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Entangled Motifs in Membrane Protein Structures.

Leonardo Salicari1,2, Antonio Trovato1,2

  • 1Department of Physics and Astronomy 'Galileo Galilei', University of Padova, Via Marzolo 8, 35031 Padova, PD, Italy.

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Entangled motifs are present in membrane proteins, similar to globular proteins. Chirality differences in double-winding motifs suggest distinct co-translational folding constraints for membrane proteins.

Keywords:
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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Entangled motifs are observed in about one-third of globular protein structures.
  • These motifs are linked to co-translational folding processes.
  • Understanding their prevalence in membrane proteins is crucial.

Purpose of the Study:

  • To investigate the presence and characteristics of entangled motifs in membrane protein structures.
  • To compare entangled motif properties between membrane and globular proteins.
  • To explore the influence of co-translational folding on membrane protein structure.

Main Methods:

  • Construction of a non-redundant dataset of membrane protein domains from existing databases.
  • Annotation of membrane proteins with labels such as monotopic/transmembrane and peripheral/integral.
  • Evaluation of entangled motifs using the Gaussian entanglement indicator.

Main Results:

  • Entangled motifs were found in one-fifth of transmembrane and one-fourth of monotopic proteins.
  • The distribution of entanglement indicator values in membrane proteins mirrors that of globular proteins.
  • Chirality bias for single-winding motifs is consistent, but reversed for double-winding motifs in membrane proteins compared to globular proteins.

Conclusions:

  • Entangled motifs are prevalent in membrane proteins, with distributions similar to globular proteins.
  • Differences in chirality bias for double-winding motifs suggest unique co-translational folding mechanisms in membrane proteins.
  • Co-translational biogenesis machinery imposes distinct constraints on membrane versus globular protein folding.