Computational design of membrane proteins using RosettaMembrane.

Protein Science : a Publication of the Protein Society
Amanda M Duran, Jens Meiler

Abstract

Computational membrane protein design is challenging due to the small number of high-resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high-throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins. Herein, Rosetta is benchmarked for membrane protein design. We evaluate strategies to cope with the often reduced quality of experimental membrane protein structures. Further, we test the usage of symmetry in design protocols, which is particularly important as many membrane proteins exist as homo-oligomers. We compare a soluble scoring function with a scoring function optimized for membrane proteins, RosettaMembrane. Both scoring functions recovered around half of the native sequence when completely redesigning membrane proteins. However, RosettaMembrane recovered the most native-like amino acid property composition. While leucine...Continue Reading

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Citations

Feb 12, 2020·Quarterly Reviews of Biophysics·Ivan V Korendovych, William F DeGrado
Sep 14, 2019·PloS One·Georg KuenzeJens Meiler
Aug 29, 2019·PLoS Computational Biology·Jonathan Yaacov WeinsteinSarel Jacob Fleishman
Apr 1, 2020·Biophysical Journal·Rebecca F AlfordJeffrey J Gray
Jul 17, 2021·Journal of Molecular Biology·Anastassia Andreevna Vorobieva
Jul 27, 2021·Journal of Chemical Theory and Computation·Rebecca F AlfordJeffrey J Gray

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