Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

Chen, Wei; Wallace, Jason A.; Yue, Zhi; Shen, Jana

doi:10.1016/j.bpj.2013.06.036

Cited by 79 publications

(167 citation statements)

References 12 publications

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“…Surprisingly, despite all approximations, predicted pK a values obtained by the FPTS are in general at least within the range of values given by different theoretical models (Stanton and Houk 2008;Chen et al 2013;Barroso da Silva and MacKernan 2017b). A recent benchmark study demonstrated that in fact even atomistic-level molecular dynamics simulations at constant pH do not obtain better results than FPTS for some protein systems.…”

Section: Titration Schemes Based On the Monte Carlo Methodsmentioning

confidence: 69%

“…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%

“…The interplay of so many titratable sites of several ionizable objects will slow down even more the already difficult sampling. The best Krieger et al (2006), Burger andAyers (2011), andOlsson et al (2011) b See Bashford (1997), Baker et al (2001), Anandakrishnan et al (2012), Wang et al (2015), and Sakalli and Knapp (2015) c See Svensson et al (1990), Kesvatera et al (1996Kesvatera et al ( , 1999Kesvatera et al ( , 2001, Teixeira et al (2010), Carnal et al (2015), Barroso da Silva et al (2017a), and Barroso da Silva and MacKernan (2017b) d See Baptista et al (1997, Baptista and Soares (2001), Machuqueiro and Baptista (2007), and Santos et al (2015) e See Lee et al (2004), Shen (2009), Dashti et al (2012), Goh et al (2013a), Chen et al (2013Chen et al ( , 2014Chen et al ( , 2016, Chen and Roux (2015), Socher and Stich (2016), and Donnini et al (2016) f See Tummanapelli and Vasudevan (2015), Kamerlin et al (2009), andLi et al (2002) alternative in this case is the MC titration schemes, particularly the FPTS. From this mesoscopic scheme, other intermediate models can also be derived in order to improve accuracy for specific tasks at higher CPU expenses.…”

Section: Comparison Between the Different Theoretical Methodsmentioning

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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Section: Titration Schemes Based On the Monte Carlo Methodsmentioning

confidence: 69%

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%

See 2 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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“…17 Most recently, an all-atom CpHMD method was developed, which uses explicit solvent to drive the dynamics in both conformational and protonation states, thus enabling the effects of ions to be explicitly taken into account. 18 Furthermore, titratable co-ions 18 or water molecules 19 are included in the simulation system to ensure charge neutrality under all pH conditions and at all time. Here we apply the all-atom CpHMD with titratable water to reexamine the titration of lauric acid in the DTA micelle.…”

Section: Introductionmentioning

confidence: 99%

Predicting proton titration in cationic micelle and bilayer environments

Eike

Murch

Koenig

et al. 2014

The Journal of Chemical Physics

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Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pK a 's in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pK a of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pK a of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs. © 2014 AIP Publishing LLC. [http://dx

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Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels

Kim

Liu

Ben‐Yoav

et al. 2016

Adv Healthcare Materials

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The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing.

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Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

Cited by 79 publications

References 12 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

Predicting proton titration in cationic micelle and bilayer environments

Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels

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