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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Yan Zhang1, Pemra Doruker1, Burak Kaynak1

  • 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA.

Current Opinion in Structural Biology
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Allosteric proteins utilize intrinsic dynamics for function, with conserved motions aiding evolutionary adaptation across species. These protein dynamics are crucial for maintaining and regulating allosteric behavior in complex organisms.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Evolutionary Biology

Background:

  • Allosteric regulation is fundamental to protein function, impacting cellular processes like metabolism and signaling.
  • Intrinsic protein dynamics, dictated by 3D structure and residue contacts, are increasingly recognized as key to allosteric mechanisms.
  • Cooperative motions within proteins often mirror their functional allosteric transitions.

Purpose of the Study:

  • To explore the relationship between intrinsic protein dynamics and allosteric behavior.
  • To investigate the evolutionary conservation and adaptation of these dynamic properties.
  • To understand how protein evolution influences allosteric regulation.

Main Methods:

  • Analysis of protein 3D structures and inter-residue contact networks.
  • Characterization of low-frequency vibrational modes (soft modes).
  • Comparative analysis of orthologous proteins across different species.

Main Results:

  • Intrinsic protein dynamics favor cooperative motions similar to functional allosteric changes.
  • These functionally relevant motions are often driven by low-frequency vibrational modes.
  • Evolutionary conservation of these dynamics suggests adaptive mechanisms.

Conclusions:

  • The intrinsic dynamics of allosteric proteins are evolutionarily conserved and play a critical role in their function.
  • Evolutionary adaptations fine-tune protein dynamics to maintain or optimize allosteric regulation.
  • Understanding these dynamics provides insights into protein evolution and regulation.