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

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.

An Algorithm for the Development of a Recombinant Antiherpetic Subunit Vaccine Combining the Crystal Structure Analysis, AlphaFold2-Based Modeling, and Immunoinformatics

“…One of the most novel, progressive, and accurate modeling applications is AlphaFold2, developed by DeepMind (London, UK) and based on both deep learning and a conventional neural network [51]. AlphaFold2 is an excellent tool that can solve various problems in modeling the three-dimensional structures of proteins and protein-containing complexes and is compatible with different experimental and computational techniques (see, e.g., [82] as one of numerous examples). The advantages of using AlphaFold2 predictions in viral research are reviewed in [83].…”

Myelin Basic Protein Attenuates Furin-Mediated Bri2 Cleavage and Postpones Its Membrane Trafficking

“…Bri2 was recently found as an interactor of myelin basic protein (MBP) [ 25 ]. MBP was identified in the early 1970s as the predominant protein of basic protein materials extracted from the whole brain or spinal cord causing experimental allergic encephalomyelitis [ 26 ].…”

“…Previously, using the yeast two-hybrid (Y2H) system, we observed interaction between MBP and Bri23 [ 25 ]. The existence of the MBP-Bri23 complex was confirmed in a reciprocal Y2H assay, and putative complexes of MBP with the β-hairpin structure of Bri23 were modeled using a combination of an AI-based AlfaFold2 protein structure modeling service [ 38 ] and a High Ambiguity Driven protein–protein DOCKing (HADDOCK) [ 25 ]. Because MBP was also found among proteins pulled down with Bri2 from the cerebral cortex [ 39 ], we hypothesized that the interaction between MBP and Bri2 was supposed to be physiologically relevant.…”

Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics

“…Previously, using the cross-linking method, we identified a number of proteins closely related to MBP, including those involved in MBP biogenesis, cytoskeleton regulation, cell adhesion, protein traffic and degradation. While the interaction of MBP with the b-hairpin C-terminal peptide of integral transmembrane protein II associated with familial British and Danish dementia (Bri2) was detected using a yeast two-hybrid system [ 26 , 27 ].…”