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Related Experiment Videos

Triggering loops and enzyme function: identification of loops that trigger and modulate movements.

K Gunasekaran1, Buyong Ma, Ruth Nussinov

  • 1Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Bldg. 469 Rm. 151, Frederick, MD 21702, USA.

Journal of Molecular Biology
|August 30, 2003
PubMed
Summary

Enzymes utilize "trigger" loops with conserved glycine residues to facilitate conformational changes in other loops, enabling function. This mechanism is conserved across diverse enzymes, suggesting evolutionary preservation of functional strategies.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Enzyme function relies on conformational changes, with loops critical for positioning catalytic residues.
  • Predicting functional loops and their roles is challenging due to poor sequence conservation in conformation-changing loops.

Purpose of the Study:

  • To investigate the role of specific loops in enzyme conformational changes.
  • To explore the conservation of mechanisms driving loop movements in enzymes.

Main Methods:

  • Molecular dynamics simulations were employed to study enzyme conformational changes.
  • Analysis focused on loop sequence conservation and structural dynamics across different enzymes.

Main Results:

  • A long, poorly conserved loop in beta1,4-Galactosyltransferase undergoes large conformational changes driven by a second, highly conserved loop rich in glycine residues.

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  • Similar glycine-rich triggering loops were identified in enolase and lipase, mediating conformational changes in other functional loops.

    • Conclusions:

    • Evolution conserves functional mechanisms, including 'trigger' loops, across diverse enzyme folds, sequences, and functions.
    • Conserved 'skillful' mechanisms, like glycine-rich loops, are fundamental to enzyme adaptation and catalytic roles.