Computational analysis and visualization of MYO5B mutations provide novel insights into the pathogenic mechanisms of MVID

Background Mutations in the MYO5B gene result in functional deficiency of myosin Vb, ultimately leading to microvillus inclusion disease (MVID). This study aimed to capture subtle conformational and dynamic changes in myosin Vb protein caused by specific MYO5B mutations through computational analysis, thereby elucidating the pathogenic mechanism of compound heterozygous variants and emphasizing correlation with the clinical phenotype of MVID. Methods A neonate suspected of MVID was admitted in 2023 with intractable diarrhea. By age two, the patient tolerated full enteral nutrition, showing an atypically mild phenotype. Whole-exome sequencing revealed novel compound heterozygous MYO5B mutations. Wild-type and mutant myosin Vb structures were modeled using AlphaFold3, and PyMOL was used to analyze mutation sites and changes in polar interactions, hydrogen bonding, and secondary structure. Docking with Rab11a was performed via HADDOCK 2.4, and interface properties were assessed using PDBe PISA. Mutational pathogenicity was evaluated with MutPred2 and PolyPhen-2. GROMACS simulations analyzed RMSF, SASA, and Rg to assess dynamic alterations in mutant proteins. Results Two previously unreported compound heterozygous mutations were identified in MYO5B: c.3599T > C (p.Leu1200Pro, paternal origin) and c.2611G > A (p.Val871Met, maternal origin). The p.Leu1200Pro (L1200P) variant reduced polar interactions with neighboring residues and altered the orientation and position of the α-helix, whereas the p.Val871Met (V871M) variant also weakened polar interactions but preserved the integrity of the secondary structure. Structural docking analysis showed that L1200P significantly weakened hydrogen bonding and salt bridge interactions with Rab11a, while V871M had comparatively milder effects. MutPred2 predicted a high pathogenic score for L1200P (0.842), and a low score for V871M (0.10). Molecular dynamics simulations further revealed that V871M increased the flexibility of the isoleucine–glutamine (IQ) domain and potentially impaired calmodulin (CaM) binding, resulting in a looser overall protein conformation. Conclusion Computational analysis confirmed the pathogenicity of the c.3599T > C mutation and revealed that c.2611G > A although less pathogenic, may still impair myosin Vb function. This compound mutation may contribute to a milder and atypical MVID phenotype. This study expands the known pathogenic spectrum of MYO5B mutations and provides molecular insights into their disease mechanisms.