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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Conformational Entropy as Collective Variable for Proteins.

Ferruccio Palazzesi1,2, Omar Valsson1,2,3, Michele Parrinello1,2,3

  • 1Department of Chemistry and Applied Biosciences, ETH Zurich c/o USI Campus , Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland.

The Journal of Physical Chemistry Letters
|September 15, 2017
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Summary
This summary is machine-generated.

The NMR S² order parameter effectively describes protein conformational changes. This method significantly accelerates protein folding and unfolding simulations, reducing computational time.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Structural biology

Background:

  • Enhanced sampling methods require accurate collective variables for protein simulations.
  • Identifying suitable descriptors for protein conformational changes remains a challenge.

Purpose of the Study:

  • To introduce the NMR S² order parameter as a descriptor for protein conformational changes.
  • To demonstrate the utility of S² in enhanced sampling techniques for protein folding and unfolding.

Main Methods:

  • Utilizing the NMR S² order parameter with metadynamics and variationally enhanced sampling.
  • Employing a surrogate for protein enthalpy alongside S².
  • Applying the free energy flooding method with S² for rate calculations.

Main Results:

  • Successfully achieved reversible folding and unfolding of a small protein.
  • Generated protein free energy landscapes significantly faster than unbiased simulations.
  • Computed peptide unfolding rates and activation energy at various temperatures.

Conclusions:

  • The NMR S² order parameter is a valid and efficient descriptor for enhanced sampling of protein dynamics.
  • This approach offers a substantial speedup for simulating protein conformational changes and calculating kinetic properties.