In Silico Structural Analysis Predicting the Pathogenicity of PLP1 Mutations in Multiple Sclerosis

Abstract

The X chromosome gene PLP1 encodes myelin proteolipid protein (PLP), the most prevalent protein in the myelin sheath surrounding the central nervous system. X-linked dysmyelinating disorders such as Pelizaeus-Merzbacher disease (PMD) or spastic paraplegia type 2 (SPG2) are typically caused by point mutations in PLP1. Nevertheless, numerous case reports have shown individuals with PLP1 missense point mutations which also presented clinical symptoms and indications that were consistent with the diagnostic criteria of multiple sclerosis (MS), a disabling disease of the brain and spinal cord with no current cure. Computational structural biology methods were used to assess the impact of these mutations on the stability and flexibility of PLP structure in order to determine the role of PLP1 mutations in MS pathogenicity. The analysis showed that most of the variants can alter the functionality of the protein structure such as R137W variants which results in loss of helix and H140Y which alters the ordered protein interface. In silico genomic methods were also performed to predict the significance of these mutations associated with impairments in protein functionality and could suggest a better definition for therapeutic strategies and clinical application in MS patients.

Keywords: functional analysis; multiple sclerosis; myelin proteolipid protein; protein structure prediction.

Figure 1

Protein flexible conformation based on the Vibrational Entropy difference (ΔΔS) between wild-type and mutant structures on the structure of PLP1. A visual representation of the chain in which the mutation occurs is also mapped. Amino acids colored according to the vibrational entropy change upon mutation. Blue represents a rigidification of the structure and red represents a gain in flexibility. (A) Normal PLP1; (B) L31P mutant; (C) L31R mutant; (D) L31V mutant; (E) R137W mutant; (F) H140Y mutant. The image is illustrated by DynaMut. The positions of the point mutations are 31, 137 and 140. Abbreviations: L is leucine; P is proline; R is arginine; V is valine; W is tryptophan; H is histidine; Y is tyrosine.

Figure 2

ConSurf analysis of conserved functional areas of the structural model of PLP1 gene-encoded protein. Amino acid at positions 31 (leucine) and 137 (arginine) are highlighted. Leucine in position 31 is a highly conserved region. Conservation score is presented in Figure S1.

Figure 3

Protein structure prediction models of PLP1 calculated by different computational methodologies. AlphaFold model presented high confidence for the residue of the protein at position 31 (pLDDT > 90), but limited confidence for the PLP1 residue at position 137 (pLDDT < 50). Model 1 showed the highest C- score (−3.95) in I-TASSER and C-I-Tasser (−3.89) servers. Phyre2 model 12 with a confidence of 16.98% was the only one that included the residues analyzed in this study.

Figure 4

Interatomic interactions for wild-type and mutant PLP1. Both wild-type and mutant residues are colored in light green and depicted as sticks, along with domains participating in any interactions surrounding them. Leucine at position 31 is hydrophobic and highly conserved: (A) wild-type residue at position 31; (B) L31V (hydrophobic); (C) L31P (nonpolar); (D) L31R (polar). Arginine at position 137 and histidine at position 140 are polar: (E) wild-type residue at position 137; (F) R137W (aromatic); (G) wild-type residue at position 140; (H) H140Y (aromatic). The image is illustrated by DynaMut. A scale of color definition for each type of interaction is provided by software: red depicts hydrogen bonds; slight red depicts water-mediated hydrogen bonds; blue depicts halogen bonds; gold depicts ionic interactions; purple depicts metal complex interactions; light blue depicts aromatic contacts; green depicts hydrophobic contacts; pink depicts carbonyl contacts. The positions of the point mutations are 31, 137 and 140. Abbreviations: L is leucine; P is proline; R is arginine; V is valine; W is tryptophan; H is histidine; Y is tyrosine.