Journal article
Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration
Structure (London), Vol.19(4), pp.523-533
2011
DOI: 10.1016/j.str.2011.01.015
PMCID: PMC3083928
PMID: 21481775
Abstract
Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.
► Electrostatics improve water molecule bonding and geometry in crystallographic refinement ► Electrostatics improves agreement with neutron data ► AMOEBA with PME has advantages over fixed charges with spherical cutoffs ► The spine of hydration in Z-DNA is disordered
Details
- Title: Subtitle
- Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration
- Creators
- Timothy D Fenn - Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USAMichael J Schnieders - Department of Chemistry, Stanford University, Stanford, CA 94305, USAMarat Mustyakimov - Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USAChuanjie Wu - Schrodinger, LLC, New York, NY 10036-4041, USAPaul Langan - Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USAVijay S Pande - Department of Chemistry, Stanford University, Stanford, CA 94305, USAAxel T Brunger - Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Resource Type
- Journal article
- Publication Details
- Structure (London), Vol.19(4), pp.523-533
- Publisher
- Elsevier Inc
- DOI
- 10.1016/j.str.2011.01.015
- PMID
- 21481775
- PMCID
- PMC3083928
- ISSN
- 0969-2126
- eISSN
- 1878-4186
- Language
- English
- Date published
- 2011
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984025284302771
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