Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs

Vögeli, Beat; Orts, Julien; Strotz, Dean; Chi, Celestine; Minges, Martina; Wälti, Marielle A.; Güntert, Peter; Riek, Roland

doi:10.1016/j.jmr.2013.11.016

Cited by 33 publications

(28 citation statements)

References 83 publications

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“…The main advantages are that it does not need any protein resonance assignment, relies on simple and interpretable NMR experiments, requires only one sample, and performs standard NMR structure calculations instead of relying on docking poses. It provides the full structure of the complex of the binding site with high accuracy, since the distance restraints are based on accurate NOEs [24,74,75]. Additionally, it is applicable to weak and strong binders in fast or slow exchange and the method is fast.…”

Section: Nmr 2 Versus Other Methods For Rapid Structure Calculations mentioning

confidence: 99%

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

Wälti

Orts

2018

Magnetochemistry

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Structural characterization of complexes is crucial for a better understanding of biological processes and structure-based drug design. However, many protein-ligand structures are not solvable by X-ray crystallography, for example those with low affinity binders or dynamic binding sites. Such complexes are usually targeted by solution-state NMR spectroscopy. Unfortunately, structure calculation by NMR is very time consuming since all atoms in the complex need to be assigned to their respective chemical shifts. To circumvent this problem, we recently developed the Nuclear Magnetic Resonance Molecular Replacement (NMR 2 ) method. NMR 2 very quickly provides the complex structure of a binding pocket as measured by solution-state NMR. NMR 2 circumvents the assignment of the protein by using previously determined structures and therefore speeds up the whole process from a couple of months to a couple of days. Here, we recall the main aspects of the method, show how to apply it, discuss its advantages over other methods and outline its limitations and future directions.

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Section: Nmr 2 Versus Other Methods For Rapid Structure Calculations mentioning

confidence: 99%

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

Wälti

Orts

2018

Magnetochemistry

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“…[5] The distances are derived from exact measurements of the nuclear Overhauser enhancement (eNOE). [9][10][11] In our initial applications of the method, we used uniformly 13 C, 15 N-labeled samples to extract distances between all protons pairs. [12] However, diagonal peak overlap becomes an increasingly limiting factor for proteins larger than ca.…”

Section: Noe Measurement and Analysismentioning

confidence: 99%

NOE‐Derived Methyl Distances from a 360 kDa Proteasome Complex

Celestine

Strotz

Riek

et al. 2018

Chemistry A European J

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Nuclear magnetic resonance spectroscopy is the prime tool to probe structure and dynamics of biomolecules at atomic resolution. A serious challenge for that method is the size limit imposed on molecules to be studied. Standard studies are typically restricted to ca. 30-40 kDa. More recent developments lead to spin relaxation measurements in methyl groups in single proteins or protein complexes as large as a mega-Dalton, which directly allow the extraction of angular information or experiments with paramagnetic samples. However, these probes are all of indirect nature in contrast to the most intuitive and easy-to-interpret structural/dynamics restraint, the internuclear distance, which can be measured by nuclear Overhauser enhancement (NOE). Herein, we demonstrate time-averaged distance measurements on the 360 kDa half proteasome from Thermoplasma acidophilium. The approach is based on exact quantification of the NOE (eNOE). Our findings open up an avenue for such measurements on very large molecules. These restraints will help in a detailed determination of conformational changes upon perturbation such as ligand binding.

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“…In general, the τ m value should be within the initial NOE build-up range (typically 80–150 ms for proteins) [21]. Nonetheless, recently developed innovative methods offering more exact conversion of NOE data to internuclear distance information, Exact NOE (eNOEs), are powerful protocols for accurate and precise protein solution structure determination [101], [102], [103]. The 3D 13 C- or 15 N-edited NOESY-HSQC spectra are widely used.…”

Section: Nmr Structure Calculationmentioning

confidence: 99%

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists

Sugiki

Kobayashi

Fujiwara

2017

Computational and Structural Biotechnology Journal

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Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data. Owing to the remarkable progress in the past decade, we can easily access suitable and popular analytical resources for NMR structure determination of proteins with high accuracy. Here, we describe the practical aspects, workflow and key points of modern NMR techniques used for solution structure determination of proteins. This review should aid NMR specialists aiming to develop new methods that accelerate the structure determination process, and open avenues for non-specialist and life scientists interested in using NMR spectroscopy to solve protein structures.

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Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs

Cited by 33 publications

References 83 publications

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

NOE‐Derived Methyl Distances from a 360 kDa Proteasome Complex

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists

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