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Related Experiment Videos

The CHAIN program: forging evolutionary links to underlying mechanisms.

Andrew F Neuwald1

  • 1The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA. aneuwald@som.maryland.edu

Trends in Biochemical Sciences
|October 27, 2007
PubMed
Summary
This summary is machine-generated.

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Proteins gain new functions through evolutionary changes, leaving distinct sequence patterns. The CHAIN program identifies these patterns and links them to atomic features, aiding in understanding protein evolution and function.

Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Structural Biology

Background:

  • Proteins evolve new functions by modifying ancestral molecular machinery.
  • Functional divergence in proteins results in conserved, divergent sequence patterns.

Purpose of the Study:

  • To present the CHAIN program for analyzing protein evolutionary divergence.
  • To link sequence divergence to selective pressures and atomic features.
  • To suggest molecular mechanisms for experimental testing.

Main Methods:

  • Multiple sequence alignment of input protein sequences.
  • Partitioning sequences into functionally divergent groups using the CHAIN program.
  • Annotating alignments to reveal selective pressures on divergent residues.

Related Experiment Videos

  • Graphical display of atomic interactions for divergent residues when atomic coordinates are provided.

    • Main Results:

    • The CHAIN program identifies functionally divergent groups within protein sequence sets.
    • Analysis reveals selective pressures on divergent residue positions.
    • Links are established between protein evolutionary divergence and critical atomic features.
    • The approach is demonstrated using bacterial clamp-loader ATPases.

    Conclusions:

    • The CHAIN program facilitates the study of protein functional evolution.
    • Connecting sequence patterns to atomic interactions provides insights into molecular mechanisms.
    • This method aids in generating hypotheses for experimental validation in protein science.