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A path from primary protein sequence to ligand recognition.

Richard Kho1, Brian L Baker, Joseph V Newman

  • 1Triad Therapeutics, Inc., San Diego, CA 92121, USA.

Proteins
|February 11, 2003
PubMed
Summary
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A new method organizes protein structures using only sequence data, creating families that reflect 3D structure and ligand binding. This approach identified 94 nicotinamide adenine dinucleotide [NAD(P)]-enzyme families, aiding proteome analysis.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Organizing protein structural information is crucial for understanding protein function and evolution.
  • Current methods often rely on experimental structure determination, which can be time-consuming and costly.
  • Sequence-based organization offers a scalable alternative for large-scale proteomic studies.

Purpose of the Study:

  • To develop and present a novel method for organizing protein structural information based solely on amino acid sequence.
  • To cluster proteins into families that correlate with three-dimensional structure and bound ligand conformation.
  • To apply this method to nicotinamide adenine dinucleotide [NAD(P)]-utilizing enzymes and analyze proteomes.

Main Methods:

  • Clustering proteins into families based on sequence similarity.

Related Experiment Videos

  • Correlating sequence families with known three-dimensional protein structures.
  • Analyzing the conformation of bound nicotinamide adenine dinucleotide [NAD(P)] within identified families.
  • Applying the method to the proteome of Mycobacterium tuberculosis.

    • Main Results:

    • Identified 94 sequence families for NAD(P)-utilizing enzymes, with 53 structurally characterized.
    • Established correlations between sequence families, protein folds (e.g., Rossmann folds, beta/alpha barrels), and NAD(P) conformation.
    • Demonstrated the utility of sequence families for proteome-wide enzyme profiling.
    • M. tuberculosis proteome analysis revealed NAD(P)-utilizing enzymes constitute ~6% of open reading frames, with short-chain dehydrogenases being the most prevalent.

    Conclusions:

    • The sequence-based method effectively organizes protein structural information and predicts fold and ligand conformation.
    • This approach facilitates the identification and characterization of enzyme families across diverse proteomes.
    • The findings for M. tuberculosis highlight the significant role of NAD(P)-utilizing enzymes, particularly short-chain dehydrogenases, in its complex cell wall biology.