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2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

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Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
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Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics  for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
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The spin state of an NMR-active nucleus can have a slight effect on its immediate electronic environment. This effect propagates through the intervening bonds and affects the electronic environments of NMR-active nuclei up to three bonds away; occasionally, even farther. This phenomenon is called spin–spin coupling or J-coupling. Coupling interactions are mutual and result in small changes in the absorption frequencies of both nuclei involved. While nuclei of the same element are involved...
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MOTOR: model assisted software for NMR structure determination.

Ulrich Schieborr1, Sridhar Sreeramulu, Bettina Elshorst

  • 1Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany.

Proteins
|July 16, 2013
PubMed
Summary

This study introduces a novel NMR strategy for determining protein structures, particularly for flexible or difficult-to-crystallize proteins. The method enhances Nuclear Overhauser Effect (NOE) assignment, enabling de novo structure determination even with incomplete data.

Keywords:
NOEalgorithmassignmentfibroblast growth factorfibroblast growth factor receptorproteinsoftwaresparse data

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Area of Science:

  • Biochemistry and Structural Biology
  • Nuclear Magnetic Resonance (NMR) Spectroscopy
  • Protein Structure Determination

Background:

  • Many biologically important eukaryotic proteins exhibit partial unstructuredness, conformational flexibility, or heterogeneity, hindering traditional crystallization and NMR structure determination.
  • Challenges in NMR include unobservable dynamics in certain protein regions and incomplete chemical shift assignments due to missing signals, which limit ab initio structure calculation from Nuclear Overhauser Effect (NOE) data.

Purpose of the Study:

  • To develop a novel protein structure determination strategy for proteins that are difficult to crystallize or analyze with standard NMR methods.
  • To create a new NOE assignment strategy that does not rely on explicit reference structures, overcoming limitations of bootstrapping algorithms.

Main Methods:

  • Developed a de novo NMR structure determination strategy employing a novel NOE assignment approach.
  • The software analyzes NOE assignment consistency based on chemical shift precision, seeking maximal consistent assignments in 3D space.
  • Utilized model structures without requiring an explicit reference structure for bootstrapping.

Main Results:

  • Validation using MptpA demonstrated robust results with 30-45% sequence identity model structures and 70% chemical shift assignments.
  • Approximately 60% of resonance assignments were sufficient to identify structural models with high conformational similarity to the actual structure.
  • Successfully determined de novo solution structures for fibroblast growth factor 21 (FGF21) and FGFR4 D2, proteins that failed crystallization and classical NMR analysis.

Conclusions:

  • The novel NMR strategy effectively determines protein structures for challenging targets, including flexible and heterogenic proteins.
  • The method provides a powerful alternative for structural biology when crystallization or standard NMR approaches fail.
  • This approach significantly advances the de novo structure determination of proteins with limited experimental data.