Molecular Modeling of Organic Matrix Proteins in Oysters


Molecular Modeling of Organic Matrix Proteins in Oysters



Anna Kathleen Benton



Three organic matrix proteins, Pearlin, Prismalin, and Shematrin, from the shell of the oyster Pinctada fucata have been isolated, characterized, and the sequences reported in the literature. These organic matrix proteins are known to interact with one another and with the mineral layers in assembly of the shell, but how the interaction occurs is unknown. This project focuses on molecular modeling of the proteins to discover how this interaction occurs by using the 3D modeling program Chem3D® (PerkinElmer). The molecular modeling program initially displays each protein in the least sterically-hindered conformation. Next, post-translational modifications were made to model the amino acid crosslinking that must occur between the proteins; the introduced post-translational modification is addition of a hydroxyl group to Tyrosine residues to form L-3,4-dihydroxyphenylalanine (L-Dopa) residues. The modifications of changing the tyrosines to L-Dopa were made to the protein sequence at random to identify any combination of alterations that would be most beneficial for the interaction between the organic matrix proteins and the mineral. After an acceptable conformation was found, the protein was replicated in the modeling program. The proteins were then rearranged to determine the most favorable electrostatic arrangement, one with polar regions of the protein interacting with one another. This modeling approach will be used in the future for proteins isolated and characterized from our experimental organism, Crassostrea virginica, the eastern oyster.

Publication Date


Project Designation

Independent Research

Primary Advisor

Karolyn M. Hansen

Primary Advisor's Department



Stander Symposium project

Molecular Modeling of Organic Matrix Proteins in Oysters