Structure and stability of the designer protein WRAP-T and its permutants

Bram Mylemans,Xiao Yin Lee,Arnout R D Voet,Christine Helsen,Ina Laier

doi:10.1038/s41598-021-98391-0

Abstract

beta -Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats (‘blades’) each consisting of a 4-stranded anti-parallel beta -sheet. So far, 4- to 12-bladed beta -propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetric beta -propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to each beta -propeller sub-family.

Highlights

Β-Propeller proteins can be found in all domains of life
We began our project before a consensus sequence of the 14 WD40-family Recently Amplified Propeller (WRAP) blades was reported by the group of Lupas[18]
The WRAP repeats show almost perfect conservation with very few mutations, and the only position which is not highly conserved is the ninth residue of the inner β-strand, where arginine and tryptophan occur often

Summary

Introduction

Β-Propeller proteins can be found in all domains of life. They consist of repeating units adopting a circular shape around a central channel. An attempt was made to create a protein that can only adopt the nine-bladed propeller fold by designing a three-fold symmetric protein instead of a nine-fold symmetric one This resulted in the Scone protein which interestingly folds as a permuted eight-bladed propeller despite nine repeats are expressed in the open reading frame[8]. These unexpected observations highlight the need for further optimization of the computational design strategies in order to accurately control the folding symmetry of β-propellers. The group of Lupas more recently reported a highly repetitive propeller with 14 repeats folding as two seven-bladed propeller domains (PDB:2ymu) in Nostoc punctiforme They named this protein “WD40-family Recently Amplified Propeller (WRAP)”. Similar to Cake this sequence possesses the ability to adopt both multimeric eight- and nine-fold symmetry, when fragments are expressed[18]

Objectives

Methods

Results

Conclusion