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Related Concept Videos

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...
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...
Nuclear Overhauser Enhancement (NOE)01:06

Nuclear Overhauser Enhancement (NOE)

Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling. This phenomenon, called the nuclear Overhauser enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring spin-active...
¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...
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...
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.

Jianyang Zeng1, Pei Zhou, Bruce Randall Donald

  • 1Department of Computer Science, Duke University, Durham, NC 27708, USA.

Journal of Biomolecular NMR
|June 28, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces NASCA, a novel algorithm for automated Nuclear Magnetic Resonance (NMR) assignments. NASCA efficiently determines protein side-chain resonance and NOE assignments, improving high-resolution structure determination.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Nuclear Magnetic Resonance (NMR) structure determination is crucial for understanding protein function.
  • Automating side-chain resonance and Nuclear Overhauser Effect (NOE) assignments is a significant bottleneck in NMR.
  • Existing methods often rely on challenging through-bond experiments (e.g., HCCH-TOCSY) that perform poorly on large proteins.

Purpose of the Study:

  • To develop a novel algorithm, NASCA (NOE Assignment and Side-Chain Assignment), for automated side-chain resonance and NOE assignments.
  • To enable high-resolution protein structure determination without relying on specific through-bond experiments for side-chain assignment.
  • To overcome limitations of current NMR assignment strategies, particularly for large protein molecules.

Main Methods:

  • Formulated the assignment problem as a Markov Random Field (MRF).
  • Applied combinatorial protein design algorithms, including dead-end elimination (DEE) and A* search, to optimize assignments.
  • Integrated NOESY spectra contact map information, RDC backbone structural data, and side-chain rotamer possibilities.
  • Utilized NASCA to resolve NOE assignment ambiguity and compute protein structures.

Main Results:

  • NASCA successfully automates both side-chain resonance and NOE assignments.
  • The algorithm achieves over 90% side-chain proton resonance assignment and approximately 80% assignment accuracy.
  • Protein structures derived from NASCA-assigned NOE restraints show backbone RMSD of 0.8-1.5 Å compared to traditional methods.

Conclusions:

  • NASCA provides an efficient and accurate automated solution for NMR side-chain resonance and NOE assignments.
  • The algorithm significantly advances high-resolution protein structure determination, especially for large proteins.
  • NASCA reduces the reliance on labor-intensive and less effective through-bond experiments for side-chain assignment.