NDLI: Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

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Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

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Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Fenn, Timothy D. Schnieders, Michael J. Mustyakimov, Marat Wu, Chuanjie Langan, Paul Pande, Vijay S. Brunger, Axel T.
Description	Country affiliation: United States Author Affiliation: Fenn TD ( Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.)
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.
File Format	HTM / HTML
ISSN	09692126
e-ISSN	18784186
DOI	10.1016/j.str.2011.01.015
Journal	Structure
Issue Number	4
Volume Number	19
Language	English
Publisher	Elsevier
Publisher Date	2011-04-13
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Molecular Biology Discipline Biochemistry Discipline Biotechnology Aldose-ketose Isomerases Chemistry Dna, Z-form Crystallography Hydrogen Bonding Models, Molecular Neutron Diffraction Nucleic Acid Conformation Protein Conformation Static Electricity Thermodynamics X-ray Diffraction Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Structural Biology Molecular Biology

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Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

X-ray Laue diffraction from crystals of xylose isomerase.

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Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of D-ribose-5-phosphate isomerase from Clostridium thermocellum.

Crystallization and preliminary X-ray crystallographic analysis of L-rhamnose isomerase with a novel high thermostability from Bacillus halodurans.

Crystallographic studies of DNA and RNA.

Crystal structure of the yeast His6 enzyme suggests a reaction mechanism.

Chiral electrostatics breaks the mirror symmetry of DNA supercoiling.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

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Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.