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Related Concept Videos

NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
Proton (¹H) NMR: Chemical Shift01:07

Proton (¹H) NMR: Chemical Shift

Organic molecules primarily contain carbon and hydrogen atoms. While all the hydrogen isotopes are NMR-active, protium or hydrogen-1 is the most abundant. It has a significant energy separation between its nuclear spin states due to its large gyromagnetic ratio. As per Boltzmann's distribution, an increase in the energy separation implies a greater excess population of nuclei available for excitation, resulting in a strong NMR absorption signal.
Absorption signals of all the protium nuclei in a...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
In chiral compounds such as 2-butanol, replacing the methylene hydrogens at C3 produces a pair of...

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Consistent blind protein structure generation from NMR chemical shift data.

Yang Shen1, Oliver Lange, Frank Delaglio

  • 1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 11, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for protein structure generation using NMR chemical shifts. This approach enables faster and more efficient protein structure determination, aiding high-throughput studies.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Protein NMR chemical shifts are sensitive indicators of local protein structure.
  • Traditional NMR structure determination relies on restraints collected later in the process.
  • Early-stage experimental data, like chemical shifts, can be leveraged for structure generation.

Purpose of the Study:

  • To develop a robust protocol for de novo protein structure generation using NMR chemical shifts.
  • To enable protein structure determination at an earlier stage of the NMR process.
  • To provide a new direction for high-throughput NMR structure determination.

Main Methods:

  • Utilizes experimental NMR chemical shifts ((13)C(alpha), (13)C(beta), (13)C', (15)N, (1)H(alpha), (1)H(N)) as input.
  • Employs an optimized procedure for selecting protein fragments from the Protein Data Bank.
  • Integrates standard ROSETTA Monte Carlo assembly and relaxation methods.

Main Results:

  • Generated full-atom protein models with backbone root mean square deviations of 0.7-1.8 Å compared to experimental structures.
  • Successfully applied the protocol in a blind manner to nine protein targets up to 15.4 kDa.
  • Demonstrated the protocol's effectiveness across 16 proteins ranging from 56 to 129 residues.

Conclusions:

  • NMR chemical shifts can be effectively used for de novo protein structure generation.
  • This chemical shift-based protocol offers a potentially faster route for structure determination.
  • The method shows promise for advancing high-throughput structural biology studies.