Publication date: Available online 8 February 2018 Source:Methods
Author(s): Julien Orts, Alvar D. Gossert
In this paper, we discuss methods for determining structures of protein-ligand complexes by NMR in solution. Our discussion is based on small ligands (<2 kDa) as for example drugs, metabolites or oligo-peptides, but most of the considerations also apply to more general cases. In NMR in solution, the kinetics of association and dissociation of the complex – the exchange rate – determines the optimal sample preparation and the NMR experimental approach. Additionally, depending on the part of the complex that will be studied (only the bound ligand, the protein, the protein-ligand interface or the entire protein-ligand complex structure), different types of NMR experiments are needed. Therefore, the choice of a combination of the appropriate experiment and a suitable sample preparation in terms of ligand to protein ratios are discussed in detail. Also, considerations for practically preparing samples of protein-ligand complexes and carrying out experiments including trouble shooting are described. For structure determination, the scope of this paper is limited to NOE-based methods and some of the most recent approaches will be covered.
[NMR paper] Structure determination of protein-ligand complexes by NMR in solution.
Structure determination of protein-ligand complexes by NMR in solution.
Structure determination of protein-ligand complexes by NMR in solution.
Methods. 2018 Feb 07;:
Authors: Orts J, Gossert AD
Abstract
In this paper, we discuss methods for determining structures of protein-ligand complexes by NMR in solution. Our discussion is based on small ligands (< 2 kDa) as for example drugs, metabolites or oligo-peptides, but most of the considerations also apply to more general cases. In NMR in solution, the kinetics of association and...
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02-11-2018 11:50 AM
[NMR paper] Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders.
Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders.
Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders.
Angew Chem Int Ed Engl. 2017 Apr 07;:
Authors: Wälti MA, Riek R, Orts J
Abstract
In early drug discovery approaches, screening hits are often weak affinity binders that are difficult to characterize in structural detail, particularly towards obtaining the 3D structure of...
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04-08-2017 10:57 AM
[NMR paper] NMR solution structure determination of large RNA-protein complexes.
NMR solution structure determination of large RNA-protein complexes.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif NMR solution structure determination of large RNA-protein complexes.
Prog Nucl Magn Reson Spectrosc. 2016 Nov;97:57-81
Authors: Yadav DK, Lukavsky PJ
Abstract
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...
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11-29-2016 12:57 AM
Determination of ligand binding modes in weak proteinâ??ligand complexes using sparse NMR data
Determination of ligand binding modes in weak proteinâ??ligand complexes using sparse NMR data
Abstract
We describe a general approach to determine the binding pose of small molecules in weakly bound proteinâ??ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of...
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11-19-2016 08:35 PM
NMR solution structure determination of large RNA-protein complexes
NMR solution structure determination of large RNA-protein complexes
Publication date: November 2016
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 97</br>
Author(s): Deepak Kumar Yadav, Peter J. Lukavsky</br>
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...
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11-19-2016 08:35 PM
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Methods Enzymol. 2011;493:241-75
Authors: Ziarek JJ, Peterson FC, Lytle BL, Volkman BF
Over the last 15years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like...
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03-05-2011 01:02 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
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Michael John, Guido Pintacuda, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting
J. Am. Chem. Soc.; 2006; 128(39) pp 12910 - 12916; (Article)
Abstract:
Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small...
Structure determination of protein-ligand complexes by NMR in solution
Linear Mode
