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Related Concept Videos

¹H NMR Signal Integration: Overview00:58

¹H NMR Signal Integration: Overview

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The intensity of a signal, which can be represented by the area under the peak, depends on the number of protons contributing to that signal. The area under each peak is shown as a vertical line called an integral, with the integral value listed under it, as seen in the proton NMR spectrum of benzyl acetate. Each integral value is divided by the smallest integral value to obtain the ratio of the number of protons producing each signal. The ratio reveals the relative number of protons and not...
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The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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Applications Of NMR In Biology01:25

Applications Of NMR In Biology

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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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¹H NMR: Pople Notation01:09

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The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
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NMR Spectroscopy Of Amines01:19

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In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is...
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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I-PINE web server: an integrative probabilistic NMR assignment system for proteins.

Woonghee Lee1, Arash Bahrami2,3, Hesam T Dashti2,4

  • 1National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA. whlee@nmrfam.wisc.edu.

Journal of Biomolecular NMR
|June 6, 2019
PubMed
Summary
This summary is machine-generated.

Integrative PINE (I-PINE) is a new web server that automates protein NMR chemical shift assignment. It supports more NMR experiments and offers enhanced visualization for protein structure and dynamics analysis.

Keywords:
Analysis of protein NMR chemical shiftsAutomationIntegrative NMRProtein NMR chemical shift assignment

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Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology
  • Nuclear Magnetic Resonance Spectroscopy

Background:

  • Protein structure and dynamics analysis heavily relies on Nuclear Magnetic Resonance (NMR) chemical shifts.
  • Automated assignment of NMR signals to protein atoms is crucial but time-consuming.
  • The Probabilistic Interaction Network of Evidence (PINE) algorithm has been a reliable tool for this task for over a decade.

Purpose of the Study:

  • To introduce Integrative PINE (I-PINE), a new web server version of the PINE algorithm.
  • To enhance automated chemical shift assignment capabilities by supporting a wider range of NMR experiments.
  • To provide improved visualization tools for protein structure and dynamics analysis based on chemical shifts.

Main Methods:

  • Development of the I-PINE web server, an extension of the PINE algorithm.
  • Integration of support for diverse NMR experiments, including 3D Nuclear Overhauser Effect (NOE) and 4D J-coupling experiments.
  • Implementation of comprehensive visualization features for chemical shift analysis.

Main Results:

  • The I-PINE server offers expanded support for NMR experiments compared to the original PINE algorithm.
  • I-PINE provides advanced visualization tools for analyzing protein structure and dynamics.
  • The web server is freely accessible with dedicated help pages, tutorials, and sample data.

Conclusions:

  • I-PINE represents a significant advancement in automated protein NMR chemical shift assignment.
  • The enhanced capabilities and accessibility of I-PINE will benefit the protein NMR research community.
  • This tool facilitates more efficient and comprehensive analysis of protein structural and dynamic properties.