Contributions of higher-order proximal distribution functions to solvent structure around proteins

The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom clus...

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Bibliographic Details
Published in:The Journal of chemical physics 2021-09, Vol.155 (10), p.104110
Main Authors: Yousefi, Razie, Lynch, Gillian C., Galbraith, Madeline, Pettitt, B. Montgomery
Format: Article
Language:English
Subjects:
Alanine
Alanine - chemistry
Algorithms
Butanes - chemistry
Density distribution
Distribution functions
Molecular dynamics
Molecular Dynamics Simulation
Myoglobin - chemistry
Myoglobins
Proteins
Proteins - chemistry
Reconstruction
Solvation
Solvents
Solvents - chemistry
Thermodynamics
Unit cell
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Summary:The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute–solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.
ISSN:0021-9606
1089-7690
1089-7690
DOI:10.1063/5.0062580