Literature DB >> 24924264

Using small angle solution scattering data in Xplor-NIH structure calculations.

Charles D Schwieters1, G Marius Clore2.   

Abstract

This contribution describes the use of small and wide angle X-ray and small angle neutron scattering for biomolecular structure calculation using the program Xplor-NIH, both with and without NMR data. The current algorithms used for calculating scattering curves are described, and the use of scattering data as a structural restraint is given concrete form as a fragment of an Xplor-NIH structure calculation script. We review five examples of the use of scattering data in structure calculation, including the treatment of single domain proteins, nucleic acids, structure determination of large proteins, and the use of ensemble representations to characterize small and large amplitude motions. Published by Elsevier B.V.

Entities:  

Keywords:  NMR restraints; SANS; SAXS; Structure determination; WAXS

Mesh:

Substances:

Year:  2014        PMID: 24924264      PMCID: PMC4057650          DOI: 10.1016/j.pnmrs.2014.03.001

Source DB:  PubMed          Journal:  Prog Nucl Magn Reson Spectrosc        ISSN: 0079-6565            Impact factor:   9.795


  36 in total

1.  Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.

Authors:  J Kuszewski; C Schwieters; G M Clore
Journal:  J Am Chem Soc       Date:  2001-05-02       Impact factor: 15.419

2.  A refined solution structure of hen lysozyme determined using residual dipolar coupling data.

Authors:  H Schwalbe; S B Grimshaw; A Spencer; M Buck; J Boyd; C M Dobson; C Redfield; L J Smith
Journal:  Protein Sci       Date:  2001-04       Impact factor: 6.725

3.  Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.

Authors:  G M Clore; A M Gronenborn
Journal:  Science       Date:  1991-06-07       Impact factor: 47.728

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

Authors:  Xiaobing Zuo; David M Tiede
Journal:  J Am Chem Soc       Date:  2005-01-12       Impact factor: 15.419

5.  Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data.

Authors:  Alexander Grishaev; Justin Wu; Jill Trewhella; Ad Bax
Journal:  J Am Chem Soc       Date:  2005-11-30       Impact factor: 15.419

6.  A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data.

Authors:  Charles D Schwieters; G Marius Clore
Journal:  Biochemistry       Date:  2007-02-06       Impact factor: 3.162

7.  Crystal structure of the phosphoenolpyruvate-binding enzyme I-domain from the Thermoanaerobacter tengcongensis PEP: sugar phosphotransferase system (PTS).

Authors:  Anselm Erich Oberholzer; Mario Bumann; Philipp Schneider; Christoph Bächler; Christian Siebold; Ulrich Baumann; Bernhard Erni
Journal:  J Mol Biol       Date:  2004-12-22       Impact factor: 5.469

8.  Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy.

Authors:  Zhengrong Wu; Frank Delaglio; Nico Tjandra; Victor B Zhurkin; Ad Bax
Journal:  J Biomol NMR       Date:  2003-08       Impact factor: 2.835

9.  Structure and dynamics of full-length HIV-1 capsid protein in solution.

Authors:  Lalit Deshmukh; Charles D Schwieters; Alexander Grishaev; Rodolfo Ghirlando; James L Baber; G Marius Clore
Journal:  J Am Chem Soc       Date:  2013-10-17       Impact factor: 15.419

10.  Crystal structure of enzyme I of the phosphoenolpyruvate sugar phosphotransferase system in the dephosphorylated state.

Authors:  Anselm E Oberholzer; Philipp Schneider; Christian Siebold; Ulrich Baumann; Bernhard Erni
Journal:  J Biol Chem       Date:  2009-09-28       Impact factor: 5.157

View more
  24 in total

Review 1.  Emerging applications of small angle solution scattering in structural biology.

Authors:  Barnali N Chaudhuri
Journal:  Protein Sci       Date:  2015-02-12       Impact factor: 6.725

2.  Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins.

Authors:  Liang Qin; Fredj Ben Bdira; Yann G J Sterckx; Alexander N Volkov; Jocelyne Vreede; Gabriele Giachin; Peter van Schaik; Marcellus Ubbink; Remus T Dame
Journal:  Nucleic Acids Res       Date:  2020-02-28       Impact factor: 16.971

3.  The PRE-Derived NMR Model of the 38.8-kDa Tri-Domain IsdH Protein from Staphylococcus aureus Suggests That It Adaptively Recognizes Human Hemoglobin.

Authors:  Megan Sjodt; Ramsay Macdonald; Thomas Spirig; Albert H Chan; Claire F Dickson; Marian Fabian; John S Olson; David A Gell; Robert T Clubb
Journal:  J Mol Biol       Date:  2015-02-14       Impact factor: 5.469

4.  Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.

Authors:  Karl T Debiec; Matthew J Whitley; Leonardus M I Koharudin; Lillian T Chong; Angela M Gronenborn
Journal:  Biophys J       Date:  2018-02-27       Impact factor: 4.033

5.  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

6.  An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.

Authors:  Shunsuke Imai; Parimal Kumar; Christopher U T Hellen; Victoria M D'Souza; Gerhard Wagner
Journal:  Nat Struct Mol Biol       Date:  2016-08-15       Impact factor: 15.369

7.  Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.

Authors:  Gabriel Cornilescu; Allison L Didychuk; Margaret L Rodgers; Lauren A Michael; Jordan E Burke; Eric J Montemayor; Aaron A Hoskins; Samuel E Butcher
Journal:  J Mol Biol       Date:  2015-12-02       Impact factor: 5.469

Review 8.  Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

Authors:  Vincenzo Venditti; Timothy K Egner; G Marius Clore
Journal:  Chem Rev       Date:  2016-01-07       Impact factor: 60.622

9.  Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering.

Authors:  Vincenzo Venditti; Charles D Schwieters; Alexander Grishaev; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-24       Impact factor: 11.205

10.  Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.

Authors:  Lalit Deshmukh; Charles D Schwieters; Alexander Grishaev; G Marius Clore
Journal:  Chemphyschem       Date:  2016-03-16       Impact factor: 3.102

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.