Many proteins can adopt multiple conformations which are important for their function. This is also true for proteins and domains that are covalently linked to each other. One important example is ubiquitin, which can form chains of different conformations depending on which of its lysine side chains is used to form an isopeptide bond with the C-terminus of another ubiquitin molecule. Similarly, ubiquitin gets covalently attached to active-site residues of E2 ubiquitin-conjugating enzymes. Due to weak interactions between ubiquitin and its interaction partners, these covalent complexes adopt multiple conformations. Understanding the function of these complexes requires the characterization of the entire accessible conformation space and its modulation by interaction partners. Long-range (1.8â??10Â*nm) distance restraints obtained by EPR spectroscopy in the form of probability distributions are ideally suited for this task as not only the mean distance but also information about the conformation dynamics is encoded in the experimental data. Here we describe a computational method that we have developed based on well-established structure determination software using NMR restraints to calculate the accessible conformation space using PELDOR/DEER data.
[NMR paper] Methods for Structure Determination of SH2 Domain-Phosphopeptide Complexes by NMR
Methods for Structure Determination of SH2 Domain-Phosphopeptide Complexes by NMR
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique to solve the structure of biomolecular complexes at atomic resolution in solution. Small proteins such as Src-homology 2 (SH2) domains have fast tumbling rates and long-lived NMR signals, making them particularly suited to be studied by standard NMR methods. SH2 domains are modular proteins whose function is the recognition of sequences containing phosphotyrosines. In this chapter, we describe the application of NMR to assess...
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[NMR paper] Probing the Binding Modes of a Multi-Domain Protein to Lipid-Based Nanoparticles by Relaxation-Based NMR.
Probing the Binding Modes of a Multi-Domain Protein to Lipid-Based Nanoparticles by Relaxation-Based NMR.
Related Articles Probing the Binding Modes of a Multi-Domain Protein to Lipid-Based Nanoparticles by Relaxation-Based NMR.
J Phys Chem Lett. 2017 May 22;:
Authors: Ceccon A, Tugarinov V, Boughton AJ, Fushman D, Clore GM
Abstract
The interactions of two model multi-domain proteins - covalently linked di-ubiquitins, Ub2 - with lipid-based nanoparticles have been quantitatively probed by the measurements of NMR lifetime...
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05-23-2017 04:45 PM
Efficient segmental isotope labeling of multi-domain proteins using Sortase A
Efficient segmental isotope labeling of multi-domain proteins using Sortase A
Abstract
NMR studies of multi-domain protein complexes provide unique insight into their molecular interactions and dynamics in solution. For large proteins domain-selective isotope labeling is desired to reduce signal overlap, but available methods require extensive optimization and often give poor ligation yields. We present an optimized strategy for segmental labeling of multi-domain proteins using the S. aureus transpeptidase Sortase A. Critical improvements compared to...
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08-29-2015 09:18 PM
[NMR paper] NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes.
NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes.
Related Articles NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes.
Prog Biophys Mol Biol. 2014 Aug 28;
Authors: Dias DM, Ciulli A
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information...
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09-02-2014 11:17 PM
NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes
NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes
Publication date: Available online 28 August 2014
Source:Progress in Biophysics and Molecular Biology</br>
Author(s): David M. Dias , Alessio Ciulli</br>
Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most...
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[NMR paper] Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination.
Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination.
Related Articles Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination.
Protein Cell. 2013 Nov 27;
Authors: Wu K, Shi C, Li J, Wang H, Shi P, Chen L, Wu F, Xiong Y, Tian C
PMID: 24282082
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A segmental labeling strategy for unambiguous determination of domainâ??domain interactions of large multi-domain proteins
A segmental labeling strategy for unambiguous determination of domainâ??domain interactions of large multi-domain proteins
Abstract NMR structural determination of large multi-domain proteins is a challenging task due to significant spectral overlap with a particular difficulty in unambiguous identification of domainâ??domain interactions. Segmental labeling is a NMR strategy that allows for isotopically labeling one domain and leaves the other domain unlabeled. This significantly simplifies spectral overlaps and allows for quick identification of domainâ??domain interaction. Here, a...
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07-08-2011 07:01 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...
Efficient determination of the accessible conformation space of multi-domain complexes based on EPR PELDOR data
Linear Mode
