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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.
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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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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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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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Structure-based protein NMR assignments using native structural ensembles.

Mehmet Serkan Apaydin1, Vincent Conitzer, Bruce Randall Donald

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

Journal of Biomolecular NMR
|March 28, 2008
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Summary
This summary is machine-generated.

This study enhances nuclear magnetic resonance (NMR) protein structure determination by using an ensemble of structures from normal mode analysis (NMA) to improve resonance and NOE assignment accuracy, even with distant templates.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Nuclear Magnetic Resonance (NMR) Spectroscopy

Background:

  • Nuclear magnetic resonance (NMR) protein structure determination requires accurate assignment of resonances and Nuclear Overhauser Effects (NOEs) to specific nuclei.
  • Structure-based assignment (SBA) methods utilize a template protein structure to expedite this assignment process.
  • Existing Nuclear Vector Replacement (NVR) frameworks achieve high accuracy with templates close to the target structure (< 2 Å backbone RMSD), but struggle with distant templates.

Purpose of the Study:

  • To extend the applicability of NVR for NMR protein structure determination when only distant template structures are available.
  • To improve the accuracy and robustness of resonance and NOE assignment in the presence of structural noise and distant templates.

Main Methods:

  • Generated an ensemble of protein structures using normal mode analysis (NMA) to represent low-frequency perturbations of a given template structure.
  • Applied Nuclear Vector Replacement (NVR) to assign resonances and sparse NOEs using each structure in the NMA-generated ensemble.
  • Aggregated assignments using a voting scheme based on maximum bipartite matching, incorporating a confidence measure derived from ensemble agreement.

Main Results:

  • Demonstrated increased assignment accuracy for human ubiquitin using distant template structures with the NMA ensemble approach.
  • Showcased improved robustness of NVR against structural noise and provided a confidence measure for assignments.
  • Successfully applied the NMA ensemble-based voting scheme to another SBA tool (MARS), increasing reliable assignments for proteins including maltose binding protein.

Conclusions:

  • The NMA ensemble-based voting scheme significantly enhances the accuracy and reliability of NMR resonance and NOE assignments, particularly with distant templates.
  • The developed method improves the convergence range of NVR and other SBA tools, making them more broadly applicable.
  • The voting scheme is mathematically proven to be a sound and optimal maximum likelihood estimator for correct assignments.