Reconstructing the protein–water interface

Макаров, Владимир Александрович; Andrews, Brian; Pettitt, B. Montgomery

doi:10.1002/(sici)1097-0282(199806)45:7<469::aid-bip1>3.0.co;2-m

Cited by 65 publications

(110 citation statements)

References 36 publications

(13 reference statements)

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“…They showed the existence of a hydration shell whose average density is around 10% larger than that of the bulk water. Molecular dynamics simulation studies also suggested that the variation in the first hydration shell density is subject to the electrostatic properties of the protein surface and local surface topography (Makarov et al, 1998(Makarov et al, , 2000Dastidar & Mukhopadhyay, 2003). However, the properties of the hydrated water shells are still the subject of many experimental and theoretical investigations.…”

Section: Introductionmentioning

confidence: 99%

Collapse of the hydration shell of a protein prior to thermal unfolding

et al. 2007

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Based on high statistical quality wide-angle X-ray scattering data for the unfolding-refolding process of hen egg-white lysozyme (HEWL), we have analysed the change of the hydration shell as a function temperature using the program CRYSOL. The present results suggest that the decrease of the hydration-shell density starts from a lower temperature than the transition temperature of the collapse of the tertiary structure of HEWL. Although the use of CRYSOL for scattering data for proteins before the transition has an apparent limitation, the collapse of the hydration shell prior to the unfolding of HEWL agrees with a slight tendency of the radius of gyration to decrease during the thermal unfolding process.

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Section: Introductionmentioning

confidence: 99%

Collapse of the hydration shell of a protein prior to thermal unfolding

et al. 2007

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“…when used in conjunction with a Voronoi-like spacial (volume) normalization 6 to the distribution's first terms, g ij (r, 1) → 1 as r → ∞, so that the approximation g ij (r) ≈ g ⊥ ij (r, 1) holds at long distance.…”

Section: Theorymentioning

confidence: 99%

“…4 Now, for the left-handed proximal distributions of the macromolecule-water distributions, the m sites are many more than if the right-handed g ij (r, n) functions were used, since n m for water, as in the more common convention. 3,4,[6][7][8] Using the larger number of macromolecular sites to expand the neighbor hierarchy in allows for the fine-grained functionalization of the excess energy per molecule over the m-member hierarchy:…”

Section: Theorymentioning

confidence: 99%

“…2 The existence of a series decomposition of the fundamental structural description of a fluid system leads naturally to the question of whether or how the series can be truncated to construct a reduced description of a fluid system which still accurately measures the thermodynamics. To this point, it has been shown [4][5][6][7][8] that the truncation of the neighbor hierarchy of the average solvent distribution around a solute at the nearest neighbor approximation, with suitable renormalization, is a reasonable approximation for the density distribution and thus the electrostatic densities and energies of small biologically interesting molecules. The resulting electrostatic free energies of solvation of the approximate density distributions a) Electronic mail: mpettitt@utmb.edu computed with linear response are within a chemically acceptable error and generally better than continuum solvent approaches.…”

Section: Introductionmentioning

confidence: 99%

“…We and others 8 have successfully used truncation of one of the series for molecules which are very different in size. Here we use a slightly different set of functions than have previously been studied 3,4,[6][7][8] to measure coarse-graining for large solutes with respect to the smaller solvent molecule interactions.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Dyer

Pettitt²

2013

The Journal of Chemical Physics

Self Cite

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In this work we examine and extend the theory of proximal radial distribution functions for molecules in solution. We point out two formal extensions, the first of which generalizes the proximal distribution function hierarchy approach to the complete, angularly dependent molecular pair distribution function. Second, we generalize from the traditional right-handed solute-solvent proximal distribution functions to the left-handed distributions. The resulting neighbor hierarchy convergence is shown to provide a measure of the coarse-graining of the internal solute sites with respect to the solvent. Simulation of the test case of a deca-alanine peptide shows that this coarse-graining measure converges at a length scale of approximately 5 amino acids for the system considered.

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Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

Schiffer

Gunsteren

1999

Proteins

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Water plays an essential role in most biological processes. Water molecules solvating biomolecules are generally in fast exchange with the environment. Nevertheless, well-defined electron density is seen for water associated with proteins whose crystal structure is determined to high resolution. The relative accessibility of these water sites is likely to be relevant to their biological role but is difficult to assess. A time-averaging crystallographic refinement simulation on basic pancreatic trypsin inhibitor successfully characterizes the relative accessibility of the crystallographic water sites. In such a refinement simulation water diffuses through the crystal lattice in a manner that is consistent with the crystallographic data. This refinement discovers that internal crystallographic waters in this particular protein are bridged to the outside protein surface via a series of progressively more accessible water sites. On the surface of the protein, water molecules exchange quickly between crystallographic water sites. Time-averaging crystallographic refinement provides a view based on experimental data of the relative accessibility of water sites in and around a protein in a crystalline environment. Proteins 1999;36:501-511.

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Reconstructing the protein–water interface

Cited by 65 publications

References 36 publications

Collapse of the hydration shell of a protein prior to thermal unfolding

Collapse of the hydration shell of a protein prior to thermal unfolding

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

Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

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