Other Common Constant Ph Simulation Methodsmentioning

confidence: 99%

Section: Other Common Constant Ph Simulation Methodsmentioning

confidence: 99%

Section: Comparison Between the Different Theoretical Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

daSilva

Dias

2017

Biophys Rev

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How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations

2019

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Physicochemical properties of proteins are controlled mainly by post‐translational modifications such as amino acid phosphorylation. Although molecular dynamics simulations have been shown to be a valuable tool for studying the effects of phosphorylation on protein structure and dynamics, most of the previous studies assumed that the phosphate group was in the unprotonated (PO32-) state, even though the protonation state could in fact vary at physiological pH. In this study, we performed molecular dynamics simulations of four different protein‐phosphorylated peptide complexes both in the PO32- and PO3H− states. Our simulations delineate different dynamics and energetics between the two states, suggesting importance of the protonation state of a phosphorylated amino acid in molecular recognition.

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Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

Chen

Shen

2014

J. Comput. Chem.

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Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma.

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Recent development and application of constant pH molecular dynamics

Cited by 114 publications

References 64 publications

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

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