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Related Concept Videos

Conservation of Protein Domains02:26

Conservation of Protein Domains

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...

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NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
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Evolutionary conservation of protein vibrational dynamics.

Sandra Maguid1, Sebastian Fernandez-Alberti, Julian Echave

  • 1Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes, Bernal, Argentina.

Gene
|June 26, 2008
PubMed
Summary

Protein dynamics show evolutionary conservation, with the most collective vibrational modes being the most stable. This explains conserved flexibility profiles and has implications for protein analysis.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Evolutionary Biology

Background:

  • Protein vibrational dynamics play a crucial role in protein function.
  • Understanding the evolutionary conservation of these dynamics is key to deciphering protein evolution.
  • Previous studies noted conserved backbone flexibility (B-factor) profiles across homologous proteins.

Purpose of the Study:

  • To investigate the evolutionary divergence of protein vibrational dynamics.
  • To systematically analyze the conservation of normal modes in proteins.
  • To understand the relationship between normal mode conservation and collectivity.

Main Methods:

  • Utilized the Gaussian Network Model (GNM).
  • Analyzed a large dataset of proteins categorized into homologous family and superfamily pairs.
  • Quantified normal mode conservation and mode collectivity.

Main Results:

  • The lowest, most collective normal modes are the most conserved.
  • A linear correlation exists between normal mode conservation and mode collectivity.
  • Conserved collective modes explain the observed conservation of B-factor profiles.

Conclusions:

  • The robustness of collective normal modes is a significant factor in protein evolution.
  • Natural selection may favor the conservation of these collective modes.
  • Findings have implications for dynamics-based protein alignment and classification.