Publication date: November 2016 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 97
Author(s): Deepak Kumar Yadav, Peter J. Lukavsky
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years. Graphical abstract
[NMR paper] Solution NMR Experiment for Measurement of 15N-1H Residual Dipolar Couplings in Large Proteins and Supramolecular Complexes.
Solution NMR Experiment for Measurement of 15N-1H Residual Dipolar Couplings in Large Proteins and Supramolecular Complexes.
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J Am Chem Soc. 2015 Aug 21;
Authors: Eletsky A, Pulavarti SV, Beaumont V, Gollnick P, Szyperski T
Abstract
NMR residual dipolar couplings (RDCs) are exquisite probes of protein structure and dynamics. A new solution NMR experiment named 2D SE2 J-TROSY is presented to...
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08-22-2015 11:20 AM
[NMR paper] Combining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in Solution.
Combining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in Solution.
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Methods Enzymol. 2015;558:279-331
Authors: Duss O, Yulikov M, Allain FH, Jeschke G
Abstract
Although functional significance of large noncoding RNAs and their complexes with proteins is well recognized, structural information for this class of systems is very scarce. Their inherent flexibility causes problems in...
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06-13-2015 11:09 PM
Fast methionine-based solution structure determination of calcium-calmodulin complexes
Fast methionine-based solution structure determination of calcium-calmodulin complexes
Abstract Here we present a novel NMR method for the structure determination of calcium-calmodulin (Ca2+-CaM)-peptide complexes from a limited set of experimental restraints. A comparison of solved CaM-peptide structures reveals invariability in CaMâ??s backbone conformation and a structural plasticity in CaMâ??s domain orientation enabled by a flexible linker. Knowing this, the collection and analysis of an extensive set of NOESY spectra is redundant. Although RDCs can define CaM domain orientation in...
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03-03-2011 02:06 AM
[NMR paper] Structure determination of protein/RNA complexes by NMR.
Structure determination of protein/RNA complexes by NMR.
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Methods Enzymol. 2005;394:525-45
Authors: Wu H, Finger LD, Feigon J
Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently...
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11-24-2010 11:14 PM
[NMR paper] Structure determination of protein complexes by NMR.
Structure determination of protein complexes by NMR.
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Methods Mol Biol. 2004;278:255-88
Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED
This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for...
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11-24-2010 09:25 PM
[NMR paper] NMR structure determination of proteins and protein complexes larger than 20 kDa.
NMR structure determination of proteins and protein complexes larger than 20 kDa.
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Curr Opin Chem Biol. 1998 Oct;2(5):564-70
Authors: Clore GM, Gronenborn AM
Recent advances in multidimensional nuclear magnetic resonance methodology to obtain 1H, 15N and 13C resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long-range order, coupled with new methods of structure refinement and novel methods...
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11-17-2010 11:15 PM
PCS-based structure determination of proteinâ??protein complexes
Abstract A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 Ã?) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure...
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08-14-2010 04:19 AM
Structure Determination of Protein Complexes by NMR
Structure Determination of Protein Complexes by NMR
D. Nietlispach, H.R. Mott, K.M. Stott, P.R. Nielsen, A. Thiru & E.D. Laue
The Department of Biochemistry, University of Cambridge
Introduction
As the structures of more proteins and domains are solved by structural genomics projects, the future of structural biology will be oriented more toward the study of macromolecular complexes. Since so many biological processes are mediated by interactions between proteins, it is important to study them at a molecular level. The study of protein-protein interactions also has applications in a...
NMR solution structure determination of large RNA-protein complexes
Linear Mode
