Solvation and cavity occupation in biomolecules

Gillian C. Lynch, John S. Perkyns, Bao Linh Nguyen, Bernard Pettitt

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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 Å3, 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. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Original languageEnglish (US)
Pages (from-to)923-931
Number of pages9
JournalBiochimica et Biophysica Acta - General Subjects
Volume1850
Issue number5
DOIs
StatePublished - 2015

Fingerprint

Solvation
Biomolecules
Occupations
Hydration
Molecular dynamics
Molecular Dynamics Simulation
Myoglobin
Proteins
Molecular Conformation
Coulomb interactions
Heme
Integral equations
Distribution functions
Conformations
X-Ray Diffraction
X ray diffraction
Atoms
Molecules
Computer simulation

Keywords

  • Integral equations
  • Molecular dynamics
  • Proximal radial distribution functions
  • Solvation

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Solvation and cavity occupation in biomolecules. / Lynch, Gillian C.; Perkyns, John S.; Nguyen, Bao Linh; Pettitt, Bernard.

In: Biochimica et Biophysica Acta - General Subjects, Vol. 1850, No. 5, 2015, p. 923-931.

Research output: Contribution to journalArticle

Lynch, Gillian C. ; Perkyns, John S. ; Nguyen, Bao Linh ; Pettitt, Bernard. / Solvation and cavity occupation in biomolecules. In: Biochimica et Biophysica Acta - General Subjects. 2015 ; Vol. 1850, No. 5. pp. 923-931.
@article{42ce3aabc6924433b1a304680f78aea4,
title = "Solvation and cavity occupation in biomolecules",
abstract = "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 {\AA}3, 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. This article is part of a Special Issue entitled Recent developments of molecular dynamics.",
keywords = "Integral equations, Molecular dynamics, Proximal radial distribution functions, Solvation",
author = "Lynch, {Gillian C.} and Perkyns, {John S.} and Nguyen, {Bao Linh} and Bernard Pettitt",
year = "2015",
doi = "10.1016/j.bbagen.2014.09.020",
language = "English (US)",
volume = "1850",
pages = "923--931",
journal = "Biochimica et Biophysica Acta - General Subjects",
issn = "0304-4165",
publisher = "Elsevier",
number = "5",

}

TY - JOUR

T1 - Solvation and cavity occupation in biomolecules

AU - Lynch, Gillian C.

AU - Perkyns, John S.

AU - Nguyen, Bao Linh

AU - Pettitt, Bernard

PY - 2015

Y1 - 2015

N2 - 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 Å3, 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. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

AB - 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 Å3, 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. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

KW - Integral equations

KW - Molecular dynamics

KW - Proximal radial distribution functions

KW - Solvation

UR - http://www.scopus.com/inward/record.url?scp=84923165835&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84923165835&partnerID=8YFLogxK

U2 - 10.1016/j.bbagen.2014.09.020

DO - 10.1016/j.bbagen.2014.09.020

M3 - Article

VL - 1850

SP - 923

EP - 931

JO - Biochimica et Biophysica Acta - General Subjects

JF - Biochimica et Biophysica Acta - General Subjects

SN - 0304-4165

IS - 5

ER -