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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...
Conserved Binding Sites01:49

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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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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

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.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Flexible backbone sampling methods to model and design protein alternative conformations.

Noah Ollikainen1, Colin A Smith, James S Fraser

  • 1Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, USA.

Methods in Enzymology
|February 21, 2013
PubMed
Summary

This study introduces methods to detect and model protein alternative conformations using Rosetta simulations. These advancements are crucial for protein engineering and understanding protein function.

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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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Structural Biology
  • Computational Biology
  • Protein Engineering

Background:

  • Understanding protein conformational ensembles is essential for protein function and engineering.
  • Accurate characterization and modeling of these ensembles are computationally and experimentally challenging.
  • Exploiting protein conformational heterogeneity requires robust methods for detection and modeling.

Purpose of the Study:

  • To describe methods for detecting alternative protein conformations.
  • To present strategies for modeling near-native conformational changes using Rosetta.
  • To demonstrate the utility of these methods in various protein modeling applications.

Main Methods:

  • Utilizing backrub-type Monte Carlo moves within the Rosetta software suite.
  • Applying Rosetta simulations to model point mutant side-chain conformations and native heterogeneity.
  • Analyzing functional conformational changes, sequence space, and protein-protein interactions.

Main Results:

  • Rosetta simulations with backrub moves enhance the modeling of side-chain conformations and heterogeneity.
  • The methods improve predictions of functional conformational changes and protein interaction specificity.
  • Demonstrated applicability to modeling amino acid covariation across protein interfaces.

Conclusions:

  • The developed methods serve as a stepping stone for exploiting protein conformational heterogeneity in design.
  • Further improvements in scoring and sampling are needed to accurately approximate protein conformational landscapes.
  • Future work should focus on modeling long-range conformational changes and designing backbone flexibility.