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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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.
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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.
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

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Published on: September 17, 2017

Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.

Falk Hoffmann1, Birgit Strodel

  • 1Institute of Complex Systems: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.

The Journal of Chemical Physics
|January 17, 2013
PubMed
Summary

This study introduces a computational method combining basin-hopping with chemical shift restraints for protein structure prediction. The approach successfully generates near-native protein structures efficiently, even with incomplete data.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Recent advancements in computational methods enable protein structure determination at atomic resolution using chemical shifts.
  • Accurate protein structure prediction is crucial for understanding biological function and disease mechanisms.

Purpose of the Study:

  • To develop and validate a novel computational approach for protein structure prediction by integrating basin-hopping global optimization with chemical shift restraints.
  • To assess the efficiency and accuracy of this method in determining near-native protein structures from extended conformations.

Main Methods:

  • The study employs the basin-hopping (BH) global optimization technique combined with chemical shift restraints formulated as a penalty function.
  • The CHARMM force field and FACTS solvation model were utilized, with optimized weighting for chemical shift penalty energy.
  • A novel function was developed to accelerate local energy minimization by dynamically adjusting the penalty function width.

Main Results:

  • The integrated approach successfully predicted near-native structures for three peptides within 10,000 basin-hopping steps, starting from fully extended conformations.
  • Secondary structure elements (alpha and beta) formed rapidly (within 1000 steps), with tertiary contacts driven by the force field.
  • The method demonstrated robustness, working effectively even with incomplete chemical shift assignments.

Conclusions:

  • The basin-hopping approach augmented with chemical shift restraints presents a promising and efficient strategy for protein structure prediction.
  • This method significantly accelerates the formation of secondary and tertiary structures, offering a valuable tool for structural biology.
  • The successful application with incomplete data highlights its potential for broader utility in protein structure determination.