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Related Concept Videos

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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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Sec61 channel partners for cotranslational translocation
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Post-translational Translocation of Proteins to the RER

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Targeting proteins to the ER
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Protein Diffusion in the Membrane

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Conserved Binding Sites01:49

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NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
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Entropy localization in proteins.

Da-Wei Li1, Scott A Showalter, Rafael Brüschweiler

  • 1Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, USA.

The Journal of Physical Chemistry. B
|November 17, 2010
PubMed
Summary
This summary is machine-generated.

Protein configurational entropy, crucial for function, was studied using molecular dynamics simulations of MDM2. Ligand binding alters motion amplitudes but conserves correlations, simplifying entropy change analysis.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Configurational entropy significantly contributes to protein free energy under physiological conditions.
  • Understanding protein dynamics and thermodynamics is key to protein function, including interactions.
  • Quantitative characterization of protein configurational entropy remains a challenge.

Purpose of the Study:

  • To investigate the configurational entropy of the oncoprotein MDM2.
  • To analyze the impact of p53-peptide ligand binding on MDM2's dynamics and entropy.
  • To establish a link between protein dynamics, thermodynamics, and ligand interactions.

Main Methods:

  • 0.4 μs molecular dynamics simulations of MDM2.
  • Simulations conducted in the presence and absence of the p53-peptide ligand.
  • Characterization of protein motions in dihedral angle space.

Main Results:

  • Ligand binding causes considerable changes in motional amplitudes of MDM2.
  • Correlations between dihedral angle motions (backbone and side-chain) are well conserved upon ligand binding.
  • The change in configurational entropy upon ligand binding can be decomposed into local contributions.

Conclusions:

  • Conserved correlations simplify the analysis of entropy changes, linking protein dynamics to thermodynamics.
  • Findings facilitate understanding of protein-ligand and protein-protein interactions.
  • Implications for deriving entropy changes from site-specific dynamics measurements using NMR spectroscopy.