A look beyond the QR code of SNARE proteins

Author:

Yadav Deepak1,Hacisuleyman Aysima1,Dergai Mykola1,Khalifeh Dany1,Abriata Luciano A.2,Peraro Matteo Dal2,Fasshauer Dirk1ORCID

Affiliation:

1. Department of Computational Biology University of Lausanne Lausanne Switzerland

2. Institute of Bioengineering, School of Life Sciences École Polytechnique FÉdÉrale de Lausanne (EPFL) Lausanne Switzerland

Abstract

AbstractSoluble N‐ethylmaleimide‐sensitive factor Attachment protein REceptor (SNARE) proteins catalyze the fusion process of vesicles with target membranes in eukaryotic cells. To do this, they assemble in a zipper‐like fashion into stable complexes between the membranes. Structural studies have shown that the complexes consist of four different helices, which we subdivide into Qa‐, Qb‐, Qc‐, and R‐helix on the basis of their sequence signatures. Using a combination of biochemistry, modeling and molecular dynamics, we investigated how the four different types are arranged in a complex. We found that there is a matching pattern in the core of the complex that dictates the position of the four fundamental SNARE types in the bundle, resulting in a QabcR complex. In the cell, several different cognate QabcR‐SNARE complexes catalyze the different transport steps between the compartments of the endomembrane system. Each of these cognate QabcR complexes is compiled from a repertoire of about 20 SNARE subtypes. Our studies show that exchange within the four types is largely tolerated structurally, although some non‐cognate exchanges lead to structural imbalances. This suggests that SNARE complexes have evolved for a catalytic mechanism, a mechanism that leaves little scope for selectivity beyond the QabcR rule.

Funder

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

Publisher

Wiley

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