Proximal distributions from angular correlations: A measure of the onset of coarse-graining

Dyer, Kippi M.; Pettitt, B. Montgomery

doi:10.1063/1.4832895

Cited by 4 publications

(7 citation statements)

References 31 publications

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“…Additionally, the average nitrogen atom category in the protein results in a smooth and gradual decrease in the water distribution with no distinct minimum or secondary peak. The effects of next nearest-neighbors can be significant …”

Section: Results and Discussionmentioning

confidence: 99%

“…In this current work, we use the NAMD molecular dynamics package and the CHARMM 27 force field parameters. , The initial protein coordinates were obtained from X-ray crystal structures with PDB codes 2mgk for myoglobin and 4azu for azurin to be consistent with our previous work. ,,, Periodic boundary condition was used. The proteins were solvated with TIP3P in a box with a 10 Å layer of water in all three directions.…”

Section: Methodsmentioning

confidence: 99%

“…The convergence of the series has been considered previously, and generally the suitably normalized first member of the hierarchy captures the major features of the distribution of solvent . The distribution of solute around solvent converges much differently …”

Section: Introductionmentioning

confidence: 99%

“…14 The distribution of solute around solvent converges much differently. 16 Depending on the thermodynamic averages sought, one can consider the water averaged around a fixed protein 17 or around a flexible protein. 13 Some have even considered a flexible reference where local protein structure is used as a reference and the rest of the protein and water is averaged.…”

Section: ■ Introductionmentioning

confidence: 99%

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Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

Nguyen

Pettitt

2015

J. Chem. Theory Comput.

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The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

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Section: Results and Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

Nguyen

Pettitt

2015

J. Chem. Theory Comput.

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“…The convergence of the series has been considered previously and generally the suitably normalized first member of the hierarchy captures the major features of the distribution of solvent [9]. The distribution of solute around solvent converges much differently [42]. …”

Section: Proximal Radial Distribution Functionsmentioning

confidence: 99%

Solvation and cavity occupation in biomolecules

Lynch

Perkyns

Nguyen

et al. 2015

Biochimica et Biophysica Acta (BBA) - General Subjects

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Background Solvation density locations are important for protein dynamics and structure. Knowledge of the preferred hydration sites at biomolecular interfaces and those in the interior of cavities can enhance understanding of structure and function. While advanced X-ray diffraction methods can provide accurate atomic structures for proteins, that technique is challenged when it comes to providing accurate hydration structures, especially for interfacial and cavity bound solvent molecules. Methods Advances in integral equation theories which include more accurate methods for calculating the long-ranged Coulomb interaction contributions to the three-dimensional distribution functions make it possible to calculate angle dependent average solvent structure, accurately, around and inside irregular molecular conformations. The proximal Radial Distribution method provides another approximate method to determine average solvent structures for biomolecular systems based on a proximal or near neighbor solvent distribution that can be constructed from previously collected solvent distributions. These two approximate methods, along with all-atom molecular dynamics simulations are used to determine the solvent density inside the myoglobin heme cavity. Discussion and Results Myoglobin is a good test system for these methods because the cavities are many and one is large, tens of Å, but is shown to have only four hydration sites. These sites are not near neighbors which implies that the large cavity must have more than one way in and out. Conclusions Our results show that main solvation sites are well reproduced by all three methods. The techniques also produce a clearly identifiable solvent pathway into the interior of the protein. General Significance The agreement between Molecular Dynamics and less computationally demanding approximate methods is encouraging.

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

Yousefi

Lynch

Galbraith

et al. 2021

The Journal of Chemical Physics

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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.

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Proximal distributions from angular correlations: A measure of the onset of coarse-graining

Cited by 4 publications

References 31 publications

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

Solvation and cavity occupation in biomolecules

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

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