Literature DB >> 15631426

Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction.

Xiaobing Zuo1, David M Tiede.   

Abstract

We report on synchrotron-based high-angle X-ray solution scattering measured to 2 A resolution for two synthetic DNA sequences for which there are conflicting X-ray crystal and solution NMR models. Our results demonstrate that high-angle X-ray scattering discriminates between differing X-ray crystal and NMR models for solution-state DNA and provides a direct, independent method for testing structural models and measuring solution-state configurational dispersions.

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Year:  2005        PMID： 15631426     DOI： 10.1021/ja044533+

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  17 in total

1.  X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation.

Authors:  Xiaobing Zuo; Guanglei Cui; Kenneth M Merz; Ligang Zhang; Frederick D Lewis; David M Tiede
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-27       Impact factor: 11.205

2.  Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.

Authors:  Friedrich Förster; Benjamin Webb; Kristin A Krukenberg; Hiro Tsuruta; David A Agard; Andrej Sali
Journal:  J Mol Biol       Date:  2008-07-31       Impact factor: 5.469

Review 3.  X-ray scattering combined with coordinate-based analyses for applications in natural and artificial photosynthesis.

Authors:  David M Tiede; Kristy L Mardis; Xiaobing Zuo
Journal:  Photosynth Res       Date:  2009 Nov-Dec       Impact factor: 3.573

Review 4.  Experimental approaches for solution X-ray scattering and fiber diffraction.

Authors:  H Tsuruta; T C Irving
Journal:  Curr Opin Struct Biol       Date:  2008-09-29       Impact factor: 6.809

5.  Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

Authors:  Katarina Hart; Nicolas Foloppe; Christopher M Baker; Elizabeth J Denning; Lennart Nilsson; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-01-10       Impact factor: 6.006

6.  Wide-angle X-ray solution scattering for protein-ligand binding: multivariate curve resolution with Bayesian confidence intervals.

Authors:  David D L Minh; Lee Makowski
Journal:  Biophys J       Date:  2013-02-19       Impact factor: 4.033

7.  All-atom polarizable force field for DNA based on the classical Drude oscillator model.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2014-04-18       Impact factor: 3.376

8.  Xplor-NIH for molecular structure determination from NMR and other data sources.

Authors:  Charles D Schwieters; Guillermo A Bermejo; G Marius Clore
Journal:  Protein Sci       Date:  2017-09-18       Impact factor: 6.725

9.  Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2015-08-26       Impact factor: 6.006

10.  Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling.

Authors:  Alexander Grishaev; Liang Guo; Thomas Irving; Ad Bax
Journal:  J Am Chem Soc       Date:  2010-11-10       Impact factor: 15.419
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