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Related Concept Videos

NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

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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...
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Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
616
Protein Organization01:24

Protein Organization

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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....
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¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

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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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¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

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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...
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Protein and Protein Structure02:15

Protein and Protein Structure

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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...
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UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.

Aleksandra L Ptaszek1,2, Jie Li3, Robert Konrat1

  • 1Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria.

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UCBShift 2.0 accurately predicts protein backbone and side chain chemical shifts. This enhanced nuclear magnetic resonance (NMR) method improves upon existing tools for protein structure analysis.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Chemistry

Background:

  • Nuclear magnetic resonance (NMR) chemical shifts provide detailed insights into protein structure and dynamics in solution.
  • Accurate prediction of chemical shifts is crucial for understanding protein conformation and function.
  • Existing methods like SHIFTX2 have limitations in accuracy and reliability for comprehensive protein analysis.

Purpose of the Study:

  • To extend the UCBShift method for predicting both backbone and side chain chemical shifts in proteins.
  • To develop a whole-protein analysis tool with improved accuracy and reliability compared to current standards.
  • To provide a versatile platform for analyzing protein structure and dynamics using NMR chemical shifts.

Main Methods:

  • The UCBShift 2.0 method integrates a transfer prediction module using sequence/structure alignments with a machine learning model.
  • Features are derived from X-ray crystal structures, incorporating physics-inspired parameters.
  • The approach was validated against well-defined test datasets for both backbone and side chain chemical shift prediction.

Main Results:

  • UCBShift 2.0 demonstrates higher accuracy and reliability in predicting protein chemical shifts compared to the SHIFTX2 method.
  • The extended method enables comprehensive whole-protein analysis, covering both backbone and side chain residues.
  • Performance validation confirmed the method's robustness and predictive power.

Conclusions:

  • UCBShift 2.0 offers a significant advancement in predicting protein chemical shifts, enhancing structural analysis capabilities.
  • The modular design and availability of protein shift-structure data allow for insights into residue-specific interactions.
  • Potential applications include validating structures from methods like AlphaFold and investigating protein dynamics.