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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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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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NMR Spectrometers: Resolution and Error Correction01:14

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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...
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¹H NMR: Interpreting Distorted and Overlapping Signals01:02

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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...
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2D NMR: Overview of Homonuclear Correlation Techniques01:16

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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.
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NMR Spectroscopy: Spin–Spin Coupling01:08

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The spin state of an NMR-active nucleus can have a slight effect on its immediate electronic environment. This effect propagates through the intervening bonds and affects the electronic environments of NMR-active nuclei up to three bonds away; occasionally, even farther. This phenomenon is called spin–spin coupling or J-coupling. Coupling interactions are mutual and result in small changes in the absorption frequencies of both nuclei involved. While nuclei of the same element are involved...
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Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
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Capturing conformational States in proteins using sparse paramagnetic NMR data.

Kala Bharath Pilla1, Julia Koehler Leman2, Gottfried Otting1

  • 1Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.

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|May 21, 2015
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Summary
This summary is machine-generated.

This study introduces a computational method using sparse pseudocontact shift (PCS) data to model protein conformational changes. The approach successfully identified distinct open and closed states of the dengue virus protease system.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein conformational changes are crucial for function but challenging to study.
  • Nuclear Magnetic Resonance (NMR) spectroscopy allows monitoring structural changes under varying conditions.
  • Paramagnetic effects in NMR provide orientation and long-range distance restraints for structural studies.

Purpose of the Study:

  • To develop and demonstrate a computational method for modeling protein conformational states using sparse pseudocontact shift (PCS) data.
  • To identify stable core structural elements and computationally complete the protein structure based on experimental restraints.
  • To validate the approach by reproducing known conformational states of a protein system.

Main Methods:

  • Utilizing sparse pseudocontact shift (PCS) data derived from NMR spectroscopy.
  • Employing a data-driven Rosetta protocol to model protein structures.
  • Identifying invariant core structural elements and computationally modeling flexible regions.
  • Applying the method to the dengue virus NS2B-NS3 protease system.

Main Results:

  • The computational protocol successfully modeled distinct closed and open conformational states of the dengue virus protease.
  • The method reproduced experimental observations by varying input PCS data without altering the computational procedure.
  • Demonstrated the ability to computationally identify protein conformational states difficult to obtain experimentally.

Conclusions:

  • Sparse PCS data combined with computational modeling is an effective strategy for characterizing protein conformational dynamics.
  • This data-driven approach provides a powerful tool for investigating protein systems with multiple conformational states.
  • The method advances the study of protein flexibility and allostery, relevant to drug discovery and understanding biological mechanisms.