A comparative analysis of key tooth proteins: exploring similarities and differences for dental research

Year 2025, Volume: 67 Issue: 2, 153 - 173, 24.12.2025

Güler Burcu Senirkentli , Gazi Erkan Bostancı , Engin Koçak

https://doi.org/10.33769/aupse.1687361

Abstract

Tooth development is orchestrated by a set of specialized proteins integral to enamel formation. In this study, we investigate the structural and functional similarities and divergences of four pivotal enamel matrix proteins—ameloblastin, amelogenin, tuftelin, and enamelin—across Homo sapiens, Mus musculus, and Rattus norvegicus, with the central aim of elucidating conserved elements and species-specific adaptations that reflect evolutionary shaping of enamel protein function. Through computational strategies, we characterize global structural convergence by Principal Component Analysis (PCA), assess flexibility via Secondary Structure Element (SSE) analysis and B-factor profiling, probe intrinsic motion patterns using Normal Mode Analysis (NMA), quantify interspecies structural deviation by Root Mean Square Deviation (RMSD), and estimate relative stability by FoldX energy minimization. Our findings reveal a pronounced structural conservation among all four proteins, particularly within core functional domains, indicative of a shared evolutionary origin, as corroborated by PCA clustering. Nonetheless, we observe clear differences in flexibility, dynamic behavior, and stability: SSE and B-factor analyses underscore species-dependent variation in plasticity, NMA demonstrates divergence in intrinsic motions, and RMSD plus FoldX data uncover subtle but meaningful stability shifts. These structural nuances likely correspond to species-specific adaptations, perhaps linked to variations in enamel thickness, tooth morphology, or timing of development. Altogether, this comparative analysis deepens our understanding of both evolutionary conservation and functional divergence among enamel matrix proteins, offering insights with potential relevance for evolutionary biology, dental tissue engineering, and regenerative medicine, as well as a conceptual foundation for the rational design of biomimetic materials that replicate the inherent properties of dental enamel.

Keywords

Tooth proteins , protein structure , dental research , simulation

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