Deconvolution of the MBP-Bri2 Interaction by a Yeast Two Hybrid System and Synergy of the AlphaFold2 and High Ambiguity Driven Protein-Protein Docking

George A Saratov,Anna A Kudriaeva,Alexey A Belogurov,Tatiana V Rakitina,Evgeniya V Smirnova

doi:10.3390/cryst12020197

Abstract

Myelin basic protein (MBP) is one of the key proteins in the development of multiple sclerosis (MS). However, very few intracellular MBP partners have been identified up to now. In order to find proteins interacting with MBP in the brain, an expression library from the human brain was screened using a yeast two-hybrid system. Here we showed that MBP interacts with the C-terminal 24-residue peptide of Integral transmembrane protein II associated with familial British and Danish dementia (ITM2B/Bri2 or Bri2). This peptide (Bri23R) was one residue longer than the known Bri23 peptide, which is cleaved from the C-terminus of Bri2 during its maturation in the Golgi and has physiological activity as a modulator of amyloid precursor protein processing. Since the spatial structures for both MBP and Bri2 were not known, we used computational methods of structural biology including an artificial intelligence system AlphaFold2 and high ambiguity driven protein-protein docking (HADDOCK 2.1) to gain a mechanistic explanation of the found protein-protein interaction and elucidate a possible structure of the complex of MBP with Bri23R peptide. As expected, MBP was mostly unstructured, although it has well-defined α-helical regions, while Bri23R forms a stable β-hairpin. Simulation of the interaction between MBP and Bri23R in two different environments, as parts of the two-hybrid system fusion proteins and in the form of single polypeptides, showed that MBP twists around Bri23R. The observed interaction results in the adjustment of the size of the internal space between MBP α-helices to the size of the β-hairpin of Bri23R. Since Bri23 is known to inhibit aggregation of amyloid oligomers, and the association of MBP to the inner leaflet of the membrane bilayer shares features with amyloid fibril formation, Bri23 may serve as a peptide chaperon for MBP, thus participating in myelin membrane assembly.

Highlights

Licensee MDPI, Basel, Switzerland.In 1971, the structural biology community established the single worldwide archive for macromolecular structure data—the Protein Data Bank (PDB)
We suggested that amyloid-like structures associated with Myelin basic protein (MBP) accumulation in the inner leaflet of the membrane bilayer can serve as a seed that attracts native Bri23 peptide and initiates its interaction with MBP
The interaction of MBP with the C-terminal peptide of Bri2 was discovered using a yeast two-hybrid system that allows the interaction of proteins in their natural environment to be detected

Summary

Introduction

In 1971, the structural biology community established the single worldwide archive for macromolecular structure data—the Protein Data Bank (PDB). Hundreds of data resources and millions of researchers, which explore fundamental biology and biomedicine, use PDB. The tremendous amount of structural information collected over 50 years was used in the creation and testing of AlphaFold2—an artificial intelligence system developed by DeepMind (https://deepmind.com, accessed on 10 October 2021) to predict the spatial with regard to jurisdictional claims in published maps and institutional affil-. Structure of proteins based on amino acid sequence [1,2,3,4]. This artificial neural network is based on the so-called “attention” approach. It should be noted that the previous advances in structural biology and, above all, protein crystallography, made it possible to obtain more than 170 thousand spatial structures of proteins, on which

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Conclusion