Keywords

EF-hand, Calcium binding, Parvalbumin, Myosin light chain, T4 lysozyme, Protein evolution, Helix-loop-helix, Ancestral motif

Reference

DOI: 10.1126/science.1111094

Abstract

In this early computational study, EF-hand calcium-binding motifs, characteristic of proteins like parvalbumin, were predicted in proteins not previously associated with calcium binding, including rabbit myosin light chains and T4 lysozyme. This finding suggests a possible evolutionary link and highlights unexpected structural conservation of EF-hand motifs even in proteins where calcium binding is not established.

Notes

1. Discovery of EF-hand-like Regions in Non-canonical Proteins

  • EF-hand: Helix-loop-helix motif, first identified in calcium-binding proteins like parvalbumin, known for its AB, CD, EF domain arrangement.
  • Using computer-based sequence and structural analysis, authors predicted three EF-hand-like motifs in rabbit myosin light chain and one EF-hand-like motif in T4 lysozyme, proteins not previously known to bind calcium.

Key insight: Structural motifs like EF-hands may be evolutionarily conserved even in proteins that no longer bind calcium — suggesting ancestral calcium-binding functions or structural roles.

2. Evolutionary Implications of EF-hand Conservation

  • EF-hand resembling motifs in non-calcium-binding proteins might reflect ancient evolutionary origins:
    • Possible gene duplication events (e.g., CD hand and EF hand duplication hypothesis).
    • EF-hands in modern calcium-binding proteins might trace back to ancestral motifs that subsequently diversified.

Evolutionary twist: EF-hands may have originated as general structural modules and later acquired specialized calcium-binding functions — a reverse evolutionary path from structural to functional specialization?

3. Possible Explanations for Non-functional EF-hands in T4 Lysozyme

  • Though T4 lysozyme contains an EF-hand-like helix-loop-helix arrangement, no evidence of Ca2+ binding was available:
    1. Fortuitous spatial arrangement of helices mimicking EF-hand fold.
    2. Inherent stability of EF-hand fold, independent of function.
    3. Degenerated ancestral EF-hand, losing calcium affinity over evolution.

Ancestral motifs may persist as structural features, even when functional relevance is lost — “molecular fossils” in protein evolution.

4. Structural and Functional Implications

  • The EF-hand signature loop (with Ca2+ coordinating oxygens) was proposed to be present in these proteins, though likely non-functional in calcium binding for lysozyme.
  • Raises the question: Does EF-hand serve structural roles even when it no longer binds calcium?
  • Interestingly, globular proteins (rich in alpha-helices) rarely display such loop-helix-loop patterns, making these EF-like regions notable exceptions.

EF-hand may serve a dual role: initially structural, then evolving into functional calcium-binding modules.

5. Early Use of Computational Structural Prediction

  • A scoring system was developed to search for sequence and structural similarity to known calcium-binding regions — pioneering bioinformatics at the time!
  • Surprise finding that high-scoring EF-hand-like motifs could exist in non-Ca2+-binding proteins, prompting rethinking of motif function and evolution.

Tech and concept: Early computational biology work, highlighting how structural motifs may be evolutionarily constrained, even when not functionally required.

Take-home Messages

  • EF-hand calcium-binding motifs may persist structurally in proteins that do not bind calcium, suggesting evolutionary remnants.
  • Rabbit myosin light chains and T4 lysozyme contain regions resembling EF-hands, expanding the understanding of EF-hand distribution.
  • Suggests EF-hands may have originated for structural purposes and later adapted for calcium sensing.
  • Raises intriguing questions about domain evolution, degeneration, and latent structural motifs in proteins.

Final Thought

Sometimes, what looks like a functional domain may be an evolutionary ghost, a relic of ancient proteins — reminding us that structure and function are not always coupled in protein evolution.