Publication date: Available online 6 November 2014 Source:Structure
Author(s): Alexander Lemak , Bin Wu , Adelinda Yee , Scott Houliston , Hsiau-Wei Lee , Aleksandras Gutmanas , Xianyang Fang , Maite Garcia , Anthony Semesi , Yun-Xing Wang , James*H. Prestegard , Cheryl*H. Arrowsmith
Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et*al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains. Teaser
Lemak et*al. describe a protocol for joint ensemble refinement of flexible multidomain protein structures against NOE, RDC, and SAXS data and apply it to a two-domain protein sf3636 from Shigella flexneri 2a. Sf3636 populates structural states with an extended arrangement of two domains that display a restricted twisting motion.
The dynamic duo: Combining NMR and small angle scattering in structural biology
The dynamic duo: Combining NMR and small angle scattering in structural biology
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of...
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04-17-2014 12:03 PM
Using Small Angle Solution Scattering Data in Xplor-NIH Structure Calculations
Using Small Angle Solution Scattering Data in Xplor-NIH Structure Calculations
Publication date: Available online 3 April 2014
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Charles D. Schwieters , G. Marius Clore</br>
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...
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04-04-2014 01:19 PM
[NMR paper] The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology.
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology.
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology.
Protein Sci. 2014 Mar 29;
Authors: Hennig J, Sattler M
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods and computational approaches now enable structural analysis of protein complexes with increasing complexity that more...
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04-02-2014 11:54 PM
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multi-disciplinary approaches are required to overcome limitations of individual methods and take advantage of...
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03-29-2014 01:00 PM
[NMR paper] Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.
Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.
Related Articles Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.
Structure. 2013 Dec 18;
Authors: Schwalbe M, Ozenne V, Bibow S, Jaremko M, Jaremko L, Gajda M, Jensen MR, Biernat J, Becker S, Mandelkow E, Zweckstetter M, Blackledge M
Abstract
The development of molecular descriptions of intrinsically...
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12-24-2013 01:04 PM
[NMR paper] Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
J Biomol NMR. 2013 Mar 3;
Authors: Hennig J, Wang I, Sonntag M, Gabel F, Sattler M
Abstract
Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic...
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03-05-2013 03:25 PM
NMR and Small Angle Scattering-based structural analysis of protein complexes in solu
NMR and Small Angle Scattering-based structural analysis of protein complexes in solution.
Related Articles NMR and Small Angle Scattering-based structural analysis of protein complexes in solution.
J Struct Biol. 2010 Nov 10;
Authors: Madl T, Gabel F, Sattler M
Structural analysis of multi-domain protein complexes is a key challenge in current biology and a prerequisite for understanding the molecular basis of essential cellular processes. The use of solution techniques is important for characterizing the quaternary arrangements and dynamics of...
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11-16-2010 04:13 PM
Multidomain Protein Structures from NMR & Solution Small-Angle X-ray Scattering
http://pubs.acs.org/isubscribe/journals/jacsat/127/i47/figures/ja054342mn00001.gif
Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data
Alexander Grishaev,* Justin Wu, Jill Trewhella, and Ad Bax*
Contribution from the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
J. Am. Chem. Soc.; 2005; 127(47) pp 16621 -...
Structural Characterization of a Flexible Two-Domain Protein in Solution Using Small Angle X-Ray Scattering and NMR Data
Linear Mode
