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Related Concept Videos

NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

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...
NMR Spectrometers: Overview01:20

NMR Spectrometers: Overview

NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...
Double Resonance Techniques: Overview01:12

Double Resonance Techniques: Overview

Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by...
NMR Spectroscopy of Aromatic Compounds01:14

NMR Spectroscopy of Aromatic Compounds

Aromatic compounds can be identified or analyzed using proton NMR and carbon‐13 NMR. Typically, aromatic hydrogens or hydrogens directly bonded to the aromatic rings are strongly deshielded by the aromatic ring current. Therefore, they absorb in the range of 6.5–8.0 ppm in proton NMR spectra. For instance, aromatic hydrogens directly bonded to the benzene ring absorb at 7.3 ppm. However, aromatic hydrogens of larger rings absorb farther upfield or downfield than the ideal range. Consider...
2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

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.
COSY90 is the standard two-dimensional (2D) COSY experiment that...

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Error tolerant NMR backbone resonance assignment and automated structure generation.

Babak Alipanahi1, Xin Gao, Emre Karakoc

  • 1David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L3G1, Canada.

Journal of Bioinformatics and Computational Biology
|February 18, 2011
PubMed
Summary

We developed IPASS, an integer linear programming system for nuclear magnetic resonance (NMR) backbone resonance assignment. IPASS enables fully automatic protein structure determination from noisy data, improving precision and recall.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Backbone resonance assignment is crucial for NMR structure determination.
  • Existing methods struggle with noisy, automatically picked peaks, hindering automated structure determination.

Purpose of the Study:

  • To develop an error-tolerant system for automated backbone resonance assignment.
  • To enable fully automatic protein structure determination using NMR data.

Main Methods:

  • Designed an integer linear programming (ILP) based assignment system (IPASS).
  • Utilized probabilistic spin system typing based on chemical shifts and secondary structure predictions.
  • Extracted connectivity information from inter-residue data and NOESY peaks to form reliable fragments.

Main Results:

  • IPASS enabled fully automatic protein structure determination for four test proteins.
  • Achieved average precision of 82% and recall of 63% on automatically picked peaks, outperforming MARS (77% precision, 36% recall).
  • Generated assignments fed into FALCON-NMR for automated 3D structure calculation with low RMSDs to native structures.

Conclusions:

  • IPASS provides a robust solution for error-tolerant backbone resonance assignment.
  • The system facilitates fully automated protein structure determination from NMR data.
  • IPASS represents a significant advancement in computational structural biology.