Charge Group Partitioning in Biomolecular Simulation

Canzar, Stefan; El-Kebir, Mohammed; Pool, René; Elbassioni, Khaled; Mark, Alan E.; Geerke, Daan P.; Stougie, Leen; Klau, Gunnar W.

doi:10.1089/cmb.2012.0239

Cited by 146 publications

(87 citation statements)

References 28 publications

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“…In contrast, the mid-level method highlighted in Figure 5, submission 529, has significantly but not dramatically worse performance by most metrics, while submission 197 is clearly worse by all metrics. Submission 529 used MD alchemical free energy calculations in explicit solvent with the GROMOS simulation package, using parameters from Automated Topology Builder[18, 2]. In contrast, submission 197 used the AMSOL solvation model[9] from the ZINC processing pipeline[13] for hydration free energy predictions, with conformations predicted by Open-Eye's Omega[11, 10, 1].…”

Section: Resultsmentioning

confidence: 99%

Blind prediction of solvation free energies from the SAMPL4 challenge

Mobley

Wymer

Lim

et al. 2014

J Comput Aided Mol Des

148

228

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Here, we give an overview of the small molecule hydration portion of the SAMPL4 challenge, which focused on predicting hydration free energies for a series of 47 small molecules. These gas-to-water transfer free energies have in the past proven a valuable test of a variety of computational methods and force fields. Here, in contrast to some previous SAMPL challenges, we find a relatively wide range of methods perform quite well on this test set, with RMS errors in the 1.2 kcal/mol range for several of the best performing methods. Top-performers included a quantum mechanical approach with continuum solvent models and functional group corrections, alchemical molecular dynamics simulations with a classical all-atom force field, and a single-confor-mation Poisson-Boltzmann approach. While 1.2 kcal/mol is still a significant error, experimental hydration free energies covered a range of nearly 20 kcal/mol, so methods typically showed substantial predictive power. Here, a substantial new focus was on evaluation of error estimates, as predicting when a computational prediction is reliable vs. unreliable has considerable practical value. We found, however, that in many cases errors are substantially underestimated, and that typically little effort has been invested in estimating likely error. We believe this is an important area for further research.

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Section: Resultsmentioning

confidence: 99%

Blind prediction of solvation free energies from the SAMPL4 challenge

Mobley

Wymer

Lim

et al. 2014

J Comput Aided Mol Des

148

228

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“…Lennard-Jones parameters and partial charges for the acid molecules were taken from the OPLS-AA library, [34,35] and their geometries were determined using the Automated Topology Builder (ATP) tool. [36][37][38] In order to be consistent with our previous studies, [24][25][26] water molecules have been represented by the five-site TIP5P model. [39] These molecules have been kept rigid in the simulations, whereas no constraint has been applied to acid molecules.…”

Section: Computational Detailsmentioning

confidence: 88%

Molecular Dynamics Simulations of the Interaction between Water Molecules and Aggregates of Acetic or Propionic Acid Molecules

et al. 2015

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Running title: interaction of water molecules with carboxylic acid aggregates * Electronic mail: sylvain.picaud@univ-fcomte.fr (S.P.) 2 Abstract:Water adsorption around small acetic and propionic acid aggregates has been studied by means of molecular dynamics simulation in the temperature range of 100-250 K as a function of the water content. Calculations have shown that acetic and propionic acid molecules behave similarly, and that both the temperature and the water content have a strong influence on the behavior of the corresponding systems.Two situations have been evidenced for the acid-water aggregates, corresponding either to water adsorption on large acid grains at very low temperatures, or to the formation of droplets consisting of acid molecules adsorbed at the surface of water aggregates at higher temperatures and high water content. At low water content and high temperature, only a partial mixing between water and acid molecules has been observed.The results of the present simulations emphasize the need for further experimental and simulation works to achieve a better characterization of the effects of both temperature and humidity on the behavior of organic aerosols in the Troposphere.3

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“…44,45 The systems were solvated using the SPC 46 water model in a cubic box of size B72.3 Â 72.3 Â 72.3. All atom molecular dynamic simulations were carried out using Gromacs 4.6.7 42 with a GROMOS 53a6 43 force field.…”

Section: Molecular Dynamics Simulation Studiesmentioning

confidence: 99%

Chelerythrine–lysozyme interaction: spectroscopic studies, thermodynamics and molecular modeling exploration

Jash

Basu

Payghan

et al. 2015

Phys. Chem. Chem. Phys.

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The binding of the iminium and alkanolamine forms of chelerythrine to lysozyme (Lyz) was investigated by spectroscopy and docking studies. The thermodynamics of the binding was studied by calorimetry. Spectroscopic evidence suggested that Trp-62 and Trp-63 in the β-domain of the protein are closer to the binding site; moreover, the binding site was at a distance of 2.27 and 2.00 nm from the iminium and alkanolamine forms, respectively, according to the Forster theory of non-radiation energy transfer. The equilibrium binding constants for the iminium and alkanolamine forms at 298 K were evaluated to be 1.29 × 10(5) and 7.79 × 10(5) M(-1), respectively. The binding resulted in an alteration of the secondary structure of the protein with a distinct reduction of the helical organization. The binding of iminium was endothermic, involving electrostatic and hydrophobic interactions, while that of alkanolamine form was exothermic and dominated by hydrogen bonding interactions. Docking studies provided the atomistic details pertaining to the binding of both forms of chelerythrine and supported the higher binding in favour of the alkanolamine over the iminium. Furthermore, molecular dynamics study provided accurate insights regarding the binding of both chelerythrine forms in accordance with the experimental results obtained. Chelerythrine binding pocket involves the catalytic region and aggregation prone K-peptide region, which are sandwiched between one another. Overall, these results suggest that both the forms of the alkaloid bind to the protein but the neutral form has higher affinity than the cationic form.

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Charge Group Partitioning in Biomolecular Simulation

Cited by 146 publications

References 28 publications

Blind prediction of solvation free energies from the SAMPL4 challenge

Blind prediction of solvation free energies from the SAMPL4 challenge

Molecular Dynamics Simulations of the Interaction between Water Molecules and Aggregates of Acetic or Propionic Acid Molecules

Chelerythrine–lysozyme interaction: spectroscopic studies, thermodynamics and molecular modeling exploration

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